变形菌门在生态功能的优势

ABSTRACT Chemolithoautotrophic members from the Campylobacteria class are dominant key players in sulfidic habitats, where they make up a stable portion of sulfide-oxidizing bacterial communities. Nevertheless, few isolates have so far been cultivated and studied in situ, and most are derived from chemosynthetic ecosystems, limiting our understanding of their physiological and metabolic features as well as ecological roles in the global marine environments. In this study, seven potentially new species were successfully isolated from mangrove sediments and further diverged into three potentially new genera within the class Campylobacteria. These isolates were obligate chemolithoautotrophs that could grow through hydrogen oxidation as well as sulfur oxidation, reduction, and disproportionation. Metabolic reconstructions revealed that these isolates contained diverse sulfide:quinone oxidoreductase and flavocytochrome c sulfide dehydrogenase for sulfide oxidation, distinct Sox gene cluster for sulfur oxidation, as well as group I, II, and IV hydrogenases for hydrogen consumption and production. Notably, these strains lacked the complete denitrification pathway, instead having all genes for nitrogen fixation, which might facilitate their survival in the nitrogen-limited mangrove sediments. Moreover, they also demonstrated the ability to adapt to low O2 conditions, such as a more efficient 2-oxoglutarate:ferredoxin oxidoreductase complex for CO2 fixation and diverse terminal oxidases including Cco, Cox, and Cyd. Metatranscriptomic analysis further confirmed their activity and different adaptation mechanisms in in situ mangrove sediments. Assessing their occurrences indicated that these lineages were globally distributed in hypoxic and anoxic environments and dominant members of marine and mangrove sediments. Overall, these results indicate that these new Campylobacteria members are metabolically versatile and play an underappreciated role in the biogeochemical cycling of carbon-rich mangrove sediments. IMPORTANCE Chemolithoautotrophic Campylobacteria spp. are generally associated with sulfide-rich environments, where they play a key role in the cycling of carbon, nitrogen, and sulfur. Yet, only a limited number of cultured isolates are currently available. In this study, we isolated seven potentially new species belonging to three new genera from mangrove sediments, which significantly expanded our understanding of the species diversity within the class Campylobacteria. These isolates demonstrated diverse and unique metabolic potentials for CO2 fixation, sulfur oxidation, hydrogen oxidation, nitrogen metabolism, and oxygen respiration, making them well adapted to the sulfur-rich, nitrogen-limited, and low-oxygen habitats they inhabit. The frequent detection of these novel species in marine and mangrove sediments, as revealed by 16S rRNA gene sequences in public databases, indicates a potential preference for oxygen-limited environments. Overall, this study promotes our understanding of the in situ function and ecological role of Campylobacteria, especially in previously overlooked carbon-rich sediment ecosystems. Chemolithoautotrophic Campylobacteria spp. are generally associated with sulfide-rich environments, where they play a key role in the cycling of carbon, nitrogen, and sulfur. Yet, only a limited number of cultured isolates are currently available. In this study, we isolated seven potentially new species belonging to three new genera from mangrove sediments, which significantly expanded our understanding of the species diversity within the class Campylobacteria. These isolates demonstrated diverse and unique metabolic potentials for CO2 fixation, sulfur oxidation, hydrogen oxidation, nitrogen metabolism, and oxygen respiration, making them well adapted to the sulfur-rich, nitrogen-limited, and low-oxygen habitats they inhabit. The frequent detection of these novel species in marine and mangrove sediments, as revealed by 16S rRNA gene sequences in public databases, indicates a potential preference for oxygen-limited environments. Overall, this study promotes our understanding of the in situ function and ecological role of Campylobacteria, especially in previously overlooked carbon-rich sediment ecosystems.

ABSTRACT Hadal trenches, the Earth’s deepest marine environments, harbor thriving microbial communities that promote the turnover of recalcitrant dissolved organic matter (RDOM) under extreme conditions. However, the effects of microbes on D-amino acid (D-AA) reservoirs, which are important components of deep-sea RDOM, remain largely unknown. To address this knowledge gap, we curated a comprehensive reference database of D-AA functional genes for accurate identification of D-AA metabolic potential from metagenomic data. Using this database, we identified the presence of various D-AA anabolic and catabolic genes that were closely correlated with central carbon metabolism and ammonia oxidation genes throughout the water column and in the sediment of the Mariana Trench. Furthermore, 93.6% of the recovered bacterial and archaeal genomes contained at least one of these D-AA functional genes, substantially expanding our understanding of potential D-AA utilizers. Notably, we discovered that glutamate racemase, an enzyme previously thought to be exclusive to bacteria, is ubiquitously present in ammonia-oxidizing archaea. This finding suggests that D-glutamate could be integrated into hadal carbon and nitrogen cycling by this crucial microbial taxon. Finally, we observed an increase in both D-AA production and degradation potential with water depth, with higher levels in near-bottom seawater than in sediment. These findings suggest that diverse microbial taxa promote increased D-AA turnover in hadal zones, potentially representing a common adaptive response to extreme hadal conditions. IMPORTANCE Deep-sea microorganisms play a crucial role in the turnover of RDOM. In this study, we investigated the metabolic potential of D-AAs, which are important constituents of RDOM and are used for indicating the recalcitrance of organic matter. By elucidating the genetic profiles of D-AA metabolism and associated microbial taxa, we observed that D-AA metabolism is a fundamental ecological function that is prevalent in the deepest ocean. Our finding of higher D-AA turnover potentials in deeper environments challenges the conventional view of the constant recalcitrance of D-AAs, suggesting that D-AA turnover may be environmentally dependent. This insight provides a new paradigm for understanding RDOM turnover, with broad implications for marine biogeochemistry. Deep-sea microorganisms play a crucial role in the turnover of RDOM. In this study, we investigated the metabolic potential of D-AAs, which are important constituents of RDOM and are used for indicating the recalcitrance of organic matter. By elucidating the genetic profiles of D-AA metabolism and associated microbial taxa, we observed that D-AA metabolism is a fundamental ecological function that is prevalent in the deepest ocean. Our finding of higher D-AA turnover potentials in deeper environments challenges the conventional view of the constant recalcitrance of D-AAs, suggesting that D-AA turnover may be environmentally dependent. This insight provides a new paradigm for understanding RDOM turnover, with broad implications for marine biogeochemistry.

The structural diversity and metabolic pathways formed by soil microbial-environmental factor interactions can be used to predict the differences in microbial ecological functions. The storage of fly ash (FA) has caused potential harm to the surrounding soil environment, whereas little is known about bacterial communities and environmental factor interactions in FA-disturbed areas. In this study, we selected two disturbed areas (DW: dry-wet deposition zone, LF: leachate flow zone) and two nondisturbed areas (CSO: control point soil, CSE: control point sediment) as the test areas and used high-throughput sequencing technology to investigate the bacterial communities. The results indicated that (1) FA disturbance significantly increased the electrical conductivity (EC), geometric mean diameter (GMD), soil organic carbon (SOC) and some potentially toxic metals (PTMs) (Cu, Zn, Se and Pb) of DW and LF and significantly decreased the AK of DW and the pH of LF (p < 0.05). (2) The relative abundance of Proteobacteria was significantly increased in the DW (p < 0.05). Similarly, the relative abundances of Proteobacteria and Firmicutes obviously increased in the LF (p < 0.001). Interestingly, the α and β diversity of LF flora and the β diversity of DW flora changed. (3) The order of influence of bacterial community structure was nutrient characteristics > physical properties > PTMs. Among all factors, AK (33.9 %) and pH (44.3 %) were the key environmental limiting factors for the bacterial community in the DW and the LF, respectively. (4) FA perturbation reduced the complexity, connectivity and modularity of the interaction network between bacteria and disturbed them by increasing the metabolic pathways that degrade pollutants. In conclusion, our results revealed the changes in the bacterial community and the main environmental driving factors under different pathways of FA disturbance; this information provides a theoretical basis for ecological environment management.

No abstract available

With the rising concerns about climate change and continuous increase in the salinity of soil, it is essential to understand the C-cycling functioning of saline soil to better predict the ecological functions and health of soil. Microbes play critical roles in C-cycling. However, limited research has been conducted to understand the impact of soil salinity on the microbial functional genes involved in C-cycling. In this study, effects of varying soil salinity levels in wetlands on the C-cycling functions and diversity of soil microbes were investigated by metagenomic sequencing. The results showed a higher relative abundance of genes related to decomposition of easily degradable organic C at low salinity. On the other hand, higher abundance of genes participating in the decomposition of recalcitrant organic C were observed at high salinity. These findings indicate distinct metabolic bias of soil microbes based on the salinity levels. Proteobacteria and Actinobacteria were dominant in soils with low to medium salinity levels, while Bacteroidetes phyla was prominent in highly saline soils. Furthermore, partial least squares path modeling (PLS-PM) identified electrical conductivity, total nitrogen, and total phosphorus as key regulators of C-cycling gene expression. Overall, the present study highlights the intricate connections between salinity, microbial attributes, and carbon metabolism in soil, suggesting that the soil microbes adapt to saline stress through divergent eco-adaptations. The findings of this study highlight the significance of exploring these microbial interactions for effective management and conservation of saline wetlands.

ABSTRACT The gut microbiota of bats is vital for their roles in health and the ecosystem, yet studies on hibernating bats in southwest China, particularly in the unique karst landscape of Guizhou, are limited. We captured three hibernating bat species—Pipistrellus (PB), Rhinolophus (RB), and Myotis (MB)—in Liping County, collecting rectal samples for 16S rRNA amplicon sequencing. Data processing involved Trimmomatic, Flash, and Qiime2 for operational taxonomic unit (OTU) standardization and species annotation via the Greengenes database. Differential abundance was analyzed using LEfSe, and diversity metrics were assessed through alpha and beta diversity analyses. The RB group was predominantly composed of Proteobacteria (80.99%), while MB and PB exhibited diverse compositions with significant OTU richness (729 in MB). Notable genera included Hafnia and Yersinia in RB and Cosenzaea myxofaciens in MB. High proportions of unclassified taxa were observed, particularly in RB (83.81%). Functional predictions indicated metabolic pathways, with a significant representation of human diseases in PB. Culturomics revealed the successful cultivation of Huaxiibacter chinensis and Enterobacter chengduensis from bats for the first time and appears to have identified a new bacterium that is likely closely related to Clostridium paraputrificum. IMPORTANCE Our research reveals significant differences in the composition and diversity of the gut microbiota among three bat groups (PB, MB, and RB) from Guizhou. While Proteobacteria predominates in all groups, its abundance varies. Notably, the high richness of operational taxonomic units (OTUs) in the MB group suggests a more diverse microbial ecosystem, underscoring the complex interactions between species diversity, diet, gut microbiota, and overall ecological dynamics in bats. Furthermore, the substantial presence of unknown bacterial species in their intestines highlights the critical importance of cultivation-based approaches. The presence of specific taxa may have potential health implications for both bats and humans. These findings emphasize the need for further investigations into the functional roles of these microbiota and their contributions to host health. Future research should focus on longitudinal studies to elucidate these intricate interactions. Our research reveals significant differences in the composition and diversity of the gut microbiota among three bat groups (PB, MB, and RB) from Guizhou. While Proteobacteria predominates in all groups, its abundance varies. Notably, the high richness of operational taxonomic units (OTUs) in the MB group suggests a more diverse microbial ecosystem, underscoring the complex interactions between species diversity, diet, gut microbiota, and overall ecological dynamics in bats. Furthermore, the substantial presence of unknown bacterial species in their intestines highlights the critical importance of cultivation-based approaches. The presence of specific taxa may have potential health implications for both bats and humans. These findings emphasize the need for further investigations into the functional roles of these microbiota and their contributions to host health. Future research should focus on longitudinal studies to elucidate these intricate interactions.

Phytoremediation of soils contaminated with high concentrations of multiple heavy metals (HCMHMs) is a promising technique. However, the microbial response mechanisms during the phytoremediation process remain poorly understood. The role of microbes in HCMHMs soil remediation may be underestimated. This study investigated microbial responses and their potential roles in HCMHMs soil remediation using the hyperaccumulator plant Sedum alfredii (S. alfredii). Soil microbial communities were characterised by 16S rRNA sequencing, and metabolic pathways and functions were predicted using PICRUSt2 analysis. The results indicated that the impact of heavy metals on bacterial community structure was more significant than that of S. alfredii. The formation of dominant phyla such as Proteobacteria and Patescibacteria played a crucial role in the bacterial remediation of HCMHMs soils. Proteobacteria utilised the Inorganic ion transport and metabolism gene clusters to translocate heavy metals or reduce their bioavailability and toxicity. Patescibacteria used the Replication, recombination and repair gene clusters to repair damaged genes, enhancing bacterial tolerance of heavy metals. The results provided new insights into the role of microbes during phytoremediation and offered a scientific basis for optimizing phytoremediation technologies. This study demonstrated that dominant phyla effectively mitigated the damage to soil ecological functions from HCMHMs soil.

Microbiome-wide association studies (MWASs) have uncovered microbial markers linked to ecosystem traits, but the mechanisms underlying their functions can remain elusive. This is largely due to challenges in validating their in situ metabolic activities and tracing such activities to individual genomes. Here, we introduced a phylogeny-metabolism dual-directed single-cell genomics approach called fluorescence-in situ-hybridization-guided single-cell Raman-activated sorting and sequencing (FISH-scRACS-seq). It directly localizes individual cells from target taxon via an FISH probe for marker organism, profiles their in situ metabolic functions via single-cell Raman spectra, sorts cells of target taxonomy and target metabolism, and produces indexed, high-coverage, and precisely-one-cell genomes. From cyclohexane-contaminated seawater, cells representing the MWAS-derived marker taxon of γ-Proteobacteria and that are actively degrading cyclohexane in situ were directly identified via FISH and Raman, respectively, then sorted and sequenced for one-cell full genomes. In such a Pseudoalteromonas fuliginea cell, we discovered a three-component cytochrome P450 system that can convert cyclohexane to cyclohexanol in vitro, representing a previously unknown group of cyclohexane-degrading enzymes and organisms. Therefore, by unveiling enzymes, pathways, genomes, and their in situ cellular functions specifically for those organisms with ecological relevance at one-cell resolution, FISH-scRACS-seq is a rational and generally applicable approach to dissecting and mining microbiota functions.

Deep-sea hydrothermal vents have been extensively explored around the globe in the past decades, and the diversity of microbial communities and their ecological functions related to hydrothermal vents have become hotspots in the study of microbial biogeochemistry. However, knowledge of dominant microbial communities and their unique metabolic characteristics adapting to hydrothermal vents is still limited. In our study, the sediment sample near the Tangyin hydrothermal vent in the southern part of the Okinawa Trough was collected, and the most abundant phyla are Proteobacteria and Desulfobacterota based on the 16S rRNA genes and metagenome sequencing. Metagenomic analysis revealed that methane metabolism, sulfur reduction, and Fe2+ uptake were abundantly distributed in hydrothermal sediment. In addition, most of the metagenomic assembly genomes (MAGs), belonging to Chloroflexota, Desulfobacterota, and Gammaproteobacteria, were found to be involved in methanogenesis, sulfur oxidation/reduction, and ferrous/ferric iron metabolisms. Among these MAGs, the two representative groups (Bathyarchaeia and Thioglobaceae) also showed distinct metabolic characteristics related to carbon, sulfur, and iron to adapt to hydrothermal environments. Our results reveal the dominant microbial populations and their metabolic features in the sediment near the Tangyin hydrothermal fields, providing a better understanding of microbial survival strategies in the extreme environment.

The γ-proteobacteria are an exceptionally diverse bacterial class whose members thrive in environments from deep-sea vents to human intestinal tracts. Rapid gene expression responses mediated by global post-transcriptional regulatory networks like the Csr/Rsm system are critical for bacterial survival in dynamic niches. CsrA/RsmA functions as a global regulatory RNA-binding protein, directly controlling hundreds to thousands of mRNA targets simultaneously across the transcriptome to coordinate systems-level metabolic and behavioral responses. Despite conservation of the CsrA/RsmA regulatory protein across γ-proteobacteria, the genes it regulates in different species remain poorly characterized. We extended a previously developed biophysical model of CsrA/RsmA-RNA binding from Escherichia coli and Pseudomonas aeruginosa to predict regulons across 16 diverse γ-proteobacterial species. While CsrA/RsmA protein structure and RNA-binding motif recognition are highly conserved, predicted target regulons diverge dramatically across species. Pathway enrichment analysis demonstrated both conserved regulation of core metabolic processes and extensive species-specific regulation of niche-adapted functions including virulence, biocontrol, and environmental stress response. Only two gene groups were shared exclusively among non-pathogens, while pathogens showed no exclusively conserved targets, indicating extensive regulon rewiring. These findings demonstrate that post-transcriptional regulatory networks evolve primarily through mutations in RNA targets that create or eliminate regulatory binding sites, rapidly adapting target repertoires to ecological demands while the regulatory protein mechanism remains conserved. Importance The CsrA/RsmA family represents one of the most influential global regulatory RNA-binding proteins in γ-proteobacteria, directly binding and regulating hundreds of mRNA targets to orchestrate systems-scale control over metabolism, virulence, and environmental adaptation, yet how this conserved mechanism adapts across diverse niches remains unclear. By predicting CsrA/RsmA targets across 16 species, we demonstrate that regulatory evolution occurs primarily through changes in targeted genes rather than the regulatory protein itself. This conserved mechanism with flexible targets may represent an efficient evolutionary strategy for optimizing gene expression for specific lifestyles, highlighting the importance of studying regulation beyond model organisms.

To investigate the vertical impacts of quizalofop-p-ethyl stress on soil bacterial communities and their ecological functional responses in wheat fields, this study collected soil samples from three depths (0–30 cm, 30–60 cm, and 60–90 cm) using a grid sampling method in typical wheat fields of Inner Mongolia Autonomous Region. Through quizalofop-p-ethyl acclimation experiments with concentration gradients (50–300 mg/L), combined with bacterial community structure and functional analyses, this study focused on revealing the dominant enrichment of Proteobacteria in deep soil and its key regulatory role in carbon (C), nitrogen (N), and phosphorus (P) cycles. The results showed that quizalofop-p-ethyl treatment significantly altered soil microbial community structure and induced obvious functional remodeling. As a core responsive taxon, the relative abundance of Proteobacteria increased significantly with increasing soil depth, becoming the absolute dominant phylum in deep soil layers. This change was significantly positively correlated with the upregulation of key metabolic pathways involved in soil C, N, and P cycles (including the citrate cycle, nitrogen metabolism, phosphonate metabolism, etc.). Functional gene analysis further indicated that the expression of multiple genes related to nitrogen assimilation and phosphorus utilization was closely associated with the abundance of Proteobacteria, directly promoting N and P cycling processes. Meanwhile, the activation of quizalofop-p-ethyl degradation-related pathways provided additional carbon sources for microorganisms, synergistically enhancing the C cycle. From the perspective of “dominant bacterial taxa driving element cycling,” this study clarified the vertical differentiation mechanism of soil microbial ecological functions under quizalofop-p-ethyl stress, which deepens the understanding of the soil microecological effects of herbicides.

Proteobacteria constitute one of the most diverse and abundant groups of microbes on Earth. In productive marine environments like deep-sea hydrothermal systems, Proteobacteria are implicated in autotrophy coupled to sulfur, methane, and hydrogen oxidation, sulfate reduction, and denitrification. Beyond chemoautotrophy, little is known about the ecological significance of poorly studied Proteobacteria lineages that are globally distributed and active in hydrothermal systems. Here we apply multi-omics to characterize 51 metagenome-assembled genomes from three hydrothermal vent plumes in the Pacific and Atlantic Oceans that are affiliated with nine Proteobacteria lineages. Metabolic analyses revealed these organisms to contain a diverse functional repertoire including chemolithotrophic ability to utilize sulfur and C1 compounds, and chemoorganotrophic ability to utilize environment-derived fatty acids, aromatics, carbohydrates, and peptides. Comparative genomics with marine and terrestrial microbiomes suggests that lineage-associated functional traits could explain niche specificity. Our results shed light on the ecological functions and metabolic strategies of novel Proteobacteria in hydrothermal systems and beyond, and highlight the relationship between genome diversification and environmental adaptation.

Salt-tolerant and halophilic microorganisms are critical drivers of ecosystem stability and biogeochemical cycling in athalassohaline environments. Lake Barkol, a high-altitude inland saline lake, provides a valuable natural setting for investigating microbial community dynamics and adaptation mechanisms under extreme salinity. In this study, we employed high-throughput metagenomic sequencing to characterize the taxonomic composition, metabolic potential, and ecological functions of microbial communities in both water and sediment samples from Lake Barkol. We reconstructed 309 metagenome-assembled genomes (MAGs), comprising 279 bacterial and 30 archaeal genomes. Notably, approximately 97% of the MAGs could not be classified at the species level, indicating substantial taxonomic novelty in this ecosystem. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Desulfobacterota, Planctomycetota, and Verrucomicrobiota, while archaeal communities were primarily composed of Halobacteriota, Thermoplasmatota, and Nanoarchaeota. Metabolic reconstruction revealed the presence of diverse carbon fixation pathways, including the Calvin-Benson-Bassham (CBB) cycle, the Arnon-Buchanan reductive tricarboxylic acid (rTCA) cycle, and the Wood-Ljungdahl pathway. Autotrophic sulfur-oxidizing bacteria, alongside members of Cyanobacteria and Desulfobacterota, were implicated in primary production and carbon assimilation. Nitrogen metabolism was predominantly mediated by Gammaproteobacteria, with evidence for both nitrogen fixation and denitrification processes. Sulfur cycling was largely driven by Desulfobacterota and Pseudomonadota, contributing to sulfate reduction and sulfur oxidation pathways. Microbial communities exhibited distinct osmoadaptation strategies. The “salt-in” strategy was characterized by ion transport systems such as Trk/Ktr potassium uptake and Na+/H+ antiporters, enabling active intracellular ion homeostasis. In contrast, the “salt-out” strategy involved the biosynthesis and uptake of compatible solutes including ectoine, trehalose, and glycine betaine. These strategies were differentially enriched between water and sediment habitats, suggesting spatially distinct adaptive responses to local salinity gradients and nutrient regimes. Additionally, genes encoding microbial rhodopsins were widely distributed, suggesting that rhodopsin-based phototrophy may contribute to supplemental energy acquisition under osmotic stress conditions. The integration of functional and taxonomic data highlights the metabolic versatility and ecological roles of microbial taxa in sustaining biogeochemical processes under hypersaline conditions. Overall, this study reveals extensive taxonomic novelty and functional plasticity among microbial communities in Lake Barkol and underscores the influence of salinity in structuring microbial assemblages and metabolic pathways in athalassohaline ecosystems.

Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.

Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety of biotechnological applications. Limnohabitans, with a ubiquitous distribution, is a metabolically versatile, fast-growing, morphologically diverse freshwater lake bacterial genera. It is especially abundant in pH-neutral and alkaline aquatic habitats, where it represents an average of 12% of freshwater bacterioplankton and plays an important role in funneling carbon from primary producers to higher trophic levels. However, no phages infecting Limnohabitans have been reported to date. Here, we describe, for the first time, three phages infecting Limnohabitans, DC31, DC33, and YIMV22061, isolated from two freshwater lakes in China and characterized using genome content analysis and comparative genomics. DC31 and DC33, recovered from the eutrophic Dianchi Lake, with auxiliary metabolic genes (AMGs), associated with nucleotide metabolism, whereas YIMV22061, isolated from the oligotrophic Fuxian Lake, carried AMGs involved in antibiotic resistance. The AMGs they carried highlight their impacts on Limnohabitans in different environments. Comparative genomic analyses indicate that DC31, DC33, and YIMV22061 represent three novel species in the Caudoviricetes class. IMG/VR database alignment further reveal that these phages are widely distributed across diverse aquatic and terrestrial ecosystems globally, suggesting their ecological significance. This study provides a basis for better understanding Limnohabitans–phage interactions.

ABSTRACT Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale. IMPORTANCE Candidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth’s prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system. Candidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth’s prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.

Mineral and organic fertilizers as well as microbial inoculations are crucial to maintain and to improve soil health and quality, ecosystem functions, and fruit yield in Camellia oleifera plantations. However, how these fertilizers shape the life strategies and functions of microbial communities in soil is unclear. Here, we conducted a one-year field experiment with three types of fertilizers: mineral (NPK), manure (Man), and microbial (MicrF), and analyzed soil properties, bacterial and fungal communities to assess microbial life strategies, functional traits and their determinants. The application of MicrF strongly increased the diversity of both soil bacterial (by 6.4%) and fungal communities (by 23%). Organic matter inputs from Man and MicrF had greater effects on the life strategies of bacteria than fungi: the dominant r-strategy bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased with Man and MicrF, but K-strategists (Acidobacteria) decreased. Conversely, the abundance of r-strategy fungi (Ascomycota) decreased, but that of K-fungi (Basidiomycota) increased. Predictions of the functions indicated that microbial fertilization accelerated the bacterial carbohydrates, carbon and nitrogen metabolism, while also increasing the prevalence of wood saprotrophic fungi. The changes in the taxonomic and functional characteristics of the microbial communities induced priming effects by co-metabolism, which were mainly regulated by contents of soil organic carbon, available phosphorus, and ammonium nitrogen, as well as carbon to nitrogen ratio. The application of MicrF is an effective approach to increase the diversity and multifunctionality of soil microbial communities in Camellia oleifera plantations, including organic matter decomposition, carbon and nitrogen metabolism. These findings provide valuable insights into the fertilizer regimes based on microbial ecological strategies and functional profiles in Camellia oleifera plantations.

Introduction Pristine soil, ornithogenic soil, intertidal sediment, and marine sediment represent four of typical habitats in the Fildes region, maritime Antarctica. However, information on bacterial community composition and function in these Antarctic habitats remain limited. Methods In this study, using a combination of 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing, 12 samples collected from various habitats in the region were analyzed. Results and discussion Bacterial community compositions in terrestrial habitats (i.e., pristine and ornithogenic soils) were found to be distinct (p < 0.01) from those in marine habitats (i.e., marine and intertidal sediments). Organic carbon (p < 0.01) and pH (p < 0.01) were two major environmental factors affecting the bacterial community composition in the diverse habitats. Proteobacteria (represented by Gamma-, Alpha-, and Betaproteobacteria; > 30%), Actinobacteria (represented by Actinobacteria; > 20%), and Bacteroidetes (represented by Flavobacteriia; > 10%) were dominant in bacteria related to carbon, nitrogen, and sulfur metabolism across all samples. Though most metabolic pathways were common in both terrestrial and marine habitats, terrestrial samples showed more diverse metabolic pathways than marine samples. However, among the top 15 abundant metabolic pathways, genes related to 11 metabolic pathways were relatively more abundant in marine habitats than in terrestrial habitats (p < 0.05). More abundant genes related to methane metabolism (e.g., pmoA), nitrification (e.g., amoA and hao), reductive citrate cycle pathway (e.g., frdA), repair of DNA damage (e.g., lexA and uvrB), salt and osmotic stress tolerance (e.g., betB, gltB, and treS), and aromatic hydrocarbon degradation (e.g., bcrC and bssA) were detected in pristine and/or ornithogenic soils, whereas genes related to sulfur metabolism (e.g., soxY, fccB, dsrAB, and sat), nitrogen fixation (e.g., nifH), acetyl-CoA metabolism (e.g., acsB, cdhD, and cdhE), carbohydrate degradation (e.g., amyA and chiA), and cold adaptation (e.g., cspA, deaD and recQ) were in higher abundance in marine and/or intertidal sediments. The influence of penguin feces on soil bacterial community composition and ecological function was observed in this study. The study findings will improve our understanding of bacterial community composition and function in various habitats in maritime Antarctica under the background of global climate change.

Bacteria in the genus Gallaecimonas are known for their ability to breakdown complex hydrocarbons, making them of particular ecological and biotechnological significance. However, few species have been isolated to date, and their ecological distribution has yet to be examined. Here, we report a novel strain of G. pentaromativorans, designated as strain 10A, which was isolated from a Pacific oyster (Magallana gigas, a.k.a. Crassostrea gigas) collected from a farm experiencing a mass mortality event in British Columbia (BC), Canada. Gallaecimonas pentaromativorans strain 10A is a rod-shaped, motile bacterium and has a circular genome of 4,322,156 bp encoding 3,928 protein-coding sequences (CDS). Phylogenetic analysis showed that strain 10A is closely related to members of G. pentaromativorans. Like other Gallaecimonas members, strain 10A is predicted to harbor specific pathways involved in degrading xenobiotic compounds including polycyclic aromatic hydrocarbons (PAHs), producing biosurfactants, and assimilating nitrate and sulfate; however, it is uniquely equipped with an additional 166 genes belonging to 147 protein families, including a putative higB-higA that likely contributes to enhanced stress response. Strain 10A also possesses Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and CRISPR-associated (Cas) system (CRISPR-Cas), prevalent in Gallaecimonas (detected in three out of four species), implying a potential defense mechanism against exogenous mobile genetic elements such as plasmids and viruses. We also mined publicly available databases to establish the widespread distribution of bacteria in the genus Gallaecimonas in seawater, sediments, and freshwater across latitude, suggesting its versatility and importance to environmental processes. Ultimately, this study demonstrates that the genome of G. pentaromativorans strain 10A, isolated from a Pacific oyster, may encode a suite of putative functions, including xenobiotic breakdown, biosurfactant production, and CRISPR-Cas defense. This plasticity and breadth in metabolic function help to explain the cosmopolitan distribution of members of this genus.

Despite being the world’s third largest ocean, the Indian Ocean is one of the least studied and understood with respect to microbial diversity as well as biogeochemical and ecological functions. In this study, we investigated the microbial community and its metabolic potential for nitrogen (N) acquisition in the oligotrophic surface waters of the Indian Ocean using a metagenomic approach. Proteobacteria and Cyanobacteria dominated the microbial community with an average 37.85 and 23.56% of relative abundance, respectively, followed by Bacteroidetes (3.73%), Actinobacteria (1.69%), Firmicutes (0.76%), Verrucomicrobia (0.36%), and Planctomycetes (0.31%). Overall, only 24.3% of functional genes were common among all sampling stations indicating a high level of gene diversity. However, the presence of 82.6% common KEGG Orthology (KOs) in all samples showed high functional redundancy across the Indian Ocean. Temperature, phosphate, silicate and pH were important environmental factors regulating the microbial distribution in the Indian Ocean. The cyanobacterial genus Prochlorococcus was abundant with an average 17.4% of relative abundance in the surface waters, and while 54 Prochlorococcus genomes were detected, 53 were grouped mainly within HLII clade. In total, 179 of 234 Prochlorococcus sequences extracted from the global ocean dataset were clustered into HL clades and exhibited less divergence, but 55 sequences of LL clades presented more divergence exhibiting different branch length. The genes encoding enzymes related to ammonia metabolism, such as urease, glutamate dehydrogenase, ammonia transporter, and nitrilase presented higher abundances than the genes involved in inorganic N assimilation in both microbial community and metagenomic Prochlorococcus population. Furthermore, genes associated with dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification and anammox were absent in metagenome Prochlorococcus population, i.e., nitrogenase and nitrate reductase. Notably, the de novo biosynthesis pathways of six different amino acids were incomplete in the metagenomic Prochlorococcus population and Prochlorococcus genomes, suggesting compensatory uptake of these amino acids from the environment. These results reveal the features of the taxonomic and functional structure of the Indian Ocean microbiome and their adaptive strategies to ambient N deficiency in the oligotrophic ocean.

In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. ABSTRACT The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.

Biofilm-dwelling microorganisms coat the surfaces of stones in river and stream ecosystems, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning1,2. Flowing water (lotic) ecosystems are under pressure from a wide range of interacting stressors including changes in land use, chemical pollution, and climate3. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are limited by a lack of understanding of their taxonomic composition and physicochemical drivers across large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England, analogous to other large-scale efforts to understand microbial biogeography across diverse environments4,5,6,7. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England’s extensive river network, revealing substantial taxonomic novelty, with ∼20% of the MAGs representing novel genera. We demonstrated that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and play a significant role in nutrient cycling with the potential for contaminant transformation. Environmental drivers, most notably geology, land cover, and nutrients, explained up to 90% of the variation in community composition. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.

Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial symbionts of plants and animals, and as ubiquitous organisms found free-living in many environments. Succeeding in these niches requires an ability to persist for potentially long periods of time in growth-arrested states when essential nutrients become limiting. The tendency of these bacteria to grow in dense biofilm communities frequently leads to the development of steep nutrient gradients and deprivation of interior cells even when the environment is nutrient rich. Surviving within host environments also likely requires tolerating growth arrest due to the host limiting access to nutrients and transitioning between hosts may require a period of survival in a nutrient-poor environment. Interventions to maximise plant-beneficial activities and minimise infections by bacteria will require a better understanding of metabolic and regulatory networks that contribute to starvation survival, and how these networks function in diverse organisms. Here we focus on carbon starvation as a growth-arresting condition that limits availability not only of substrates for biosynthesis but also of energy for ongoing maintenance of the electrochemical gradient across the cell envelope and cellular integrity. We first review models for studying bacterial starvation and known strategies that contribute to starvation survival. We then present the results of a survey of carbon starvation survival strategies and outcomes in ten bacterial strains, including representatives from the orders Enterobacterales and Pseudomonadales (both Gammaproteobacteria) and Burkholderiales (Betaproteobacteria). Finally, we examine differences in gene content between the highest and lowest survivors to identify metabolic and regulatory adaptations that may contribute to differences in starvation survival.

Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.

Background Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques. Results Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle. Conclusions The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract

The deciphering of the phylogenetic diversity and metabolic features of the abundant bacterial taxa is critical for exploring their ecological importance and application potential. Qipengyuania is a genus of frequently isolated heterotrophic microorganisms with great industrial application potential. Numerous strains related to the genus Qipengyuania have been isolated from diverse environments, but their genomic diversity and metabolic functions remain unclear. ABSTRACT Members of the genus Qipengyuania are heterotrophic bacteria frequently isolated from marine environments with great application potential in areas such as carotenoid production. However, the genomic diversity, metabolic function, and adaption of this genus remain largely unclear. Here, 16 isolates related to the genus Qipengyuania were recovered from coastal samples and their genomes were sequenced. The phylogenetic inference of these isolates and reference type strains of this genus indicated that the 16S rRNA gene was insufficient to distinguish them at the species level; instead, the phylogenomic reconstruction could provide the reliable phylogenetic relationships and confirm 15 new well-supported branches, representing 15 putative novel genospecies corroborated by the digital DNA-DNA hybridization and average nucleotide identity analyses. Comparative genomics revealed that the genus Qipengyuania had an open pangenome and possessed multiple conserved genes and pathways related to metabolic functions and environmental adaptation, despite the presence of divergent genomic features and specific metabolic potential. Genetic analysis and pigment detection showed that the members of this genus were identified as carotenoid producers, while some proved to be potentially aerobic anoxygenic photoheterotrophs. Collectively, the first insight into the genetic diversity and metabolic potentials of the genus Qipengyuania will contribute to better understanding of the speciation and adaptive evolution in natural environments. IMPORTANCE The deciphering of the phylogenetic diversity and metabolic features of the abundant bacterial taxa is critical for exploring their ecological importance and application potential. Qipengyuania is a genus of frequently isolated heterotrophic microorganisms with great industrial application potential. Numerous strains related to the genus Qipengyuania have been isolated from diverse environments, but their genomic diversity and metabolic functions remain unclear. Our study revealed a high degree of genetic diversity, metabolic versatility, and environmental adaptation of the genus Qipengyuania using comparative genomics. Fifteen novel species of this genus have been established using a polyphasic taxonomic approach, expanding the number of described species to almost double. This study provided an overall view of the genus Qipengyuania at the genomic level and will enable us to better uncover its ecological roles and evolutionary history.

Introduction Karst subterranean systems are vulnerable ecosystems that have not yet been studied adequately at the microbial functional level. Cave sediments deposited over different time periods host diverse microbial communities that play a critical role in nutrient cycling and pollutant degradation. Methods In this study, we investigated microbial diversity and metabolic capacity in recently deposited alluvial sediments and an ancient palaeo-river deposit in a karst cave system. Using 16S rRNA gene amplicon metagenomic analysis, community-level physiological profiling (CLPP), and chemical characteristics of the environment, the influence of key environmental factors on microbial community composition and substrate degradation, concentrating particularly upon sediment age, oxygen availability, and temperature, was assessed. Results The results showed different microbiome compositions and metabolic characteristics between sites. The old alluvial sediment exhibited low taxonomic and functional diversity, accompanied by elevated heavy-metal concentrations, suggesting that sediment age might act as a geochemical filter, limiting microbial function. In contrast, a periodically flooded site showed high metabolic versatility and taxonomic diversity, emphasizing the ecological role of hydrological pulses in maintaining functional microbial diversity. CLPP metrics linked community structure to functional potential, revealing adaptive traits in key taxa such as Polaromonas, Methylibium, and Beggiatoa. Discussion These results demonstrated the value of integrating functional and taxonomic approaches in subsurface environments and provide insights into microbial resilience, biogeochemical processes, and the potential for applied environmental use.

Elucidating the interactions between algal and microbial communities is essential for understanding the dynamic mechanisms regulating algal blooms in the marine environment. Shifts in bacterial communities when a single species dominates algal blooms have been extensively investigated. However, bacterioplankton community dynamics during bloom succession when one algal species shift to another is still poorly understood. In this study, we used metagenomic analysis to investigate the bacterial community composition and function during algal bloom succession from Skeletonema sp. to Phaeocystis sp. The results revealed that bacterial community structure and function shifted with bloom succession. The dominant group in the Skeletonema bloom was Alphaproteobacteria, while Bacteroidia and Gammaproteobacteria dominated the Phaeocystis bloom. The most noticeable feature during the successions was the change from Rhodobacteraceae to Flavobacteriaceae in the bacterial communities. The Shannon diversity indices were significantly higher in the transitional phase of the two blooms. Metabolic reconstruction of the metagenome-assembled genomes (MAGs) showed that dominant bacteria exhibited some environmental adaptability in both blooms, capable of metabolizing the main organic compounds, and possibly providing inorganic sulfur to the host algae. Moreover, we identified specific metabolic capabilities of cofactor biosynthesis (e.g., B vitamins) in MAGs in the two algal blooms. In the Skeletonema bloom, Rhodobacteraceae family members might participate in synthesizing vitamin B1 and B12 to the host, whereas in the Phaeocystis bloom, Flavobacteriaceae was the potential contributor for synthesizing vitamin B7 to the host. In addition, signal communication (quorum sensing and indole-3-acetic acid molecules) might have also participated in the bacterial response to bloom succession. Bloom-associated microorganisms showed a noticeable response in composition and function to algal succession. The changes in bacterial community structure and function might be an internal driving factor for the bloom succession.

High-resolution 16S rRNA tag pyrosequencing was used to obtain seasonal snapshots of the bacterial diversity and community structure at two locations in Gosung Bay (South Sea, Korea) over a one year period. Seasonal sampling from the water column at each site revealed highly diverse bacterial communities containing up to 900 estimated Operational Taxonomic Units (OTUs). The Alphaproteobacteria and Gammaproteobacteria were the most abundant groups, and the most frequently recorded OTUs were members of Pelagibacter and Glaciecola. In particular, it was observed that Arcobacter, a genus of the Epsilonproteobacteria, dominated during summer. In addition, Psedoalteromonadaceae, Vibrionaceae and SAR11-1 were predominant members of the OTUs found in all sampling seasons. Environmental factors significantly influenced the bacterial community structure among season, with the phosphate and nitrate concentrations contributing strongly to the spatial distribution of the Alphaproteobacteria; the Gammaproteobacteria, Flavobacteria, and Actinobacteria all showed marked negative correlations with all measured nutrients, particularly silicon dioxide and chlorophyll-a. The results suggest that seasonal changes in environmental variables contribute to the dynamic structure of the bacterial community in the study area.

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This study investigated the microbial structure in the surface seawater from five coastal sites around Xiamen Island, China, over four seasons to evaluate seasonal environmental fluctuations impact on them. This subtropical island is characterized by long, hot, humid summers, and short, mild, dry winters. All sites were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes; microbial community composition was similar across four seasons. However, larger proportions of Gammaproteobacteria and Bacillus were observed during the summer than during any other season. The high ratio of Bacillus, Bacteroidetes, and Clostridia richness to Alphaproteobacteria richness in the summer, suggested that the sites we tested were heavily affected by waste water to other seasons. Correlation-based network analyses among the bacterial species and environmental variables indicated important connections between physiochemical variables and specific taxonomic groups. Collectively, our results suggested that seasonal shifts and wastewater pollution together shape the structures of the microbial communities around Xiamen Island.

Algae-associated microbiomes are underexplored, limiting our understanding of their influence on the large-scale microalgae reactors. Over two 8-month periods, microbial dynamics were monitored three times per week in two microalgae raceways inoculated with Desmodesmus armatus. One reactor received wastewater, while the other used clean water and fertilizers. The sampled culture volume was filtered into pico and nano size fractions before DNA extraction. Metabarcoding of the 18S and 16S rRNA genes revealed a high microbial diversity across the two time series and a complex eukaryotic and prokaryotic community growing alongside the microalga. Chlorophyta and Fungi were the dominant eukaryotic groups, while Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Bacteroidia dominated the prokaryotic communities. Contrasting Amplicon Sequence Variants (ASVs) were found between healthy (D. armatus abundance > 70 %) and unhealthy (D. armatus abundance 10-20 %) conditions across reactors and time series. Network analysis identified up to 10 potential ecological interactions among D. armatus and its microbiome, predominantly positive. Specific ASVs associated with a healthy condition were positively correlated with D. armatus, while other ASVs linked to an unhealthy condition were negatively correlated. Potentially pathogenic bacteria included Mycobacterium and Flavobacterium, whereas potentially beneficial taxa included Geminocystis, Thiocapsa, Ahniella, and Bosea. Several fungal ASVs showed context-specific associations, whereas specific fungi such as Paraphelidium tribonemae, Aphelidium parallelum, Aphelidium desmodesmi, Aphelidiomycota sp., Rozellomycota sp., and Rhizophidium sp, were identified as potentially harmful. This study reveals the striking diversity and complexity of microalgae-associated microbiomes within raceways, providing valuable insights for optimizing industrial production processes, particularly for wastewater treatment and sustainable green biomass generation.

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Abstract. Susanto I, Jayanegara A, Ridwan R, Wiryawan IKG, Laconi EB. 2025. Metagenomic insights into microbial community dynamics of fermented Indigofera zollingeriana supplemented with probiotics and phytobiotics. Biodiversitas 26: 2684-2695. Silage fermentation is an effective method for preserving forage by utilizing microbial activity under anaerobic conditions to maintain its nutritional value and prolong storage stability. Indigofera zollingeriana is a high-protein and fibre-rich forage, making it a promising candidate for silage. However, fermentation success depends on microbial communities involved in organic matter degradation. This study employed Next-Generation Sequencing (NGS) with the Illumina platform to analyze the microbial composition of Indigofera silage, enabling precise genus-level identification via 16S rRNA sequencing. The study evaluated microbial diversity and population shifts in silage supplemented with phytobiotics, probiotics, and their combination. The results showed that Gammaproteobacteria dominated all treatments (>90%), with Bacilli and Alphaproteobacteria present in smaller proportions. The combination treatment exhibited the highest microbial diversity, with increased Betaproteobacteria and Actinomycetes, which aid fibre degradation. The low presence of Clostridia suggested well-controlled fermentation. At the family level, Enterobacteriaceae were dominant in single LAB and phytobiotic treatments, while the combination treatment reduced Enterobacteriaceae and increased Moraxellaceae and Enterococcaceae, which support fermentation stability. At the genus level, Enterobacter was prevalent, but the combination treatment increased Pantoea and Leclercia, indicating a more balanced fermentation ecosystem. Alpha diversity and Principal Coordinates Analysis (PCoA) confirmed that the combination treatment promoted microbial diversity and fermentation stability while suppressing Enterobacter cloacae. Treatment using acacia bark extract showed effectiveness in the smallest Costridia population (2%). These findings highlight the importance of combining probiotics and phytobiotics to enhance silage quality and microbial balance, emphasizing the need for further research on microbial interactions in fermentation.

An atypical winter Cerataulina pelagica bloom outbroke in Laizhou Bay (LZB), southern Bohai Sea during Nov. 2021 and Feb. 2022, which caused a significant economic loss of aquaculture industry. Here, we conducted three large-scale cruise surveys (summer, autumn, and winter) and a one-year surveys (control, pre-bloom, bloom, and post-bloom) in LZB, and used 16S and 18S rRNA genes high-throughput sequencing techniques to reveal the dynamics of microbial communities during the C. pelagica blooms. Our results showed that microbial diversity decreased during algal blooms in both surveys. In addition, there were significant differences between microbial communities at each stage. In the large-scale surveys, the dominant phytoplankton groups changed from Chlorophyta and Dinoflagellate to Bacillariophyta (mainly Cerataulina) with the occurrence of algal blooms in winter. Alphaproteobacteria (Rhodobacteraceae and Clade I) and Actinobacteriota (Actinomarinaceae and Microbacteriaceae) were the most abundant bacterial taxa. In the one-year surveys, Cerataulina were, as expected, the dominant phytoplankton group during the bloom period. Rhodobacteraceae and Bacteroidota (Flavobacteriaceae) were the dominant bacterial groups during the peak period of blooms, whereas Microbacteriaceae gradually enriched with the decline of blooms. A variety of environmental factors (temperature, salinity, and nutrients) had significant effects on microbial communities. In addition, co-occurrence network analysis revealed positive relationships within microbial communities during algal blooms. The microbial prediction function mainly included phototrophy, chemoheterotrophy, and nitrogen and sulfur metabolisms, and there were significant changes in different stages. Overall, this study further reveals the interaction mechanisms and ecological effects of microbial communities during algal blooms.

Introduction The study explores the indirect impact of climate change driven by gentoo’s penguin colonization pressure on the microbial communities of moss banks formed by Tall moss turf subformation in central maritime Antarctica. Methods Microbial communities and chemical composition of the differently affected moss banks (Unaffected, Impacted and Desolated) located on Galindez Island and Сape Tuxen on the mainland of Kyiv Peninsula were analyzed. Results The native microbiota of the moss banks’ peat was analyzed for the first time, revealing a predominant presence of Acidobacteria (32.2 ± 14.4%), followed by Actinobacteria (15.1 ± 4.0%) and Alphaproteobacteria (9.7 ± 4.1%). Penguin colonization and subsequent desolation of moss banks resulted in an increase in peat pH (from 4.7 ± 0.05 to 7.2 ± 0.6) and elevated concentrations of soluble nitrogen (from 1.8 ± 0.4 to 46.9 ± 2.1 DIN, mg/kg) and soluble phosphorus compounds (from 3.6 ± 2.6 to 20.0 ± 1.8 DIP, mg/kg). The contrasting composition of peat and penguin feces led to the elimination of the initial peat microbiota, with an increase in Betaproteobacteria (from 1.3 ± 0.8% to 30.5 ± 23%) and Bacteroidota (from 5.5 ± 3.7% to 19.0 ± 3.7%) proportional to the intensity of penguins’ impact, accompanied by a decrease in community diversity. Microbial taxa associated with birds’ guts, such as Gottschalkia and Tissierella, emerged in Impacted and Desolated moss banks, along with bacteria likely benefiting from eutrophication. The changes in the functional capacity of the penguin-affected peat microbial communities were also detected. The nitrogen-cycling genes that regulate the conversion of urea into ammonia, nitrite oxide, and nitrate oxide (ureC, amoA, nirS, nosZ, nxrB) had elevated copy numbers in the affected peat. Desolated peat samples exhibit the highest nitrogen-cycle gene numbers, significantly differing from Unaffected peat (p < 0.05). Discussion The expansion of gentoo penguins induced by climate change led to the replacement of acidophilic microbiomes associated with moss banks, shaping a new microbial community influenced by penguin guano’s chemical and microbial composition.

The activated sludge system used in wastewater treatment plants has demonstrated partial removal capabilities for various contaminants of emerging concern (CECs). However, existing research primarily focuses on the removal efficiency individual or combined CECs, with limited research addressing their impact on microbial community. In this study, three activated sludge systems were developed to investigate the effects of low concentrations of CECs, including five types of antibiotics and five types of non-antibiotic CECs. The results showed that activated sludge could effectively degrade non-antibiotic CECs within 3 -5 days even in the third cycle, whereas the degradation of antibiotics was more variable. Compared to the AA-Group, Alphaproteobacteria, Anaerolineae, Planctomycetes, Gammaproteobacteria, and Bacteroidia shifted to connector in the non-AA treatment as keystones species. Variance partitioning and co-occurrence network analysis showed that CECs exert significant deterministic influences, surpassing traditional environmental factors. Notably, antibiotics promoted microbial interactions more than other CECs, the finding was further validated by null model analysis. Our study provides novel insights into the differential impacts of low-concentration CECs on microbial community dynamics and interactions. Findings highlight the necessity to better understand the complex microbial processes driven by CECs, particularly antibiotics, to further develop more efficient biological treatment processes for CECs removal.

The earthworm species Lumbricus terrestris L. feeds on plant litter mixed with surrounding soil. Here, we analyzed with a mesocosm approach and soil incubations how that activity and subsequent ageing of casts (feces) affects the abundance and diversity of the soil microbiome. Earthworms were fed either with straw of sainfoin (SA, Onobrychis viciifolia; C/N ratio 22) or winter wheat (WW, Triticum aestivum , C/N ratio 101). The gut transit increased the abundances of bacteria and fungi, but reduced archaea. As indicated at the DNA and RNA level, main beneficiaries of the facilitated access to nutrients were members of Bacteroidota, especially Flavobacter-iales with an estimated generation time of only 2 h. While Alphaproteobacteria were reduced, Gammaproteo-bacteria also increased in abundance and activity. SA was more nutritious for L. terrestris , and supported a higher bacterial abundance, probably because more N was available for growth and denitrification. During cast ageing, prokaryotic community compositions became increasingly similar to bulk soil communities. However, they remained distinguishable even after 168 d, suggesting that effects can last beyond a vegetation period. Dry-wet conditions preserved these differences better than continuous moisture. During ageing, more complex prokaryotic networks were detected with WW and dry-wet conditions. Thus, N and water limitations appeared to enhance cooperation rather than competition between the prokaryotes. Overall, this study demonstrates that earthworm soil interactions strongly affect the diversity and temporal dynamics of the soil microbiome. Legacy effects of earthworm activities should thus be kept in mind when investigating the environmental variation of soil microbiomes.

Marine macroalgae and their associated microbial communities are pivotal in shaping coastal ecosystems and facilitating biogenic elements' biochemical cycles. In this study, we implemented the high-throughput sequencing technology to sequence bacterial 16S rRNA gene to comprehensively analyze the bacterial communities of healthy and diseased macroalgae as well as the surrounding seawaters. The results revealed that Proteobacteria and Bacteroidota were the two main phylum in all samples. Alphaproteobacteria, Gammaproteobacteria and Bacteroidota were the predominant bacterial classes. This observation underscored that the composition of bacterial communities remains comparably consistent at higher taxonomic levels, regardless of variations in their health statuses. The alpha-diversity indices of seawater bacterial communities, epiphytic communities, and endophytic communities showed no significant differences. Epiphytic bacterial communities harbored a greater proportion of colonized bacteria, such as Vibrio and Pseudomonas. While endophytic bacterial communities contained a higher presence of tissue-degrading microbial assemblages, the primary bacterial communities were predominantly affiliated with Rhodobacteraceae and Flavobacteriaceae. Temperature, salinity, nitrate and nitrite concentration were the most significant properties correlated with seawater, epiphytic and endophytic bacterial communities in different health statuses revealed by Canonical correspondence analysis. A PICRUSt analysis demonstrated the metabolic functional prediction. Nitrogen and sulfate reduction genes were mainly concentrated in epiphytic bacterial communities in good health. Endophytic bacterial communities in disease had higher carbon and nitrogen fixation potentials. These results confirmed that bacteria, macroalgae, and environmental properties had an interactive relationship, all related to the momentous ecological benefits of macroalgae.

Simple Summary Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are promising molecular biomarkers widely applied in paleoenvironmental reconstruction. However, their biological origins within marine ecosystems remain poorly understood. In this study, both ‘living’ intact polar lipid-derived brGDGTs (IPL-brGDGTs) and ‘fossil’ core brGDGTs (CL-brGDGTs), together with bacterial community compositions, were analysed across multiple sediment cores collected along a nearshore-to-offshore gradient in the East China Sea (ECS). The results suggest that Gammaproteobacteria, Dehalococcoidia, Alphaproteobacteria, Bacilli, and Actinobacteria are the primary potential producers of brGDGTs in nearshore environments. In contrast, Anaerolineae, Phycisphaerae, and Desulfobacteria dominate as likely producers in offshore regions. The distribution of brGDGTs is primarily shaped by variations in bacterial community composition. Furthermore, the vertical distribution profiles of both bacterial communities and IPL-brGDGTs—believed to be predominantly synthesised in situ—indicate that physical disturbance processes, such as wave action, tidal forces, and storm events, significantly influence the distributions of bacterial communities and IPL-brGDGTs in near-surface sediments. This study provides new insights into the biological sources of brGDGTs in marine environments. It highlights the importance of considering physical disturbance effects when interpreting sedimentary brGDGT records for paleoenvironmental reconstructions in marginal seas, such as the ECS.

Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown. Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms. The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.

Soil pH critically regulates microbial community structure and activity, thereby influencing carbon transformation processes in terrestrial ecosystems. However, the mechanisms underlying pH-mediated shifts in microbial metabolic functions and cellulose-degrading functional genes remain poorly understood. This study investigated the responses of bacterial communities, metabolic profiles, and the abundance of cellobiohydrolase I (cbhI) and glycoside hydrolase family 48 (GH48) genes to varying pH levels in fluvo-aquic and red soils. High-throughput sequencing, PICRUSt-based metabolic prediction, and quantitative PCR were employed to analyze microbial composition, functional traits, and gene dynamics. Network analysis clarified linkages between functional genes, pathways, and taxa. The results revealed that elevated pH significantly increased CO2 emissions and dissolved organic carbon (DOC) content in both soils. Dominant taxa, including Alphaproteobacteria, Bacteroidetes, Xanthomonadaceae, and Mycoplasma, exhibited pH-dependent enrichment. Metabolic predictions indicated that pH positively influenced genes linked to biodegradation and xenobiotic metabolism in fluvo-aquic soil but suppressed energy-metabolism-related genes. Contrastingly, in red soil, cbhI and GH48 gene abundance declined with rising pH, suggesting that acidic conditions favor cellulolytic activity. Network analysis identified strong positive correlations between CO2 emissions and Caulobacteraceae, while cbhI and GH48 genes were closely associated with taxa such as Xanthomonadaceae, Comamonadaceae, and Micromonosporaceae, which drive organic matter decomposition. These findings underscore pH as a pivotal regulator of microbial community structure and functional gene expression, with soil-specific responses highlighting the need for tailored strategies to optimize carbon cycling and sequestration in agricultural ecosystems.

Seagrass meadows produce organic carbon and deposit it on the seabed through the decaying process. Microbial activity is closely related to the process of eelgrass death and collapse. We investigated the microbial community structure of eelgrass during the eelgrass decomposition process by using a microcosm containing raw seawater and excised eelgrass leaves collected from a Zostera marina bed in Futtsu, Chiba Prefecture, Japan. The fast-growing microbes (i.e., Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia) rapidly adhered to the eelgrass leaf surface and proliferated in the first two weeks but gradually decreased the relative abundance as the months moved on. On the other hand, the slow-growing microbes (i.e., Cytophagia, Anaerolineae, Thaumarchaeota, and Actinobacteria) became predominant over the eelgrass surface late in the culture experiment (120, 180 days). The fast-growing groups of Gammaproteobacteria and Flavobacteriia appear to be closely related to the initial decomposition of eelgrass, especially the rapid decomposition of leaf-derived biopolymers. Changes in nitrogen content due to the bacterial rapid consumption of readily degradable organic carbon induced changes in the community structure at the early stage of eelgrass decomposition. In addition, shifts in the C/N ratio were driven by microbial community changes during later decomposition phases.

Abstract Marine microorganisms are drivers of biogeochemical cycles in the world’s oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.

Radiation (e.g., nuclear leakage) is a common harmful factor in the ocean that potentially affects the microbial community in nearby benthic hosts such as jellyfish polyps, which is essential for the maintenance of jellyfish populations and high-quality medusae. After comparison with the microbial community of medusae, the effect of 60Co-γ on the microbial community in Aurelia coerulea polyps was dynamically tested using 16S rRNA gene sequencing. Our results suggested that Proteobacteria (76.19 ± 3.24%), Tenericutes (12.93 ± 3.20%) and Firmicutes (8.33 ± 1.06%) are most abundant in medusae, while Proteobacteria (29.49 ± 2.29%), Firmicutes (46.25 ± 5.59%), and Bacteroidetes (20.16 ± 2.65%) are the top three phyla in polyps. After 60Co-γ radiation, the proportion of Proteobacteria increased from 29.49 ± 2.29% to 59.40 ± 3.09% over 5 days, while that of Firmicutes decreased from 46.25 ± 5.59% to 13.58 ± 3.74%. At the class level, Gammaproteobacteria continually increased during the 5 days after radiation exposure, whereas Bacilli declined, followed by partial recovery, and Alphaproteobacteria and Flavobacteriia remained almost unchanged. Intriguingly, Staphylococcus from Firmicutes and three other genera, Rhodobacter, Vibrio, and Methylophaga, from Proteobacteria greatly overlapped according to their KEGG functions. It is concluded that the microbial community in A. coerulea polyps is distinct from that in the medusae and is greatly affected by 60Co-γ exposure, with a growth (0-3 d) period and a redistribution (3-5 d) period. The dynamic change in the microbial community is probably an important self-defense process in response to external interference that is regulated by the host's physiological characteristics and the intense interspecific competition among symbiotic microbes with similar functions and functional redundancies.

Marine microorganisms are vital to biogeochemical cycles and food web dynamics, with their community structure shaped by environmental factors such as temperature, light, and salinity. While microbial dynamics in the western Antarctic Peninsula are relatively well- studied, the northwestern region remains underexplored, particularly in long-term, multidomain analyses. To fill this gap, we investigated microbial communities encompassing all three domains of life (Bacteria, Archaea, and Eukarya) in the Northwestern Antarctic Peninsula. Using the universal primer set 515Y/926R, we sequenced unfractionated seawater from ten sites over a six-year period (2013–2019). Environmental parameters, temperature and salinity, showed minimal variation across the study. However, microbial diversity and composition, especially among eukaryotic phytoplankton, displayed significant temporal changes among seasons and years. The prokaryotic community, by contrast, was relatively stable, with Gammaproteobacteria— particularly the Nitrincolaceae family—maintaining high relative abundance throughout all sampling periods, but a few distinct ASVs. In contrast, no eukaryotic group exhibited consistently high relative abundance across sampling periods. The summer of 2016, marked by a strong El Niño event, presented the most distinct microbial community structure, underscoring the sensitivity of these communities to extreme climatic conditions. These results highlight the importance of integrated, long-term studies to better understand the dynamics, interactions, and resilience of microbial ecosystems in the rapidly changing Antarctic environment. IMPORTANCE This study provides a unique long-term perspective on microbial community dynamics in the Northwestern Antarctic Peninsula, a region still poorly explored through a multidomain lens. By investigating the temporal variability of Bacteria, Archaea, and Eukaryotes over six years, we reveal distinct stability patterns between these groups, with phytoplankton showing the highest variability and prokaryotes remaining relatively stable. The strong response of the microbial community to the 2016 El Niño event highlights its sensitivity to extreme climate conditions, reinforcing the importance of understanding how Antarctic ecosystems will respond to future climate shifts. The consistent presence of Nitrincolaceae, a key bacterial taxon, suggests its ecological relevance in the region, while fluctuations in phytoplankton composition may impact food web dynamics. These findings emphasize the need for continued long-term monitoring to predict how microbial communities will adapt to environmental changes, which is crucial for assessing the future functioning of polar marine ecosystems.

Accurate characterization of the movement of water through catchments, particularly during precipitation event response, is critical for hydrological efforts such as contaminant transport modeling or prediction of extreme flows. Abiotic hydrogeochemical tracers are commonly used to track sources and ages of surface waters but provide limited details about transit pathways or the spatial dynamics of water storage and release. Alternatively, biotic material in streams is derived from thousands of taxa originating from a variety of environments within watersheds, including groundwater, sediment, and upslope terrestrial environments, and this material can be characterized with genetic sequencing and bioinformatics. We analyzed the stable water isotopes (δ18O and δ2H) and microbiome composition (16S rRNA gene amplicon sequencing) of the Marys River of western Oregon, USA during an early season storm to describe the processes, storage, and flowpaths that shape surface water hydrology. Stable water isotopes (δ18O and δ2H) typified an event response in which stream water is composed largely of ‘old’ water introduced to the catchment before the storm, a common though not well understood phenomenon. In contrast, microbial biodiversity spiked during the storm, consisting of early- and late-event communities clearly distinguishable from pre-event communities. We applied concentration-discharge (cQ) analysis to individual microbial taxa and found that most Alphaproteobacteria sequences were positively correlated (i.e., were mobilized) with discharge, whereas most sequences from phyla Gammaproteobacteria and Bacteroidota were negatively correlated with discharge (i.e., were diluted). Source predictions using the prokaryote habitat preference database ProkAtlas found that freshwater-associated microbes composed a smaller fraction of the microbial community during the stream rise and a larger fraction during the recession, while soil and biofilm-associated microbes increased during the storm and remained high during recession. This suggests that the “old” water discharged during the storm was likely stored and released from, or passed through, soil- and biofilm-rich environments, demonstrating that this approach adds new, biologically derived tracer information about the hydrologic pathways active during and after this event. Overall, this study demonstrates an approach for integrating information-rich DNA into water resource investigations, incorporating tools from both hydrology and microbiology to demonstrate that microbial DNA is useful not only as an indicator of biodiversity but also functions as an innovative hydrologic tracer.

Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.

Amphibian microbial communities are known to be shaped by host physiology and environmental factors, yet the relative roles of sexual dimorphism and tissue specialization remain poorly understood. Using 16S rRNA gene sequencing, we compared the gastrointestinal and integumentary microbiomes of a monomorphic Chinese frog population, Odorrana schmackeri, inhabiting identical montane streams. Our results showed distinct phylogenetic stratification between niches: Proteobacteria dominated both environmental microbiota and O. schmackeri gut and skin microbiotas but with differential sub-phylum specialization. The soil microbiota was dominated by unclassified_Vicinamibacteraceae, the water microbiota was Limnohabitans-dominated, the skin microbiota was dominated by Bordetella, and the gut microbiota was led by Acinetobacter. Alpha diversity analysis revealed significant tissue- and environmental-based divergences but no sexual differentiation, a pattern confirmed by beta diversity assessments showing stronger microbial community separation by tissue and environmental compartmentalization than by sex. Functional metagenomic prediction indicated convergent enrichment of metabolic pathways across host-associated and environmental communities. These results suggest that microbial community structure in O. schmackeri is principally governed by tissue-specific ecological selection pressures rather than host sexual characteristics. Our findings enhance understanding of microbiome assembly rules in vertebrate ectotherms and identify potential connections between microbiota in different ecological niches.

Foreign AT-rich genes drive bacterial adaptation to new niches while challenging the existing regulation network. Here we report that MucR, a conserved regulator in α-proteobacteria, balances adaptation and regulatory integrity in Sinorhizobium fredii, a facultative microsymbiont of legumes. Chromatin immunoprecipitation sequencing coupled with transcriptomic data reveal that average transcription levels of both target and non-target genes, under free-living and symbiotic conditions, increase with their conservation levels. Targets involved in environmental adaptation and symbiosis belong to genus or species core and can be repressed or activated by MucR in a condition-dependent manner, implying regulatory integrations. However, most targets are enriched in strain-specific genes of lower expression levels and higher AT%. Within each conservation levels, targets have higher AT% and average transcription levels than non-target genes and can be further up-regulated in the mucR mutant. This is consistent with higher AT% of spacers between −35 and −10 elements of promoters for target genes, which enhances transcription. The MucR recruitment level linearly increases with AT% and the number of a flexible pattern (with periodic repeats of Ts) of target sequences. Collectively, MucR directly represses AT-rich foreign genes with predisposed high transcription potential while progressive erosions of its target sites facilitate regulatory integrations of foreign genes.

ABSTRACT The Hadal Zone is acknowledged for its extreme environmental conditions, especially high hydrostatic pressures. The dominant scavengers in the Hadal Zone, Hadal amphipods, fulfill vital roles in the Hadal food web and ecological niches. However, research on the gut microbiota of amphipods related to ecological functions and environmental adaptation is still limited. Here, we used 16S rRNA sequencing technology and a culture-dependent method to analyze the composition of the gut microbiota in Amphipoda living in the Mariana Trench. A total of 16 bacterial genera were identified. Among them, Firmicutes and Proteobacteria were the predominant phyla. The adaptability of gut probiotics to the environment was investigated. Pediococcus pentosaceus XY62 was picked up as the representative strain to elucidate the ecological functions of gut microbes in amphipods. The ProBio database and the K-B agar diffusion method indicated that P. pentosaceus XY62 exhibited the highest probiotic activity compared with all other isolated strains. Specific metabolic pathways and transporter systems that contribute to a range of environmental adaptation strategies have been revealed by genomic analysis of P. pentosaceus XY62. The environmental response genes and a specialized KDP transport system allow it to adapt to the challenging conditions of the Hadal Zone. In addition, the presence of antibacterial compounds and antibiotic resistance genes, as well as the ability to form a biofilm, facilitated the successful colonization of P. pentosaceus XY62 in the gut environment. IMPORTANCE Amphipods are widely distributed in the Hadal trenches, and the study of their gut microbes has garnered considerable scientific interest. Our research breaks away from traditional omics approaches, innovatively combining sequencing technologies with culture-dependent methods to analyze the gut microbiome structure of amphipods from the Mariana Trench. This not only complements the current omics-dominated field but also paves the way for future resource development of extreme microbes. Furthermore, by conducting genomic analyses and functional validations on a representative strain, we have uncovered its probiotic effects and strategies for adapting to extreme environments. This provides new insights into the theoretical study of the ecological functions of deep-sea bacteria. Overall, our findings offer a fresh perspective on the microbial community structure and environmental adaptation strategies of gut microorganisms in the Hadal Zone. Amphipods are widely distributed in the Hadal trenches, and the study of their gut microbes has garnered considerable scientific interest. Our research breaks away from traditional omics approaches, innovatively combining sequencing technologies with culture-dependent methods to analyze the gut microbiome structure of amphipods from the Mariana Trench. This not only complements the current omics-dominated field but also paves the way for future resource development of extreme microbes. Furthermore, by conducting genomic analyses and functional validations on a representative strain, we have uncovered its probiotic effects and strategies for adapting to extreme environments. This provides new insights into the theoretical study of the ecological functions of deep-sea bacteria. Overall, our findings offer a fresh perspective on the microbial community structure and environmental adaptation strategies of gut microorganisms in the Hadal Zone.

Endophytic bacteria play an important role in the growth, stress tolerance, and metabolic function of salt-tolerant peanuts, yet their community assembly across different saline–alkali soils and plant organs remains poorly characterized. In this study, the V3–V4 variable region of the endophytic bacteria 16S rRNA gene in three organs (roots, leaves, and pods) of high-oleic-acid peanut variety Huayu9118 from three saline–alkali locations (Xinjiang, Jilin, and Shandong, China) was analyzed by high-throughput sequencing. A total of 1,360,313 effective sequences yielded 19,449 amplicon sequence variants (ASVs), with Proteobacteria (45.86–84.62%), Bacteroidota (6.52–13.90%), and Actinobacteriota (3.97–10.87%) dominating all samples. Niche strongly influenced microbial diversity: the roots exhibited the highest level of richness (Chao 1/ACE indices), while the leaves showed the greatest diversity (Shannon/Simpson indices) in XJ samples. Significant compositional differences were observed between aerial (leaves) and underground (roots/pods) organs. Geographic location also markedly shaped endophytic communities, with stronger effects in roots and pods than in leaves—a pattern supported by PCoA combined with ANOSIM (R (roots) = 1, R (pods) = 0.874, R (leaves) = 0.336, respectively, p < 0.001). Saline–alkali adaptation led to a marked enrichment of Novosphingobium in roots and pods and of Halomonas in leaves compared to non-saline–alkali-grown peanuts. Furthermore, the endophytic communities within the same organ type varied significantly across the three saline–alkali sites. Redundancy analysis (RDA) identified the key environmental factors shaping bacterial community composition in the root samples from each location: available phosphorus (AP) and sulfate (SO42−) were the strongest predictors in XJ; available potassium (AK) and chloride (Cl−) in DY; and hydrolyzed nitrogen (HN), pH, soil organic matter (SOM), and bicarbonate (HCO3−) in JL. These findings demonstrate that niches and geographical conditions determined the composition and relative abundance of endophytic bacteria in salt-tolerant peanuts, providing new insights into microbial ecological adaptation in saline–alkali ecosystems.

ABSTRACT Gastrointestinal microorganisms play a crucial role in host survival and adaptation, but information on host-specific selection or environmental factors that shape the microbiome in natural populations is limited. In this study, we employed 16S rRNA gene amplicon sequencing to investigate the composition and predicted the functions of gut microbiota of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) from cold-water habitats across three geographically distant sea areas in the Northern Pacific Ocean. We also explored the potential influence of the host and environment on the microbiota. The two ophiuroids possessed diverse microbial communities, with Proteobacteria being the most dominant phylum in all four groups. Aliivibrio was the predominant genus in O. sarsii from the Bering Sea, while Candidatus Hepatoplasma was the dominant genus in O. sarsii from the Japan Sea and O. sarsii vadicola from the Yellow Sea. Predicted bacterial functions indicated that most of the pathways with significant differences belonged to metabolism and genetic information processing. Notably, no significant difference was observed between the two coexisting ophiuroid species in the Japan Sea. The high similarity in microbial communities between O. sarsii from the Japan Sea and O. sarsii vadicola from the Yellow Sea may be attributed to their analogous ecological niche. The host and the environment jointly shape the composition of the gut microbial community. The presence of specific microorganisms supports the ecological success of ophiuroids across diverse environments, providing a foundation for host adaptation to cold-water habitats. IMPORTANCE Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species. Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.

Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3–V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.

This study investigates the gut microbiota composition and functional adaptations in three indigenous fish species from the Kizil River, Xinjiang: Schizothorax biddulphi (SB), Diptychus maculatus (DM), and Triplophysa yarkandensis (TY), recognizing their ecological significance and the need for conservation insights. Shotgun metagenomics was employed to profile the gut microbiota and functional potential. Taxonomic and functional annotations were analyzed, including identification of dominant taxa, biomarkers (LEfSe), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for metabolic functions, and Carbohydrate-Active enZymes (CAZy) database annotations. Environmental parameters (crude oil pollution, nitrogen levels, pathogen presence) were assessed, and dietary shifts during overwintering were characterized. Distinct gut microbiota profiles were identified: Proteobacteria, Acinetobacter, and Pseudomonas were dominant overall. Species-specific biomarkers were Micromonospora (DM); Proteobacteria, Firmicutes, Aeromonas, and Bacillus (SB); and Mucoromycota, Vibrio, and Alcanivorax (TY). DM and SB exhibited significantly higher Firmicutes/Bacteroidetes ratios and enhanced nutrient utilization capabilities compared to TY. Key functional pathways included enriched fructose/mannose metabolism (SB) and oxidative phosphorylation (DM). CAZy analysis revealed high CE3 abundance across species, with GT6/GT10 (SB) and PL22 (TY) serving as unique enzymatic biomarkers. Dietary shifts during overwintering occurred: DM and TY transitioned towards herbivory, while SB retained carnivorous tendencies despite increased plant consumption. All species showed reduced immunity, with DM and SB particularly vulnerable to Acinetobacter-related infections. Environmental analysis revealed crude oil pollution, elevated nitrogen levels, and contamination with A. baumannii. TY demonstrated notable salinity adaptability but heightened sensitivity to pollution. Host phylogeny exerted a strong influence on microbiota composition and metabolic functions. The results demonstrate host-specific microbial adaptation driven by phylogeny. The distinct functional profiles (nutrient utilization, key metabolic pathways like fructose/mannose metabolism and oxidative phosphorylation, CAZy enzymes) reflect ecological niche specialization. The observed dietary shifts and reduced winter immunity, compounded by environmental stressors (crude oil, nitrogen, A. baumannii), highlight critical vulnerabilities, especially for DM and SB. TY’s salinity adaptation is counterbalanced by pollution sensitivity. This study provides essential insights for developing targeted conservation strategies and sustainable aquaculture practices for these indigenous species within their natural habitat, emphasizing the need for pollution mitigation.

Abstract Background: The Aromatoleum/Azoarcus/Thauera (AAT) cluster comprises anaerobic degradation specialists (Aromatoleum, Thauera) and N2-fixing endophytes (Azoarcus). Omics-based and genetic studies with associated model strains implicate stringent response (SR) in adaptation to nutrient limitation and plant colonization. SR is well-studied in standard bacteria such as Escherichia coli and known as adaptive strategy to nutrient limitations by adjusting e.g., transcription and stress response. SR involves the alarmone (p)ppGpp, whose cellular level is controlled by the synthetases/hydrolases RelA/SpoT and the noncanonical transcription factor DksA, whose interaction with RNA polymerase (RNAP) binding of (p)ppGpp enhances. Summary: DksA-mediated SR occurs across Proteobacteria and other phylogenetic groups such as Myxococcia and Spirochaetia, mostly applying to pathogens. Furthermore, all three DksA variants (four, two or one cysteine residue(s) for Zn2+-binding) were found. Genes encoding SR components are present in all studied 37 genomes representing 31 species from the AAT cluster. Each genome encodes a synthesizing RelA, a hydrolyzing SpoT, a four cysteine-containing DksA, and mostly also a one cysteine-containing DksA. Opposing functions of RelA and SpoT in Aromatoleum aromaticum EbN1T, Aromatoleum sp. strain CIB, Azoarcus olearius BH72, and Thauera aromatica K172T (also entire AAT cluster) are implicated by full conservation of amino acids (E and D vs. 2H2D motif and ED diad) essential for catalysis by their synthetase versus hydrolase domains. Likewise, functionality of the predicted C4-type DksAs from these four model strains was visually assessed by structural modeling and comparison of key features (binding sites for Zn2+/(p)ppGpp; CC tip for RNAP interaction) to those of the available E. coli DksA cryo-EM structure. Key Messages: SR as a global adaptation strategy should contribute to the success of the AAT cluster in its distinct habitats: complex and highly variable soils/sediments (high molecular and microbial diversity, fluctuating nutrient availabilities and redox states) of the free-living degradation specialists versus the defined endorhizosphere (more stable conditions, less complex community) of the endophytes. A noteworthy exception is Aromatoleum sp. strain CIB by combining degradation and endophytic features. Thus, future investigations into the role of SR in the habitat success of such bacteria reflecting their divergent environmental niches are needed as well as promising.

Microbial communities in river ecosystems regulate biogeochemical cycling and serve as natural bioremediators for environmental pollutants. However, accurately predicting their dynamic responses to changing conditions remains a significant scientific challenge because of the complexity of microbial interactions and ecosystem-scale feedbacks. Here, a novel compositional neural encoder-decoder (cNED) framework was developed, coupling environmental variables with microbial profiles based on an extensive collection of 473 samples from the upper Yangtze River. A total of 157 core bacterial OTUs were identified from 27,932 OTUs by the occupancy-frequency method, which were predominantly governed by deterministic assembly processes. The identified core microbiome demonstrated significant functional associations with carbon and nitrogen cycling. Compared with conventional modeling approaches (multilayer perceptron, random forests, linear regression), the cNED framework demonstrated superior predictive performance, achieving high accuracy in taxonomic prediction and functional profile prediction (carbon cycling: R² = 0.85; nitrogen cycling: R² = 0.52). The Shapley additive explanations (SHAP) analysis identified spatial gradients and temperature as key environmental drivers. Generalized Additive Models uncovered phylum- and function-specific tipping points: Proteobacteria exhibited a dual-threshold thermal niche (20.5-27 °C), while functions like methylotrophy and nitrogen fixation responded nonlinearly to temperature and TN, revealing unimodal or monotonic transitions. The cNED framework developed in this study establishes an interpretable predictive framework for forecasting microbial community and functional responses to environmental perturbations, offering valuable insights for evidence-based river ecosystem management and climate adaptation strategies.

Abstract Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.

ABSTRACT Microbial communities within animals provide nutritional foundation and energy supply for the hydrothermal ecosystem. The peltospirid snail Gigantopelta aegis forms large aggregation in the Longqi vent field on the Southwest Indian Ridge. This endemic species is characterized by a changeable diet and morphology, especially reflected in internal organs such as remarkably enlarged esophageal glands. Here, 16S full-length rRNA gene analysis was performed to compare the variations in esophageal gland microbiota between two body size groups (small and large) of G. aegis. Phyla Proteobacteria and Bacteroidetes were the dominant featured bacteria contributing to the microbial community. No significant differences between the small and large groups were revealed by the diversity index and principal component analysis (PCA) clustering. The differences were in the relative abundance of bacteria. Compared with small-sized snails, the larger ones housed more Thiogranum (9.94% to 34.86%) and fewer Sediminibacterium (29.38% to 4.54%). Functional prediction for all of the microbiota showed that the pathways related to metabolism appeared highly abundant in smaller G. aegis. However, for the larger ones, the most distinctive pathways were those of environmental information processing. Facultative symbiotic Sulfurovum was marked as a core node in the co-occurrence network and suggested an influence on habitat selection of G. aegis in hydrothermal fields. In summary, variations in bacteria composition and potential functions possibly reflected changes in the anatomical structure and dietary habits of G. aegis. These dominant bacteria shared capabilities in nutritional supplementation and ecological niche expansion in the host, potentially a key adaptation for hydrothermal survival. IMPORTANCE Dominant in the Longqi hydrothermal vent Southwest Indian Ridge, Gigantopelta aegis was observed to undergo unique and significant morphological changes and diet shifts known as cryptometamorphosis. During this process, G. aegis developed a specialized bacteria-housing organ, the esophageal gland, in the later life stages. Our research discovered variations in esophageal gland microbes between different body size groups of snails. These bacteria were closely related to the development and health of G. aegis. Full-length 16S rRNA gene analysis revealed more Thiogranum and fewer Sediminibacterium, suggesting a potential association with environmental adaptation. In the small-sized group, the potential functions were enriched in metabolism, while in larger G. aegis individuals, predictions indicated adaptive functions such as environmental information processing. Also, symbiotic Sulfurovum could be one of the factors influencing the habitat selection of G. aegis. Understanding the complex relationship between benthic macrofauna and microbes helps us describe the mechanisms of survival in extreme environments. Dominant in the Longqi hydrothermal vent Southwest Indian Ridge, Gigantopelta aegis was observed to undergo unique and significant morphological changes and diet shifts known as cryptometamorphosis. During this process, G. aegis developed a specialized bacteria-housing organ, the esophageal gland, in the later life stages. Our research discovered variations in esophageal gland microbes between different body size groups of snails. These bacteria were closely related to the development and health of G. aegis. Full-length 16S rRNA gene analysis revealed more Thiogranum and fewer Sediminibacterium, suggesting a potential association with environmental adaptation. In the small-sized group, the potential functions were enriched in metabolism, while in larger G. aegis individuals, predictions indicated adaptive functions such as environmental information processing. Also, symbiotic Sulfurovum could be one of the factors influencing the habitat selection of G. aegis. Understanding the complex relationship between benthic macrofauna and microbes helps us describe the mechanisms of survival in extreme environments.

Abstract Coral–bacterial interaction is a major driver in coral acclimatization to the stressful environment. 16S rRNA High‐throughput sequencing was used to classify the role of different coral reef compartments; sediment, water, and tissue; in the South China Sea (SCS), as well as different locations in shaping the microbial community. The majority of OTUs significantly shifted at impacted sites and indicated distinction in the relative abundance of bacteria compartment/site‐wise. Richness and diversity were higher, and more taxa were enriched in the sediment communities. Proteobacteria dominated sediment samples, while Cyanobacteria dominated water samples. Coral tissue showed a shift among different sites with Proteobacteria remaining the dominant Phylum. Moreover, we report a dominance of Chlorobium genus in the healthy coral tissue sample collected from the severely damaged Site B, suggesting a contribution to tolerance and adaptation to the disturbing environment. Thus, revealing the complex functionally diverse microbial patterns associated with biotic and abiotic disturbed coral reefs will deliver understanding of the symbiotic connections and competitive benefit inside the hosts niche and can reveal a measurable footprint of the environmental impacts on coral ecosystems. We hence, urge scientists to draw more attention towards using coral microbiome as a self‐sustaining tool in coral restoration.

Simple Summary Mangrove forests are unique ecosystems located in tropical and subtropical tidal areas worldwide. In mangrove ecosystems, the bacterial community mediates nutrient transformation and therefore is essential for mangrove productivity and maintenance. The bacterial community structure in mangrove soil that is influenced by environmental factors thus merits comprehensive study. Illumina next-generation sequencing detected the unique biomarkers and predominant genera that established distinct niches in the mangrove soils along the Upper Gulf of Thailand. The bacterial diversity and community structure of the Mae Klong Estuary site were most dissimilar to those of the other sites, while the bacterial communities of Chaopraya Estuary, Laemphakbia Promontory, and Pranburi forest park sites were closer to each other. The Kungkrabaen Bay and Black Sand Beach sites had bacterial communities which were closest to each other. The mangrove soils were found variable with respect to pH and had low amounts of organic matter (OM). Soil OM was the major factor that modulated the bacterial community structure. The groups of ammonia-oxidizing, sulfate-reducing, and methanogenic bacteria were the significant biomarkers distributed in these mangrove soils. Abstract The comprehensive data for the dynamic adaptation of bacterial community structure in response to environmental factors is important for the maintenance of the mangrove ecosystem. This aspect was investigated with soils and surface water from six mangrove forests in six provinces along the Upper Gulf of Thailand shoreline. Mangrove soils were variable with respect to pH (acidic to slightly alkaline) and had low amounts of organic matter (OM). Illumina next-generation sequencing attested that the number of observed species as well as the bacterial diversity and richness among all sites were not significantly different. The gamma-, alpha-Proteobacteria, Desulfobacteria, Bacteroidia, Anaerolineae, Bathyarchaeia, Acidobacteriae, Nitrososphaeria, Clostridia, and Thermoplasmata were more abundant bacterial classes present in all sites. Soil OM was the major factor that mostly modulated the bacterial community structure, while salinity influenced the number of observed species and bacterial richness. These results provide informative data on the bacterial community, in response to both environmental factors and heavy metal pollutants, that is prominent for sustainable development and management of mangrove forests.

ABSTRACT Soil microorganisms mediate several biological processes through the secretion of natural products synthesized in specialized metabolic pathways, yet functional characterization in ecological contexts remains challenging. Using culture-independent metagenomic analyses of microbial DNA derived directly from soil samples, we examined the potential of biosynthetic gene clusters (BGCs) from six bacterial communities distributed along an altitudinal gradient of the Andes Mountains in the Atacama Desert. We mined 38 metagenome-assembled genomes (MAGs) and identified 168 BGCs. Results indicated that most predicted BGCs were classified as non-ribosomal-peptides (NRP), post-translational modified peptides (RiPP), and terpenes, which were mainly identified in genomes of species from Acidobacteriota and Proteobacteria phyla. Based on BGC composition according to types of core biosynthetic genes, six clusters of MAGs were observed, three of them with predominance for a single phylum, of which two also showed specificity to a single sampling site. Comparative analyses of accessory genes in BGCs showed associations between membrane transporters and other protein domains involved in specialized metabolism with classes of biosynthetic cores, such as resistance-nodulation-cell division (RND) multidrug efflux pumps with RiPPs and the iron-dependent transporter TonB with terpenes. Our findings increase knowledge regarding the biosynthetic potential of uncultured bacteria inhabiting pristine locations from one of the oldest and driest nonpolar deserts on Earth. IMPORTANCE Much of what we know about specialized metabolites in the Atacama Desert, including Andean ecosystems, comes from isolated microorganisms intended for drug development and natural product discovery. To complement research on the metabolic potential of microbes in extreme environments, comparative analyses on functional annotations of biosynthetic gene clusters (BGCs) from uncultivated bacterial genomes were carried out. Results indicated that in general, BGCs encode for structurally unique metabolites and that metagenome-assembled genomes did not show an obvious relationship between the composition of their core biosynthetic potential and taxonomy or geographic distribution. Nevertheless, some members of Acidobacteriota showed a phylogenetic relationship with specific metabolic traits and a few members of Proteobacteria and Desulfobacterota exhibited niche adaptations. Our results emphasize that studying specialized metabolism in environmental samples may significantly contribute to the elucidation of structures, activities, and ecological roles of microbial molecules. Much of what we know about specialized metabolites in the Atacama Desert, including Andean ecosystems, comes from isolated microorganisms intended for drug development and natural product discovery. To complement research on the metabolic potential of microbes in extreme environments, comparative analyses on functional annotations of biosynthetic gene clusters (BGCs) from uncultivated bacterial genomes were carried out. Results indicated that in general, BGCs encode for structurally unique metabolites and that metagenome-assembled genomes did not show an obvious relationship between the composition of their core biosynthetic potential and taxonomy or geographic distribution. Nevertheless, some members of Acidobacteriota showed a phylogenetic relationship with specific metabolic traits and a few members of Proteobacteria and Desulfobacterota exhibited niche adaptations. Our results emphasize that studying specialized metabolism in environmental samples may significantly contribute to the elucidation of structures, activities, and ecological roles of microbial molecules.

Abstract The Chenier Islands are depositional areas within intertidal zones, characterized by unique soil textures and distinctive environmental conditions that shape specific vegetation distribution patterns. However, the adaptive mechanisms of Phragmites australis (common reed) and Suaeda salsa (L.) Pall. (common seepweed) two prevalent plant species in this region—in saline stress environments, as well as the composition and functional characteristics of their rhizosphere bacterial communities, remain largely unclear. In this study, rhizosphere soil samples were collected from common reed and common seepweed. DNA was extracted and subjected to high-throughput sequencing to analyze the composition and predictive functional profiles of the rhizosphere microbial communities. The results indicated that no significant differences were observed in the alpha diversity indices (Chao1, ACE, Simpson, and Shannon), indicating similar microbial species richness and evenness in the rhizospheres of common reed and common seepweed. Taxonomic analysis at the phylum level showed that the dominant bacterial phyla shared by both plants were Proteobacteria, Bacteroidota, Chloroflexota, and Actinomycetota. Notably, Acidobacteriota and Cyanobacteria were uniquely enriched in the common reed and common seepweed rhizospheres, respectively. At the genus level, the microbial communities of both plants were largely composed of unclassified taxa and minor groups, with Zeaxanthinibacter being the only cultivable dominant genus identified. Principal Coordinates Analysis (PCoA) explained 75.02% of the total β-diversity variance, and the clear separation of samples along the first coordinate axis revealed visually distinct community structures between the two plants. PERMANOVA further confirmed that plant species significantly influenced microbial community assembly, with a moderate explanatory strength (R2 = 0.205, p = 0.008). Integrated results from LEfSe, PICRUSt2, and FAPROTAX analyses demonstrated that common seepweed rhizospheres were enriched with 19 photosynthesis-related biomarkers, suggesting a stronger photoautotrophic potential compared to common reed. In contrast, the common reed rhizosphere retained only two oligotrophic degraders Acidobacteriota and Chloroflexota. Although PICRUSt2 predictions indicated high overlap in core metabolic pathways between the two plants, FAPROTAX profiling revealed markedly divergent energy-acquisition strategies. Specifically, the common seepweed microbiome exhibited a “photoautotrophy nitrogen fixation” coupling strategy, whereas common reed relied predominantly on a “chemoheterotrophy nitrate reduction” pathway, reflecting niche partitioning in the saline environment. It should be noted that functional predictions derived from PICRUSt2 and FAPROTAX are computational inferences rather than empirical measurements, and thus mechanistic interpretations should be treated with caution. This study identifies a rhizosphere bacterial community assembly pattern characterized by “structural differentiation but functional convergence” offering valuable insights into microbial-mediated plant adaptation to saline stress.

Microbial communities are closely related to plant performance and numerous studies have shown their involvement with the growth and development of host plants, resistance to pathogen invasion and adaptation to environmental stress. Here we described in detail the ecological process of the microbial community assembly in hyperaccumulator plant Sedum plumbizincicola. We divided the microbiota into four ecological compartments (bulk soil, rhizosphere, root endosphere and aboveground endosphere). The results showed that host selection strongly controlled the aggregation of microbial community. So that microbes occupied different niches from the bulk soil to the aboveground endosphere, and bacterial diversity and network complexity decreased gradually. Soil types were the second influencing factor, especially for the microbial community in the root endosphere. The SourceTracker analysis further confirmed the vertical migration of microbes from bulk soil to aboveground endosphere. In addition, under the condition of heavy metal pollution, the microbial community of S. plumbizincicola tended to form a microbial pool dominated by Proteobacteria and Actinobacteria. Ellin6067, Sphingomonas, Ralstonia, SC-I-84_uncultured bacterium, Burkholderiaceae_Undibacterium and Pedosphaeraceae_uncultured bacterium etc. were identified as the vital biomarker taxa. Among these genera, the relative abundance of last three was significantly positively correlated with the activation and transfer of cadmium, and they mainly enriched in paddy soil. This study provides evidence for the mechanism by which the microbial community assembly occurs and experience for regulating the microbial community and increasing the accumulation efficiency of potentially toxic metals in S. plumbizincicola.

Burkholderia harbors versatile Gram‐negative species and is β‐Proteobacteria. Recently, it was proposed to split the genus in two main branches: one of animal and plant pathogens and another, Paraburkholderia, harboring environmental and plant‐beneficial species. Currently, Paraburkholderia comprises more than 70 species with ability to occupy very diverse environmental niches. Herein, we sequenced and analyzed the genome of Paraburkholderia kururiensis type strain KP23T, and compared to P. kururiensis M130, isolated in Brazil, and P. kururiensis susbp. thiooxydans, from Korea. This study focused on the gene content of the three genomes with special emphasis on their potential of plant‐association, biocontrol, and bioremediation. The comparative analyses revealed several genes related to plant benefits, including biosynthesis of IAA, ACC deaminase, multiple efflux pumps, dioxygenases, and degradation of aromatic compounds. Importantly, a range of genes for protein secretion systems (type III, IV, V, and VI) were characterized, potentially involved in P. kururiensis well documented ability to establish endophytic association with plants. These findings shed light onto bacteria‐plant interaction mechanisms at molecular level, adding novel information that supports their potential application in bioremediation, biofertilization, and biocontrol of plant pathogens. P. kururiensis emerges as a promising model to investigate adaptation mechanisms in different ecological niches.

Multipartite genomes, consisting of more than one replicon, have been found in approximately 10 % of bacteria, many of which belong to the phylum Proteobacteria. Many aspects of their origin and evolution, and the possible advantages related to this type of genome structure, remain to be elucidated. Here, we performed a systematic analysis of the presence and distribution of multipartite genomes in the class Gammaproteobacteria, which includes several genera with diverse lifestyles. Within this class, multipartite genomes are mainly found in the order Alteromonadales (mostly in the genus Pseudoalteromonas ) and in the family Vibrionaceae . Our data suggest that the emergence of secondary replicons in Gammaproteobacteria is rare and that they derive from plasmids. Despite their multiple origins, we highlighted the presence of evolutionary trends such as the inverse proportionality of the genome to chromosome size ratio, which appears to be a general feature of bacteria with multipartite genomes irrespective of taxonomic group. We also highlighted some functional trends. The core gene set of the secondary replicons is extremely small, probably limited to essential genes or genes that favour their maintenance in the genome, while the other genes are less conserved. This hypothesis agrees with the idea that the primary advantage of secondary replicons could be to facilitate gene acquisition through horizontal gene transfer, resulting in replicons enriched in genes associated with adaptation to different ecological niches. Indeed, secondary replicons are enriched both in genes that could promote adaptation to harsh environments, such as those involved in antibiotic, biocide and metal resistance, and in functional categories related to the exploitation of environmental resources (e.g. carbohydrates), which can complement chromosomal functions.

Our skin and mucosal surfaces are colonized by diverse microbial communities, collectively known as the microbiota [1]. The microbiota provides benefits as microbial metabolites contribute to host nutrition and immune education, although the viability of germ-free animals conjectures that these two functions are not essential for life. However, environmental exposure makes germ-free animals prone to lethal infection, illustrating that the microbiota confers a third function that is often vital, namely, the ability to confer colonization resistance against pathogens [2]. Colonization resistance is an acquired trait, because the microbiota is assembled after birth by attaining maternal and environmental microbes [3]. To coexist, each species within the microbial community needs to be able to utilize a critical resource better than any other member of the microbiota, and the abundance of this growth-limiting resource determines the abundance of the species, a concept known as the nutrient-niche hypothesis [4]. The conceptual framework of the nutrient-niche hypothesis suggests that the neonate microbiota will mature until all discrete nutrient-niches have been filled with a suitable occupant, thereby reaching an equilibrium state [5]. Assuming the same anatomical location in different individuals exposes similar nutrient-niches, the nutrient-niche hypothesis further predicts that the metabolic pathways that enable each member within the microbial community to utilize its growth-limiting nutrient must be conserved between different individuals. Consistent with this prediction, metabolic pathways encoded by the microbiota are very similar between individuals [1]. However, carriage of microbial taxa varies greatly within a healthy population [1], an observation that is not explained by the nutrient-niche hypothesis and remains poorly understood. Priority effects generate variation in taxa carriage Host genetic variation explains only a small fraction of taxonomic microbiota variation between individuals, whereas environmental influences dominate this trait [6]. An important environmental influence in the gastrointestinal tract is the diet, which determines the availability of a subset of growth-limiting nutrients, thereby adding or subtracting nutrient-niches [7, 8]. For example, microbiota-accessible carbohydrates found in dietary fiber determine the abundance of fiber-consuming saccharolytic bacteria in the gut microbiota, and prolonged dietary fiber starvation can lead to an irreversible extinction of species specialized in devouring this critical resource by eliminating their nutrient-niche [8]. Although diet can generate statistically significant changes in the taxonomic composition of the gut microbiota, these changes are small compared to the variation observed between individuals. Furthermore, diet does not provide a plausible explanation for the taxonomic diversity observed in microbial communities outside the gastrointestinal tract [1]. Instead, a critical factor generating taxonomic microbiota diversity between individuals is the order of species arrival and timing by which host surfaces are colonized early in life [9]. The colonization order influences both the outcome of microbial community assembly and the ecological success of individual microbes [3, 9]. These priority effects are preserved in mice lacking adaptive immunity, suggesting that acquired host responses are not a major source of taxonomic diversity in the microbiota composition [9]. Priority effects are mediated through niche preemption or niche modification and can involve the genetic adaptation of microbes to a niche [9, 12], but the underlying mechanisms are incompletely understood. Mechanistic insights into this “first come, first serve” phenomenon suggest that the microbe that initially occupies a nutrient-niche in a neonate gains priority access to the growth-limiting nutrient that defines its nutrient-niche [10]. A growth-limiting resource that determines the abundance of facultative anaerobic Enterobacteriaceae (phylum Proteobacteria) within the microbiota of the large intestine is the availability of respiratory electron acceptors, such as oxygen [11]. Escherichia coli (family Enterobacteriaceae) has access to oxygen in the ceca of neonate chicks when it is inoculated one day prior to challenge with Salmonella enterica (family Enterobacteriaceae) but not when neonate chicks receive both species at the same time [10], suggesting that order and timing of gut colonization determine whether growth-limiting resources are accessible to a microbe. Henceforth we will refer to the concept that the founding occupant gains priority access to the growth-limiting resource that defines its nutrient-niche as the “founder hypothesis.” The founder hypothesis suggests that stochastic effects that govern the initial exposure of neonates to microbes that become founding occupants of each nutrient-niche are a prominent source of taxonomic variation in the microbiota composition between individuals (Fig 1) [3]. Open in a separate window Fig 1 The founder hypothesis. The principles of the founder hypothesis are shown schematically for a single nutrient-niche. Stochastic effects governing microbial exposure during infancy determine which microbial species (red or blue rods) establishes residency in the nutrient-niche, thereby generating diversity in taxa carriage between individuals. The founding occupant gains priority access to the growth-limiting resource that defines its nutrient-niche. These priority effects enable the occupant to confer colonization resistance against environmental exposure to microorganisms that are suitable contenders for the same nutrient-niche. The resulting resistance to stress imposed through environmental exposure to microorganisms produces microbiota resistance.

Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions. ABSTRACT Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named “Methylotetracoccus oryzae” C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems. IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.

Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating that NAB may be active participants contributing to the bloom dynamics. Our statistical results suggested that salinity, temperature and nitrate may be some of the key environmental factors controlling the composition and dynamics of the marine NAB communities.

This study investigated the diversity and metabolic potential of microbial communities in the Eastern Indian Ocean (EIO) through 16S rDNA gene sequencing and metagenomics analyses. Water samples were collected from the surface waters (5 m depth) and 150 m depth layer in the EIO between March 20th and June 6th, 2019. This study reveals microbial-driven biogeochemical dynamics in the oligotrophic Eastern Indian Ocean, where vertically stratified communities (Cyanobacteria/Proteobacteria-dominated surface vs. diversified Proteobacteria at 150 m) and latitudinal diversity gradients reflect nutrient limitations. Metagenomics identified four carbon fixation strategies: the Calvin cycle dominated epipelagic CO2 assimilation, while the 3-hydroxypropionate bicycle showed elevated surface activity, alongside reductive citrate and Wood-Ljungdahl pathways involving novel Actinobacteria. Nitrogen cycling exhibited spatial heterogeneity: nifH-dominated nitrogen fixation in the surface waters, prevalent narGHI nitrate reduction, and divergent nirS/nirK/nosZ distributions tied to nutrient gradients. Proteobacteria and Actinobacteria were key nitrogen fixers, with novel Actinobacteriota diazotrophs expanding known diversity. Elevated nosZ abundance in the Bay of Bengal underscored regional nitrous oxide consumption hotspots. These findings underscore microbial mediation of carbon-nitrogen fluxes in oligotrophic systems, providing genomic insights into ecosystem responses to climate-driven ocean changes.

Arid and semi-arid regions comprise nearly one-fifth of the earth's terrestrial surface. However, the diversities and functions of their soil microbial communities are not well understood, despite microbial ecological importance in driving biogeochemical cycling. Here, we analyzed the geochemistry and microbial communities of the desert soils from Tarim Basin, northwestern China. Our geochemical data indicated half of these soils are saline. Metagenomic analysis showed that bacterial phylotypes (89.72% on average) dominated the community, with relatively small proportions of Archaea (7.36%) and Eukaryota (2.21%). Proteobacteria, Firmicutes, Actinobacteria, and Euryarchaeota were most abundant based on metagenomic data, whereas genes attributed to Proteobacteria, Actinobacteria, Euryarchaeota, and Thaumarchaeota most actively transcribed. The most abundant phylotypes (Halobacterium, Halomonas, Burkholderia, Lactococcus, Clavibacter, Cellulomonas, Actinomycetospora, Beutenbergia, Pseudomonas, and Marinobacter) in each soil sample, based on metagenomic data, contributed marginally to the population of all microbial communities, whereas the putative halophiles, which contributed the most abundant transcripts, were in the majority of the active microbial population and is consistent with the soil salinity. Sample correlation analyses according to the detected and active genotypes showed significant differences, indicating high diversity of microbial communities among the Tarim soil samples. Regarding ecological functions based on the metatranscriptomic data, transcription of genes involved in various steps of nitrogen cycling, as well as carbon fixation, were observed in the tested soil samples. Metatranscriptomic data also indicated that Thaumarchaeota are crucial for ammonia oxidation and Proteobacteria play the most important role in other steps of nitrogen cycle. The reductive TCA pathway and dicarboxylate-hydroxybutyrate cycle attributed to Proteobacteria and Crenarchaeota, respectively, were highly represented in carbon fixation. Our study reveals that the microbial communities could provide carbon and nitrogen nutrients for higher plants in the sandy saline soils of Tarim Basin.

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen problem” that is growing at a similar trajectory to the “carbon problem”. As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life’s ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants.

Abstract Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya. Amplicon-based taxonomic classification revealed the dominance of the phyla Proteobacteria, Bacteroidota, and candidate Patescibacteria in the glacial sites. Further, eight good-quality metagenome-assembled genomes (MAGs) of Proteobacteria, Patescibacteria, Acidobacteriota, and Choloflexota retrieved from the metagenomes elucidated the microbial contributions to nutrient cycling. The ERG MAGs showed aerobic respiration as a primary metabolic feature, accompanied by carbon fixation and complex carbon degradation potentials. Pathways for nitrogen metabolism, chiefly dissimilatory nitrate reduction and denitrification, and a complete sulphur oxidation enzyme complex for sulphur metabolism were identified in the MAGs. We observed that DNA repair and oxidative stress response genes complemented with osmotic and periplasmic stress and protein chaperones were vital for adaptation against the intense radiation and stress conditions of the extreme Himalayan niche. Current findings elucidate the microbiome and associated functional potentials of a vulnerable glacier, emphasizing their significant ecological roles in a changing glacial ecosystem.

Free-living bacterial community and abundance have been investigated extensively under different soil management practices. However, little is known about their nitrogen (N) fixation abilities, and how their contributions to N budgets impact plant growth, yield, and carbon (C) and N cycling enzymes in a long-term consecutive sugarcane monoculture farming system, under contrasting amendments, along different soil horizons. Here, nifH gene amplicon was used to investigate diazotrophs bacterial community and abundance by leveraging high-throughput sequencing (HTS). Moreover, edaphic factors in three soil depths (0–20, 20–40, and 40–60 cm) under control (CK), organic matter (OM), biochar (BC), and filter mud (FM) amended soils were investigated. Our analysis revealed that β-glucosidase activity, acid phosphatase activity, ammonium (NH_4^+-N), nitrate (NO_3^–N), total carbon (TC), total nitrogen (TN), and available potassium (AK) were considerably high in 0–20 cm in all the treatments. We also detected a significantly high proportion of Proteobacteria and Geobacter in the entire sample, including Anabaena and Enterobacter in 0–20 cm soil depth under the BC and FM amended soils, which we believed were worthy of promoting edaphic factors and sugarcane traits. This phenomenon was further reinforced by network analysis, where diazotrophs bacteria belonging to Proteobacteria exhibited strong and positive associations soil electrical conductivity (EC), soil organic matter content (SOM) available phosphorus (AP), TN, followed by NH4^+-N and NO_3^–N, a pattern that was further validated by Mantel test and Pearson’s correlation coefficients analyses. Furthermore, some potential N-fixing bacteria, including Burkholderia , Azotobacter , Anabaena, and Enterobacter exhibited a strong and positive association with sugarcane agronomic traits, namely, sugarcane stalk, ratoon weight, and chlorophyll content. Taken together, our findings are likely to broaden our understanding of free-living bacteria N-fixation abilities, and how their contributions to key soil nutrients such as N budgets impact plant growth and yield, including C and N cycling enzymes in a long-term consecutive sugarcane monoculture farming system, under contrasting amendments, along different soil horizons.

The cultivation of grasslands can modify both bacterial community structure and impact on nutrient cycling as well as the productivity and diversity of plant communities. In this study, two pristine New Zealand grassland sites dominated by indigenous tall tussocks (Chionochloa pallens or C. teretifolia) were examined to investigate the extent and predictability of variation of the bacterial community. The contribution of free-living bacteria to biological nitrogen fixation is predicted to be ecologically significant in these soils; therefore, the diazotrophic community was also examined. The C. teretifolia site had N-poor and poorly-drained peaty soils, and the C. pallens had N-rich and well-drained fertile soils. These soils also differ in the proportion of organic carbon (C), Olsen phosphorus (P) and soil pH. The nutrient-rich soils showed increased relative abundances of some copiotrophic bacterial taxa (including members of the Proteobacteria, Bacteroidetes and Firmicutes phyla). Other copiotrophs, Actinobacteria and the oliogotrophic Acidobacteria showed increased relative abundance in nutrient-poor soils. Greater diversity based on 16S rRNA gene sequences and the Tax4Fun prediction of enhanced spore formation associated with nutrient-rich soils could indicate increased resilience of the bacterial community. The two sites had distinct diazotrophic communities with higher diversity in C. teretifolia soils that had less available nitrate and ammonium, potentially indicating increased resilience of the diazotroph community at this site. The C. teretifolia soils had more 16S rRNA gene and nifH copies per g soil than the nutrient rich site. However, the proportion of the bacterial community that was diazotrophic was similar in the two soils. We suggest that edaphic and vegetation factors are contributing to major differences in the composition and diversity of total bacterial and diazotrophic communities at these sites. We predict the differences in the communities at the two sites will result in different responses to environmental change.

Carbon (C), nitrogen (N), and phosphorus (P) are key soil nutrients whose synergistic interactions regulate ecosystem nutrient cycling, yet the functional gene-level coordination and driving factors of these cycles remain poorly understood. This study addresses this gap by investigating the dynamic changes in C, N, and P cycling functional genes and their microbial and environmental drivers across Robinia pseudoacacia plantations of different restoration stages (10, 20, 30, and 40 years) on the Loess Plateau. We analyzed soil physicochemical properties and conducted metagenomic sequencing, redundancy analysis (RDA), and Partial Least Squares Structural Equation Modeling (PLS-SEM). Results showed that P-cycling functional genes, particularly pqqC and spoT, exhibited the highest network centrality, indicating their dominant role in regulating nutrient dynamics. Compared with farmland, STC, SOC, SAP, pH, and SWC significantly changed (p < 0.05) with restoration age, directly shaping key microbial groups such as Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. These microbial shifts were strongly correlated with the synergistic changes in C, N, and P functional gene abundance (p < 0.01). The findings highlight the central role of phosphorus-solubilizing genes in linking C, N, and P cycles and emphasize the microbial community responses to soil environmental changes as a key driver of nutrient cycling during ecological restoration. This study provides novel insights into microbial functional gene interactions and their ecological significance in soil nutrient dynamics, offering theoretical support for improving restoration strategies on the Loess Plateau.

Microbial activities and biochemical reactions are responsible for the biodeterioration of stone cultural heritage, but information on microbial metabolic potentials remains elusive. Here we profiled microbial community signatures and its functional traits on stone cultural heritage from different climate zones globally using sequencing datasets available publicly. Bacterial community on stone cultural heritage shows a significant separation between BSk (cold semi-arid climate) and Cfb (temperate oceanic climate) with Aw (tropical savanna climate) as a transition region. Importantly, the ubiquity of ammonia oxidizers and nitrite oxidizers on stone cultural heritage under different climates supports the active production and accumulation of nitrates while ammonia/ammonium can be supplied by dinitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA), together with the hydrolysis of urea, arginine, formamide and cyanate. Sulfate accumulation on stone cultural heritage is mainly resulted from the microbial-driven transformation of organosulfur and thiosulfate, with little dissimilatory reduction of sulfate. Pseudorhodoplanes was identified and reported in elemental sulfur turnover for the first time. Notably, carbon sequestration via the reductive tricarboxylic acid (rTCA) cycle and an incomplete 3-hydroxypropionate/4-hydroxybutynate (HP/HB) cycle other than the Calvin Benson-Bassham (CBB) cycle is also significant on stone cultural heritage under relatively humid climate. These results advance our understanding of microbial metabolic potentials and their genetical partitioning patterns on stone cultural heritage of different climate zones globally.

The Sundarbans, the world’s largest tidal mangrove forest, acts as a crucial ecosystem for production, conservation, and the cycling of carbon and nitrogen. The study explored the hypothesis that microbial communities in mangrove ecosystems exhibit unique taxonomic and functional traits that play a vital part in carbon cycling and ecosystem resilience. Using metagenomic analysis to evaluate microbial communities in mangrove and non-mangrove environment, evaluating their composition, functional functions, and ecological relevance. The analysis revealed distinct microbial profiles, in mangrove and non-mangrove environments, with bacteria, proteobacteria, and viruses being the most prevalent groups, with varying abundances in each environment. Functional and taxonomical analysis identified genes involved in carbon regulation, including Triacylglycerol lipase, NarG, DsrB, DNA-binding transcriptional dual regulator CRP, Vanillate O-demethylase oxygenase, succinate-CoA ligase, Tetrahydrofolate ligase, Carboxylase, Ribulose-1,5-bisphosphate carboxylase/oxygenase, Glycine hydroxymethyltransferase, MAG: urease, Endosymbiont of Oligobrachia haakonmosbiensis, Ribulose bisphosphate carboxylase, Aconitate hydratase AcnA, and nitrous oxide reductase, suggesting the metabolic versatility of these microbial communities for carbon cycling. The findings emphasize the key role of microbial activity in preserving mangrove ecosystem health and resilience, highlighting the intricate interplay between microbial diversity, functional capabilities, and environmental factors.

The living soil system is fundamental to sustainable agriculture, with soil quality reflecting environmental stability and food security. However, soil health is declining due to unsustainable practices and climatic stresses such as drought and salinity. Soil microorganisms play a vital role in nutrient mobilization, solubilization, and improved nutrient availability. The rhizosphere, a dynamic root zone, fosters crucial microbe - plant interactions that enhance soil biodiversity, disease suppression, and physicochemical properties like *Rhizobium spp.*, *Azotobacter chroococcum* which enhances nitrogen fixation, *Bacillus megaterium*, *Pseudomonas fluorescens* converts insoluble phosphate to soluble phosphorus form etc. Beneficial microbes like plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) boost crop productivity and tolerance to abiotic stress. Microbial communities also enhance soil structure, water retention, and organic matter dynamics. As sensitive indicators of soil health, microbes are key to sustainable agriculture. Future research should focus on identifying efficient microbial strains and understanding their metabolites to improve plant-soil interactions and support sustainable food production.

Deoxygenation is tied to organic carbon (Corg) supply and utilization in marine systems. Under oxygen-depletion, bacteria maintain Corg respiration using alternative electron acceptors such as nitrate. Since anaerobic respiration’s energy yield is lower, Corg remineralization may be reduced and its residence time increased. We investigated the influence of oxygen and alternative electron acceptors’ availability on Corg cycling by heterotrophic bacteria during a continuous culture experiment with Shewanella baltica, a facultative anaerobic γ-Proteobacteria in the Baltic Sea. We tested six different oxygen levels, from suboxic (<5 µmol L-1) to fully oxic conditions, using a brackish (salinity=14 g L-1) media supplied with high (HighN) or low (LowN) inorganic nitrogen concentrations relative to glucose as labile Corg source. Our results show that suboxia limited DOC (glucose) uptake and cell growth only under LowN, while higher availability of alternative electron acceptors seemingly compensated oxygen limitation under HighN. N-loss was observed under suboxia in both nitrogen treatments. Under HighN, N-loss was highest and a C:N loss ratio of ~2.0 indicated that Corg was remineralized via denitrification. Under LowN, the C:N loss ratio under suboxia was higher (~5.5), suggesting the dominance of other anaerobic respiration pathways, such as dissimilatory nitrate reduction to ammonium (DNRA). Bacterial growth efficiency was independent of oxygen concentration but higher under LowN (34 ± 3.0%) than HighN (26 ± 1.6%). Oxygen concentration also affected dissolved organic matter (DOM) cycling. Under oxic conditions, the release of dissolved combined carbohydrates was enhanced, and the amino acid-based degradation index (DI) pointed to more diagenetically altered DOM. Our results suggest bacterial Corg uptake in low-oxygen systems dominated by S. baltica can be limited by oxygen but compensated by high nitrate availability. Hence, suboxia diminishes Corg remineralisation only when alternative electron acceptors are lacking. Under high nitrate:Corg supply, denitrification leads to a higher N:C loss ratio, potentially counteracting eutrophication in the long run. Low nitrate:Corg supply may favour other anaerobic respiration pathways like DNRA, which sustains labile nitrogen in the system, potentially intensifying the cycle of eutrophication. Going forward, it will be crucial to establish the validity of our findings for S. baltica in natural systems with diverse organic substrates and microbial consortia.

Microorganisms can mediate arsenic (As) and antimony (Sb) transformation and thus change the As and Sb toxicity and mobility. The influence of As and Sb on the innate microbiome has been extensively characterized. However, how microbial metabolic potentials are influenced by the As and Sb co-contamination is still ambiguous. In this study, we selected two contrasting sites located in the Shimen realgar mine, the largest realgar mine in Asia, to explore the adaptability and response of the soil microbiome to As and Sb co-contamination and the impact of co-contamination on microbial metabolic potentials. It is observed that the geochemical parameters, including the As and Sb fractions, were the driving forces that reshaped the community composition and metabolic potentials. Bacteria associated with Bradyrhizobium, Nocardioides, Sphingomonas, Burkholderia, and Streptomyces were predicted to be tolerant to high concentrations of As and Sb. Co-occurrence network analysis revealed that the genes related to C fixation, nitrate/nitrite reduction, N fixation, and sulfate reduction were positively correlated with the As and Sb fractions, suggesting that As and Sb biogeochemical cycling may interact with and benefit from C, N, and S cycling. The results suggest that As and Sb co-contamination not only influences As-related genes, but also influences other genes correlated with microbial C, N, and S cycling.

Plant economics, the way plants allocate and utilize resources, affect multiple soil processes through interactions with root and associated microbial communities. However, the interplay between plant economics and microbial ecological strategies remains poorly understood, which is crucial for integrated manipulation of plant‐ and microbe‐mediated functions in mitigating climate change and sustaining soil health. We used a field experiment with 11 cover crop species grown monocultures in the same base soil to test whether microbial ecological strategies are associated with plant economic strategies and if their interactions are linked to soil functions. A principal component analysis (PCA) was performed on root and leaf traits to identify the loadings of cover crop species on the plant trait space. Metagenomic analysis of rhizosphere microbial communities was conducted to infer their ecological strategies based on genetically encoded community‐aggregated traits. We found a synchronous relationship between the conservation gradient of plant economic strategies and the trade‐offs in microbial ecological strategies. Conservative plant strategists, such as Lolium multiflorum, Triticum turgidum and Brassica juncea, fostered microbial communities characterized by high growth yield potentials (Y‐strategies). This included increased microbial carbon fixation pathways, citrate cycle, ribosome and valine, leucine and isoleucine biosynthesis. As a result, microbial metabolic efficiency improved, shown by higher microbial biomass carbon content and a lower metabolic quotient (qCO2), led to enhanced soil organic carbon accumulation. In comparison, acquisitive plants like Astragalus sinicus, Vicia villosa, Trifolium incarnatum and Medicago sativa stimulated microbial resource‐acquisition strategies (A‐strategies). This included enhanced bacterial chemotaxis, secretion systems, biotin metabolism and cell motility pathways, which in turn increased soil exoenzyme activity and accelerated soil nitrogen mineralization. Consequently, these species enhanced soil nitrogen availability and had substantial feedbacks on subsequent main crop productivity. Synthesis. This study demonstrates how plant economic strategies influence the balance between different microbial ecological strategies, specifically the trade‐offs in Y‐ and A‐strategies. These interactions exert control over carbon and nitrogen dynamics in the soil ecosystem. The findings provide insights for implementing nature‐based solutions to improve agroecosystem management practices.

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ABSTRACT Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous Arcobacteraceae based on our deep-sea in situ incubations and the global data. The phylogenomic tree of Arcobacteraceae is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea in situ incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of Arcobacteraceae in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized Arcobacteraceae to carbon, nitrogen, and sulfur cycling in global oceans. IMPORTANCE Marine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the “hot time” of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths. Marine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the “hot time” of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.

While metagenomics can provide insight into microbial community metabolic potential, understanding factors that influence gene abundance is necessary to maximize the information gained from this analysis. Gene abundances are influenced by chemical or physical conditions along with other factors, such as copy number variation between taxa, methodological biases, or issues associated with identification and classification. Here, we identify major drivers of spatiotemporal shifts in microbial gene relative abundance from multiple months, sites, and depths within Chesapeake Bay in 2017 using shotgun metagenomics. We compared changes in relative abundance of key genes for bacterial photosynthesis, nitrogen, and sulfur metabolism with each other and measured environmental variables. Major drivers of differences in key metabolic gene abundances are associated with environmental variables that largely change with depth and season (e.g., temperature, oxygen, phosphate). For sulfur oxidation, bacterial photosynthesis, and denitrification, genes within each process are generally significantly correlated with each other and with several environmental variables. For other processes, such as nitrification, nitrogen fixation, and dissimilatory nitrate reduction to ammonium, genes that encode enzymes within the same pathway are not well correlated. The lack of correlation typically results from differences in identified taxa carrying these genes, suggesting modular pathway structure, methodological errors, or discrepancies in gene copy number between taxonomic groups. To be suitable indicators of biogeochemical processes for models, genes or pathways should be strongly correlated with environmental variables and specific to and inclusive of all taxa mediating the associated process.

Mangrove ecosystems play an important role in carbon (C) sequestration and nitrogen (N) removal. Although Spartina alterniflora has successively invaded native mangrove habitats during the preceding two decades, the effects of this invasion on the microbial functional potential involved in nutrient cycling remain unclear. In this study, metagenomic sequencing was used to investigate microbial C and N cycling in sediments derived from S. alterniflora and three native mangrove species (Kandelia obovata, Avicennia marina, and Aegiceras corniculatum). Greater differences in functional profiles of C and N cycling-related genes were observed between S. alterniflora and mangrove sediments than between different mangrove sediments. Functional diversity was lower in S. alterniflora sediments than in native mangrove sediments. The growth of Thaumarchaeota and Proteobacteria, was enhanced due to their resilience to diversity loss, while the growth of oligotrophs, such as Chloroflexi and Firmicutes, was inhibited in S. alterniflora sediments. Compared to mangrove sediments, the abundance of genes involved in C fixation and methane production was lower in S. alterniflora sediments. However, S. alterniflora significantly increased the gene abundance of pmo which controlled the oxidation process of CH4 to carbon dioxide. Additionally, genes involved in nitrification were enriched, whereas genes involved in N reduction processes, such as denitrification and dissimilatory nitrate reduction to ammonium, N immobilization, and N mineralization, were depleted in S. alterniflora sediments compared to mangrove sediments. Partial least squares regression models demonstrated that the decrease in soil organic C and increase in pH after S. alterniflora invasion induced the loss of microbial functional diversity, which was the main driver of changes in the abundances of genes involved in C and N cycling. Overall, our findings indicate that S. alterniflora invasion modifies the microbial functional profile of nutrient cycling in native mangrove ecosystems and potentially weakens the capacity of mangroves to sequester carbon and remove nitrogen.

Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits. Sphagnum mosses harbor a diverse assemblage of microbial partners, including N2‐fixing (diazotrophic) and CH4‐oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. Here, we investigate the response of the Sphagnum phytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO2 (+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH4, CO2) and nitrogen (NH4‐N) cycling from the belowground environment up to Sphagnum and its associated microbiome, we identified a series of cascading impacts to the Sphagnum phytobiome triggered by warming and elevated CO2. Under ambient CO2, warming increased plant‐available NH4‐N in surface peat, excess N accumulated in Sphagnum tissue, and N2 fixation activity decreased. Elevated CO2 offset the effects of warming, disrupting the accumulation of N in peat and Sphagnum tissue. Methane concentrations in porewater increased with warming irrespective of CO2 treatment, resulting in a ~10× rise in methanotrophic activity within Sphagnum from the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane‐induced N2 fixation and significant losses of keystone microbial taxa. In addition to changes in the Sphagnum microbiome, we observed ~94% mortality of Sphagnum between the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N‐availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of the Sphagnum phytobiome to rising temperatures and atmospheric CO2 concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands.

Nitrogen-fixing cyanobacteria (NFC) are photosynthetic prokaryotic microorganisms capable of nitrogen fixation. They can be used as biofertilizers in paddy fields, thereby improving the rice tillering capacity and yield. To reveal the microbiological mechanisms by which nitrogen-fixing cyanobacteria alter soil carbon storage, we conducted a field experiment using NFC as a partial substitute for nitrogen fertilizer in paddy fields in the Sanjiang Plain of Northeast China's Mollisols region. Using metagenomic sequencing technology and Biolog Ecoplate™ carbon matrix metabolism measurements, we explored the changes in the soil microbial community structure and carbon utilization in paddy fields. The results indicated that the replacement of nitrogen fertilizer with NFC predisposed the soil microbial community to host a great number of copiotrophic bacterial taxa, and Proteobacteria and Actinobacteria were closely associated with the metabolism of soil carbon sources. Moreover, through co-occurrence network analysis, we found that copiotrophic bacteria clustered in modules that were positively correlated with the metabolic level of carbon sources. The addition of NFC promoted the growth of copiotrophic bacteria, which increased the carbon utilization level of soil microorganisms, improved the diversity of the microbial communities, and had a potential impact on the soil carbon stock. The findings of this study are helpful for assessing the impact of NFC on the ecological function of soil microbial communities in paddy fields in the black soil area of Northeast China, which is highly important for promoting sustainable agricultural development and providing scientific reference for promoting the use of algal-derived nitrogen fertilizers.

Intercropping systems can improve soil fertility and health, however, soil microbial communities and functional genes related to carbon, nitrogen and phosphorus cycling under the intercropping system of mesquite and perilla have not been studied. Therefore, in the present study, different planting densities and varieties of Perilla frutescens (L.) Britt and kiwifruit were used for intercropping, and changes in soil microbial communities and carbon, nitrogen, and phosphorus cycling genes in kiwifruit inter-roots under inter-cropping conditions were investigated by macro-genome sequencing technology. The results showed that intercropping with Perill caused a decrease in most soil nutrients, soil enzyme activities, and had a significant impact on the microbial (bacteria and fungi) diversity. Inter-cropping increased the relative abundance of the dominant bacterial phylum “Proteobacteria” and “Actinobacteria” by 47 and 57%, respectively, but decreased the relative abundance of the dominant fungal phylum “Chordata” and “Streptophyta” by 11 and 20%, respectively, in the inter-root soil of kiwifruit, and had a significant impact on the microbial (bacteria and fungi) diversity. In addition, inter-cropping could greatly increase the inter-root soil carbon sequestration (PccA, korA/B/C/D, fhs, and rbcl/s), carbon degradation (abfD), organic nitrogen mineralization (GDH2), denitrification (napA/B, nirB, norB), organic phosphorus mineralization (phop, phn), and inorganic phosphorus solubilization (gcd, ppk) gene abundance. The gene co-occurrence network indicated that soil korB, nirB, and gnd key functional genes for carbon, nitrogen, and phosphorus cycling in kiwifruit inter-root soils and their expression was up-regulated in the inter-cropping group. Structural equation (SEM) further showed that soil total nitrogen, organic matter, total carbon and acid phosphatase had significant effects on microbial diversity (p < 0.05) and soil carbon cycling gene korB and phosphorus cycling gene purH (p < 0.001), while korB and purH had positive effects on kiwifruit quality. In conclusion, intercropping perilla in kiwifruit orchards changed the structure of bacterial and fungal communities in the inter-root soil of kiwifruit, but I believe that intercropping perilla stimulates carbon degradation, leading to carbon emission and serious loss of soil nutrients, and that prolonged intercropping may adversely affect the quality of kiwifruit, and thus its limitations should be noted in future studies.

Soil microbial carbon (C) fixation represents a vital yet uncertain component of forest carbon cycling, and its underlying mechanisms especially depth-specific responses remain unclear. To address this, we integrated metagenomics and machine learning to examine these relationships along a tree species richness gradient (1–8 species), analyzing both topsoil (0–10 cm) and subsoil (10–20 cm). Results revealed distinct vertical stratification in soil properties and microbial carbon fixation strategies. Microbial carbon fixation gene abundance was primarily driven by soil organic carbon (SOC) and nitrate nitrogen (NO₃−-N), exhibiting a nonlinear threshold at ~85 g kg−1 SOC. The promoting effect of SOC peaked at moderate richness (3–5 species) but declined at higher richness. Depth-resolved analysis revealed that the Calvin cycle gene rbcL responded mainly to richness in topsoil, whereas rTCA cycle genes (korA, korC) were more sensitive in subsoil These findings demonstrate that tree diversity enhances microbial carbon fixation through nutrient-mediated mechanisms, but these effects are nonlinear, context-dependent, and depth-specific. Incorporating such complexity is essential for accurately predicting forest carbon sequestration.

Diazotrophic communities contribute inorganic nitrogen for the primary productivity of the marine environment by biological nitrogen fixation (BNF). They play a vital role in the biogeochemical cycle of nitrogen in the marine ecological environment. However, there is still an incomplete understanding of BNF and diazotrophs in artificial seaweed farms. Therefore, this study comprehensively investigated the temporal variations of BNF associated with Gracilariopsis lemaneiformis, as well as the diazotrophic communities associated with macroalgae and its surrounding seawater. Our results revealed that a total of 13 strains belonging to Proteobacteria and Bacteroidetes were identified as N2-fixing bacteria using azotobacter selective solid medium and nifH gene cloning. Subsequently, BNF and diazotrophic communities were characterized using the acetylene reduction method and high-throughput sequencing of the nifH gene, respectively. The results showed that nitrogenase activity and nifH gene abundance of epiphytic bacteria on G. lemaneiformis varied significantly among four different cultivation periods, i.e., Cultivation Jan. (CJ), Cultivation Feb. (CF), Cultivation Mar. (CM), Cultivation Apr. (CA). Among them, the nitrogenase activity and nifH gene abundance of epiphytic bacteria on G. lemaneiformis in CM were significantly higher than those in CJ, CF, and CA, indicating that the BNF of eiphytic bacteria on G. lemaneiformis was markedly enhanced. Combined with the data on environmental factors, it was found that the low concentration of nitrogen and phosphorus in CM might considerably boost the BNF of epiphytic bacteria in G. lemaneiformis. The sequencing results of the nifH gene showed that the α-diversity of diazotrophic communities associated with G. lemaneiformis and seawater in CM was higher than that in other cultivation periods. In addition, the diazotrophic communities on G. lemaneiformis were significantly different in CJ, CF, CM, and CA, and they were significantly diverse from diazotrophic communities in seawater. LEfSe analysis indicated that Rhodobacterales, Hyphomonadaceae, Robiginitomaculum, and Robiginitomaculum antarcticum within α-proteobacteria played a remarkable role in BNF in response to nitrogen nutrient deficiency. Taken together, these results provide a unique insight into the interaction between macroalgae and its epiphytic bacteria and lay a foundation for further research on the mechanism of action of nitrogen-cycling microorganisms associated with macroalgae.

Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes. The mechanisms underlying plant-microbe interactions in coastal ecosystems are little explored. Here, the authors use multi-omics and biogeochemical measurements to investigate the saltmarsh cordgrass root microbiome and its role in coupling nitrogen fixation and sulfur cycling.

Biological nitrogen fixation (BNF) represents a sustainable alternative to the capital- and energy-intensive Haber-Bosch process, which dominates industrial fertilizer production but contributes significantly to global carbon emissions. While Geobacter sulfurreducens has been identified as a promising diazotroph, its BNF efficiency remains untapped. Here, we engineered G. sulfurreducens by deleting the ammonium transporter gene amtB (strain ΔamtB), achieving a record-high BNF rate of 20.57 ± 0.87 mg N L-1 day-1, approximately twice that of the wild-type strain and exceeding those of all reported free-living diazotrophs and synthetic catalysts for ambient nitrogen fixation. 15N isotope labeling and nitrogenase activity assays confirmed enhanced fixation, whereas biofertilizer trials demonstrated the ability of ΔamtB as a biofertilizer to support Arabidopsis thaliana growth. Mechanistic studies revealed that amtB deletion (1) amplified cellular nitrogen assimilation, (2) alleviated ammonium-mediated suppression of nitrogenase activity, and (3) disrupted energy-intensive futile ammonium cycling, conserving cell energy. This study establishes ΔamtB as a scalable BNF platform for sustainable agriculture, offering a viable pathway to decarbonize fertilizer production.

In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

Background Atopic dermatitis (AD) interferes with quality of life and is influenced by important factors like skin microbiome. The results of the skin microbiome composition and diversity in AD varied in some studies. Purpose This study aims to determine the composition and diversity of the skin microbiome in Indonesian AD patients. Patients and Methods Genomic deoxyribonucleic acid (DNA) preparations were obtained from skin swabs of the cubital fossa of 16 subjects, nine of which were having mild AD, three moderate AD, and four healthy individuals. DNA extraction and sequencing of the 16S ribosomal ribonucleic acid (rRNA) gene using next-generation sequencing and bioinformatics analysis were further performed. Results Firmicutes (p), Bacilli (c), Bacillales (o), Staphylococcaceae (f), and Staphylococcus (g) were dominant in moderate AD. On the contrary, Proteobacteria (p), Gammaproteobacteria (c), Pseudomonadales (o), Moraxellaceae (f), and Acinetobacter (g) were dominant in mild AD. Staphylococcus aureus was found in the highest number in individuals with moderate AD. Interestingly, Ensifer adhaerens was found in mild AD. Microbial diversity was decreased in moderate AD. Conclusion Metagenomic analysis in this study identified microbes in moderate and mild AD and showed a low diversity of skin microbiomes in moderate AD. Interestingly, this is the first time that the bacteria Ensifer adhaerens was detected on the human skin.

Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.

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Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

The objective of this present study was to explore the initial establishment of metabolically active bacteria and subsequent evolution in four fractions: rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) through early weaning and supplementing rhubarb root powder in 7 different age groups (1, 10, 20, 38, 41, 50, and 60 d) during rumen development. Results of the 16S rRNA sequencing based on RNA isolated from the four fractions revealed that the potentially active bacterial microbiota in four fractions were dominated by the phyla Proteobacteria, Firmicutes, and Bacteroidetes regardless of different ages. An age-dependent increment of Chao 1 richness was observed in the fractions of RL and RE. The principal coordinate analysis (PCoA) indicated that samples in four fractions all clustered based on different age groups, and the structure of the bacterial community in RE was distinct from those in other three fractions. The abundances of Proteobacteria decreased significantly (P < 0.05) with age, while increases in the abundances of Firmicutes and Bacteroidetes were noted. At the genus level, the abundance of the predominant genus Mannheimia in the Proteobacteria phylum decreased significantly (P < 0.05) after 1 d, while the genera Quinella, Prevotella, Fretibacterium, Ruminococcus, Lachnospiraceae NK3A20 group, and Atopobium underwent different manners of increases and dominated the bacterial microbiota across four fractions. Variations of the distributions of some specific bacterial genera across fractions were observed, and supplementation of rhubarb affected the relative abundance of various genera of bacteria.

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Tibetan Chickens should have unique gastrointestinal microbiota because of their particular habitats. Thus, the aim of this study was to investigate the cecal microbiota of Tibetan Chickens from five typical high‐altitude regions of China. Lohmann egg‐laying hens (LMs) and Daheng broiler chickens (DHs) were chosen as controls. The cecal bacterial populations of Tibetan Chickens were surveyed by high‐throughput sequencing (HTS) of the bacterial 16S rRNA hypervariable region V3‐V4 (16S rRNAV3‐V4) combined with community‐fingerprinting analysis of the 16S rRNA gene based on polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE). The results revealed that the majority of cecal microbiota differed between the Tibetan Chicken and LM/DH. The microbial communities in the cecum were composed of 16 phyla, 28 classes, 36 orders, 57 families, 101 genera, and 189 species. Represented phyla were Bacteroidetes (>47%), Firmicutes (>18.8%), Spirochaetae (>0.3%), and Proteobacteria (>0.4%). Bacteroides and the RC9 gut group were the two most abundant genera. There were relatively more Christensenellaceae, Subdoligranulum, Spirochaeta, and Treponema in Tibetan Chickens, whereas there were more Phascolarctobacterium, Faecalibacterium, Megamonas, and Desulfovibrio in LMs and DHs. The cecal microbiota of Tibetan Chicken have slightly diverged due to exposure to different geographic environments. Differences in the intestinal bacterial communities of Tibetan Chicken and LM/DH were noted.

No abstract available

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12–14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.

No abstract available

Rabbit can produce meat, fur and leather, and serves as an important biomedical animal model. Understanding the microbial community of rabbits helps to raise rabbits healthily and better support their application as animal models. In this study, we selected 4 healthy Belgium gray rabbits to collect the microbial samples from 12 body sites, including skin, lung, uterus, mouth, stomach, duodenum, ileum, jejunum, colon, cecum, cecal appendix and rectum. The microbiota across rabbit whole body was investigated via 16S rRNA gene amplicon sequencing. After quality control, 46 samples were retained, and 3,148 qualified ASVs were obtained, representing 23 phyla and 264 genera. Based on the weighted UniFrac distances, these samples were divided into the large intestine (Lin), stomach and small intestine (SSin), uterus (Uter), and skin, mouth and lung (SML) groups. The diversity of Lin microbiota was the highest, followed by those of the SSin, Uter and SML groups. In the whole body, Firmicutes (62.37%), Proteobacteria (13.44%) and Bacteroidota (11.84%) were the most predominant phyla. The relative abundance of Firmicutes in the intestinal tract was significantly higher than that in the non-intestinal site, while Proteobacteria was significantly higher in the non-intestinal site. Among the 264 genera, 35 were the core microbiota distributed in all body sites. Sixty-one genera were specific in the SML group, while 13, 8 and 1 were specifically found in the Lin, SSin and Uter groups, respectively. The Lin group had the most difference with other groups, there were average 72 differential genera between the Lin and other groups. The functional prediction analysis showed that microbial function within each group was similar, but there was a big difference between the intestinal tracts and the non-intestinal group. Notably, the function of microorganism in uterus and mouth were the most different from those in the gastrointestinal sites; rabbit’s coprophagy of consuming soft feces possibly resulted in little differences of microbial function between stomach and large intestinal sites. Our findings improve the knowledge about rabbit microbial communities throughout whole body and give insights into the relationship of microbial communities among different body sites in health rabbits.

Summary Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re‐evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time‐series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers.

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and a range of fitness in fish, but little is known about the gut microbial community in Antarctic fish. In this study, the composition of intestinal microbial community in four species of Antarctic fish was detected based on 16S rRNA gene sequencing. As a result, 1 004 639 sequences were obtained from 13 samples identified into 36 phyla and 804 genera, in which Proteobacteria, Actinobacteria, Firmicutes, Thermi, and Bacteroidetes were the dominant phyla, and Rhodococcus, Thermus, Acinetobacter, Propionibacterium, Streptococcus, and Mycoplasma were the dominant genera. The number of common OTUs (operational taxonomic units) varied from 346 to 768, while unique OTUs varied from 84 to 694 in the four species of Antarctic fish. Moreover, intestinal bacterial communities in individuals of each species were not really similar, and those in the four species were not absolutely different, suggesting that bacterial communities might influence the physiological characteristics of Antarctic fish, and the common bacterial communities might contribute to the fish survival ability in extreme Antarctic environment, while the different ones were related to the living habits. All of these results could offer certain information for the future study of Antarctic fish physiological characteristics.

Organochlorine pesticides (OCPs) contaminated sites pose great threats to both human health and environmental safety. Targeted bioremediation in these regions largely depends on microbial diversity and activity. This study applied metagenomics to characterize the microbial communities and functional groups composition features during independent or simultaneous rapeseed oil and tartaric acid applications, as well as the degradation kinetics of OCPs. Results showed that: the degradation rates of α-chlordane, β-chlordane and mirex were better when (0.50% w/w) rapeseed oil and (0.05 mol L-1) tartaric acid were applied simultaneously than singular use, yielding removal rates of 56.4%, 53.9%, and 49.4%, respectively. Meanwhile, bio-stimulation facilitated microbial enzyme (catalase/superoxide dismutase/peroxidase) activity in soils significantly, promoting the growth of dominant bacterial communities. Classification at phylum level showed that the relative abundance of Proteobacteria was significantly increased (p < 0.05). Network analysis showed that bio-stimulation substantially increased the dominant bacterial community's proportion, especially Proteobacteria. The functional gene results illustrated that bio-stimulation facilitated total relative abundance of degradation genes, phosphorus, carbon, nitrogen, sulfur metabolic genes, and iron transporting genes (p < 0.05). In metabolic pathways, functional genes related to methanogenesis and ammonia generation were markedly upregulated, indicating that bio-stimulation promoted the transformation of metabolic genes, such as carbon and nitrogen. This research is conducive to exploring the microbiological response mechanisms of bio-stimulation in indigenous flora, which may provide technical support for assessing the microbial ecological remediation outcomes of bio-stimulation in OCP contaminated sites.

As a natural hibernator, the Chinese alligator (Alligator sinensis) is an ideal and intriguing model to investigate changes in microbial community structure and function caused by hibernation. In this study, we used 16S rRNA profiling and metagenomic analysis to compare the composition, diversity, and functional capacity in the gut microbiome of hibernating vs. active Chinese alligators. Our results show that gut microbial communities undergo seasonal restructuring in response to seasonal cycles of feeding and fasting in the Chinese alligator, but this animal harbors a core gut microbial community primarily dominated by Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes across the gut regions. During hibernation, there is an increase in the abundance of bacterial taxa (e.g., the genus Bacteroides) that can degrade host mucin glycans, which allows adaptation to winter fasting. This is accompanied by the enrichment of mucin oligosaccharide-degrading enzyme and carbohydrate-active enzyme families. In contrast, during the active phase (feeding), active Chinese alligators exhibit a carnivore gut microbiome dominated by Fusobacteria, and there is an increase in the relative abundance of bacteria (e.g., Cetobacterium somerae) with known proteolytic and amino acids-fermentating functions that improve host protein-rich food digestion efficiency. In addition, seasonal variations in the expression of β-defensins play a protective role in intestinal immunity. These findings provide insights into the functional adaptations of host–gut microbe symbioses to seasonal dietary shifts to maintain gut homeostasis and health, especially in extreme physiological states.

Vehicle-wash wastewater can contain petroleum-derived residues that accumulate in drainage sludge and pose persistent environmental risks. In this study, shotgun metagenomics of drainage sludge from a vehicle-wash ditch were combined with isolate level validation to assess indigenous hydrocarbon biodegradation potential. Taxonomic profiling revealed a community dominated by Proteobacteria (notably Gammaproteobacteria), while Bacillus was detected only at low relative abundance at the genus level. Functional annotation indicated strong genetic potential for alkane activation and downstream processing, together with multiple enzymes associated with aromatic?ring transformation. To link this community-level potential with experimentally verifiable activity, an indigenous isolate recovered from the sludge was identified as Bacillus amyloliquefaciens MD3.3 based on 16S rRNA gene sequencing (GenBank: PV550465). In microcosms prepared with wastewater from the same drainage source, GC-MS analysis demonstrated marked attenuation of mineral oil n-alkanes over 0-7-14 days. ?n?alkanes decreased from 185,346.63 ± 11,120.80 µg/L at Day 0 to 21,498.48 ± 3,224.77 µg/L at Day 7 and 260.82 ± 52.16 µg/L at Day 14, corresponding to 88.44 ± 1.05% and 99.86 ± 0.02% removal, respectively (n = 3). In contrast, abiotic sterilized controls showed only minor non-biological losses (4.23 ± 3.54% and 5.97 ± 0.75% removal at Days 7 and 14). Collectively, these results support the feasibility of site-relevant bioremediation for vehicle-wash wastewater.

Abstract. Afandi, Suhandono S, Septiani P, Fibriani A. 2025. Polystyrene biodegradation and functional biodiversity of gut microbial consortia in Tenebrio molitor with metagenomic and metabolomic insights. Biodiversitas 26: 3994-4016. Polystyrene (PS), a persistent plastic pollutant, can be biodegraded by Tenebrio molitor larvae through gut microbiome-mediated processes. This study employed integrated shotgun metagenomics and metabolomics to elucidate the microbial taxa, enzymes, and metabolic pathways involved in PS degradation. In vivo trials demonstrated a PS mass reduction of 6.38%, while in vitro experiments using gut microbial consortia resulted in a 3.49% mass loss. Surface erosion of the PS film was confirmed via scanning electron microscopy. Taxonomic profiling identified 334 bacterial genera under the PS diet and 329 under rice bran, with 93 genera unique to PS treatment. Dominant phyla included Proteobacteria (53.87%), Actinobacteria (6.44%), and Aquificae (6.42%). Hydrocarbon-degrading genera enriched under the PS diet included Burkholderia (3.94%), Nocardioides (2.67%), and Oceanobacter, the latter being exclusive to PS-fed larvae. Biodiversity metrics revealed high genus-level diversity (Shannon Index H? = 3.79-3.81), moderate Evenness (E = 0.65-0.66), and low Dominance (D = 0.06), indicating a complex yet balanced microbial ecosystem under xenobiotic stress. Functional annotations identified xenobiotic degradation pathways, including styrene metabolism (0.56%) and toluene metabolism (1.40%), driven by key enzymes such as monooxygenases and phenylacetaldehyde dehydrogenase. Metabolomic profiling identified 39 metabolites in larval frass and 20 degradation intermediates in the liquid medium, with lactic acid and benzyl alcohol being the primary products associated with the breakdown of aromatic compounds. These findings underscore the functional biodiversity and ecological adaptability of the gut microbiome in plastic detoxification, highlighting insect-microbe symbioses as promising agents for sustainable bioremediation strategies.

The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB’s eastern coast, viz., Saint Martin and Cox’s Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas , Methylophaga , Anaerospora , Marivita , and Vibrio dominating in Cox’s Bazar and Pseudoalteromonas , Nautella , Marinomonas , Vibrio , and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox’s Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox’s Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.

Most of the discarded waste material paves their way to the utmost common dumping grounds, Landfills. Despite their widespread use, the landfill microbiomes are still not well characterized. Metagenomics approach provides insight into the identification of operational parameters influencing the microbiome composition and their biodegradation competencies. The metagenomic DNA was prepared to explore taxonomical community structure, phylogenetic relationships, and functional profile at the same time. A total of 100,021,052 high-quality filtered reads were acquired with a GC abundance of 62.59%. Taxonomical abundance revealed the dominance of phylum Proteobacteria and genes involved in biomolecules metabolism, aromatic compound degradation, stress tolerance, xenobiotic biodegradation etc. were revealed functionally. The intricate heterogeneous environment of landfill revealed well flourished biogeochemical metabolic profiles including nitrogen metabolism. This is the first study for the generated metagenome of Ghazipur landfill and the obtained results propose that microbial communities in landfill settings are far more intricate than expected. It remain mostly unexplored which demands the usage of multiple platforms for a better understanding.

Identifying the microbial community and their functional potential from different stages of common effluent treatment plants (CETP) can enhance the efficiency of wastewater treatment systems. In this study, wastewater metagenomes from 8 stages of CETP were screened for microbial diversity and gene profiling along with their corresponding degradation activities. The microbial community displayed 98.46% of bacterial species, followed by Eukarya (0.10%) and Archaea 0.02%. At the Phylum level, Proteobacteria (28.8%) was dominant, followed by Bacteroidetes (16.1%), Firmicutes (11.7%), and Fusobacteria (6.9%) which are mainly capable of degrading the aromatic compounds. Klebsiella pneumoniae, Wolinella succinogenes, Pseudomonas stutzeri, Desulfovibrio vulgaris, and Clostridium sticklandii were the most prevalent species. The functional analysis further demonstrated the presence of enzymes linked with genes/pathways known to be involved in the degradation/metabolization of aromatic compounds like benzoate, bisphenol, 1,2-dichloroethane phenylalanine. This information was further validated with the whole genome analysis of the bacteria isolated from the CETP. We anticipate that integrating both shotgun and whole-genome analyses can reveal the rich reservoir for novel enzymes and genes present in CETP effluent that can contribute to designing efficient bioremediation strategies for the environment in general CETP system, in particular.

Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.

Background Obesity-related alterations in the gut microbiota have been linked to cognitive decline, yet their relationship with attention remains poorly understood. Objective To evaluate the possible relationships among gut metagenomics, plasma metabolomics and attention. Design We conducted faecal shotgun metagenomics and targeted plasma tryptophan metabolomics across three independent cohorts (n=156, n=124, n=804) with functional validations in preclinical models, including three faecal microbiota transplantation (FMT) experiments in mice and Drosophila melanogaster. Results Obesity was consistently associated with reduced attention. Metagenomics analyses identified Proteobacteria species and microbial functions related to tryptophan biosynthesis from anthranilic acid (AA) as negatively associated with attention in obesity. Plasma tryptophan metabolic profiling and machine learning revealed that 3-hydroxyanthranilic acid (3-HAA) was positively associated with attention, particularly in obesity, while AA showed a negative association. Bariatric surgery improved attention and enriched microbial species linked to attention. In mice, diet-induced obesity (DIO) and microbiota depletion reduced 3-HAA and 5-hydroxy-indole acetic acid (5-HIAA) concentrations in the prefrontal cortex (PFC), which were restored by FMT. Global metabolic profiling (>600 metabolites) of PFC from the FMT group identified 3-HAA and the tryptophan and tyrosine pathways among the most significant in mice receiving microbiota from high-attention donors. A second FMT experiment also revealed a consistent enrichment of the tryptophan and tyrosine metabolism at the transcriptional level in the PFC, with Haao (3-hydroxyantrhanilic acid dioxygenase) and Aox4 (aldehyde oxidase 4), key in 3-HAA and 5-HIAA degradation, among the significantly regulated genes. In a third FMT study, attentional traits were transmitted from humans to mice alongside modulation of serotonergic and dopaminergic pathways. In Drosophila, mono-colonisation with Enterobacter cloacae and DIO induced attention deficit-like behaviours, which were mitigated by 3-HAA supplementation. Conclusions We have identified the microbiota and 3-HAA as potential therapeutic targets to improve attention, especially in obesity.

Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.

Background Mangrove sediment microbes are increasingly attracting scientific attention due to their demonstrated capacity for diverse bioremediation activities, encompassing a wide range of environmental contaminants. Materials and methods The microbial communities of five Avicennia marina mangrove sediment samples collected from Al Rayyis White Head, Red Sea (KSA), were characterized using Illumina amplicon sequencing of the 16S rRNA genes. Results Our study investigated the microbial composition and potential for organohalide bioremediation in five mangrove sediments from the Red Sea. While Proteobacteria dominated four microbiomes, Bacteroidetes dominated the fifth. Given the environmental concerns surrounding organohalides, their bioremediation is crucial. Encouragingly, we identified phylogenetically diverse organohalide-respiring bacteria (OHRB) across all samples, including Dehalogenimonas , Dehalococcoides, Anaeromyxobacter, Desulfuromonas, Geobacter , Desulfomonile , Desulfovibrio , Shewanella and Desulfitobacterium . These bacteria are known for their ability to dechlorinate organohalides through reductive dehalogenation. PICRUSt analysis further supported this potential, predicting the presence of functional biomarkers for organohalide respiration (OHR), including reductive dehalogenases targeting tetrachloroethene (PCE) and 3-chloro-4-hydroxyphenylacetate in most sediments. Enrichment cultures studies confirmed this prediction, demonstrating PCE dechlorination by the resident microbial community. PICRUSt also revealed a dominance of anaerobic metabolic processes, suggesting the microbiome’s adaptation to the oxygen-limited environment of the sediments. Conclusion This study provided insights into the bacterial community composition of five mangrove sediments from the Red Sea. Notably, diverse OHRB were detected across all samples, which possess the metabolic potential for organohalide bioremediation through reductive dehalogenation pathways. Furthermore, PICRUSt analysis predicted the presence of functional biomarkers for OHR in most sediments, suggesting potential intrinsic OHR activity by the enclosed microbial community.

High salinity, low fertility and poor structure in saline-alkali soils led to nutrient cycling slow and microbial activity loss. The application of amendments has proven effective in enhancing soil nutrients, which significantly affects soil nitrogen and phosphorus cycling process. However, the specific impact of different amendments on the microbial functional potential related to nutrient cycling in saline-alkali soils remains unclear. Hence, metagenomics sequencing was used to investigate soil microbial communities and nitrogen and phosphorus cycling genes in response to different amendments, and to examine the influence of soil physicochemical properties on functional genes in the Hetao irrigation district of China. The results showed that amendments application enriched the Proteobacteria abundance, while inhibiting oligotrophic groups such as Chloroflexi. Compared to the control (CK), the combined application of desulfurization gypsum and cattle manure (DC) notably increased nasA (assimilatory nitrate reduction) and nirB (dissimilatory nitrate reduction), as well as phoD and phoA genes (organic P mineralization). Furthermore, soil AK and AP were primary factors affecting microbial communities and N and P cycling genes. Overall, this study offers valuable insights into soil nitrogen and phosphorus cycling genes and their interactions in response to different amendments, where the application of amendments affects nitrogen and phosphorus cycling by altering soil nutrient availability.

The eastern Arabian Sea (EAS) is known for its unique oceanographic features such as the seasonal monsoonal winds, upwelling of nutrient-rich waters and a significant increase in primary productivity during the monsoon season. In this study, we utilised the shotgun metagenomics approach to determine the seasonal variations in bacterial taxonomic and functional profiles during the non-monsoon and monsoon seasons in the EAS. Significant seasonal variations in the bacterial community structure were observed at the phylum and genera levels. These findings also correspond with seasonal shifts in the functional profiles of the bacterial communities based on the variations of genes encoding enzymes associated with different metabolic pathways. Pronounced seasonal variation of bacterial taxa was evident with an increased abundance of Idiomarina, Marinobacter, Psychrobacter and Alteromonas of Proteobacteria, Bacillus and Staphylococcus of Firmicutes during the non-monsoon season. These taxa were linked to elevated nucleotide and amino acid biosynthesis, amino acid and lipid degradation. Conversely, during the monsoon, the taxa composition changed with Alteromonas, Candidatus Pelagibacter of Proteobacteria and Cyanobacteria Synechococcus; contributing largely to the amino acid and lipid biosynthesis, fermentation and inorganic nutrient metabolism which was evident from functional analysis. Regression analysis confirmed that increased seasonal primary productivity significantly influenced the abundance of genes associated with carbohydrate, protein and lipid metabolism. These highlight the pivotal role of seasonal changes in primary productivity in shaping the bacterial communities, their functional profiles and driving the biogeochemical cycling in the EAS.

No abstract available

The Limpopo province, located in the arid-tropical region in northeastern South Africa, is renowned for its diverse natural wetlands, some of which are currently unprotected. These wetlands play a crucial role in preserving biodiversity, purifying water, controlling floods, and supporting agricultural production for rural communities. Unfortunately, human activities such as agricultural effluents, run-offs, domestic wastewater, and plastics pollution, along with the impacts of climate change, are mounting pressures on these ecosystems. However, there is limited information on the microbial ecology of natural wetlands in this region, considering the changing anthropogenic activities. The data presented represents the first report on the microbial and functional diversity of sediment microbiomes associated with unprotected arid-tropical natural wetlands in South Africa. Metagenomic shotgun sequencing was performed on sediment samples from ten different wetlands using the Illumina NextSeq 2000 platform. Taxonomic profiling of 328,625,930 high-quality sequencing reads using the MetaPhlAn v3.0 pipeline revealed that Bacteria were the most abundant kingdom (54.5 %), followed by Viruses (0.40 %), Archaea (0.01 %), and Eukaryota (0.36 %). Among bacteria, the most prevalent taxa belonged to the phylum Proteobacteria, particularly the classes Gammaproteobacteria and Betaproteobacteria, which accounted for 83 % of bacterial sequences. The Terrabacteria group, consisting of the phyla Firmicutes and Actinobacteria, made up 3 % of the bacterial population. The abundance of these top bacterial taxa varied across different wetland samples, both at the genus and species levels. In addition, hierarchical clustering based on Bray-Curtis dissimilarity distances of fungal, protist, archaea, and virus species showed distinct clustering of sediment samples from different wetlands. Functional annotation of the metagenomes identified 1224–1702 enzyme classes, 84,833–198,397 gene families, and 280–400 pathways across the various wetland sediments. The data provide crucial baseline information on the microbial and functional diversity of sediment communities in arid tropical wetlands. This knowledge will contribute to a better understanding of these unique environments and can aid in their management and conservation efforts in rural South Africa.

Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC. 8JzsRQQL6mihmS_qxcrFZs Video abstract Video abstract

No abstract available

Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.

No abstract available

Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.

Traditionally preserved meat products are common food items in Sikkim state of India. We studied the high-throughput sequencing of four traditionally preserved meat products viz. beef kargyong, pork kargyong, yak satchu and khyopeh to profile the bacterial communities and also inferred their predictive functional profiles. Overall abundant OTUs in samples showed that Firmicutes was the abundant phylum followed by Proteobacteria and Bacteroidetes. Abundant species detected in each product were Psychrobacter pulmonis in beef kargyong, Lactobacillus sakei in pork kargyong, Bdellovibrio bacteriovorus and Ignatzschinera sp. in yak satchu and Lactobacillus sakei and Enterococcus sp. in khyopeh. Several genera unique to each product, based on analysis of shared OTUs contents, were observed among the samples except in khyopeh. Goods coverage recorded to 1.0 was observed, which reflected the maximum bacterial diversity in the samples. Alpha diversity metrics showed a maximum bacterial diversity in khyopeh and lowest in pork kargyong Community dissimilarities in the products were observed by PCoA plot. A total of 133 KEGG predictive functional pathways was observed in beef kargyong, 131 in pork kargyong, 125 in yak satchu and 101 in khyopeh. Metagenome contribution of the OTUs was computed using PICTRUSt2 and visualized by BURRITO software to predict the metabolic pathways. Several predictive functional profiles were contributed by abundant OTUs represented by Enterococcus, Acinetobacter, Agrobacterium, Bdellovibrio, Chryseobacterium, Lactococcus, Leuconostoc, Psychrobacter, and Staphylococcus.

Ulcerative colitis (UC) has become a global epidemic, and the lack of an effective cure highlights the necessity and urgency to explore novel therapies. Sijunzi Decoction (SJZD), a classical Chinese herbal formula, has been comprehensively applied and clinically proven effective in treating UC; however, the pharmacological mechanism behind its therapeutic benefits is largely obscure. Here, we find that SJZD can restore microbiota homeostasis and intestinal barrier integrity in DSS-induced colitis. SJZD significantly alleviated the colonic tissue damage and improved the goblet cell count, MUC2 secretion, and tight junction protein expressions, which indicated enhanced intestinal barrier integrity. SJZD remarkedly suppressed the abundance of phylum Proteobacteria and genus Escherichia-Shigella, which are typical features of microbial dysbiosis. Escherichia-Shigella was negatively correlated with body weight and colon length, and positively correlated with disease activity index and IL-1[Formula: see text]. Furthermore, through gut microbiota depletion, we confirmed that SJZD exerted anti-inflammatory activities in a gut microbiota-dependent manner, and fecal microbiota transplantation (FMT) validated the mediating role of gut microbiota in the SJZD treatment of UC. Through gut microbiota, SJZD modulates the biosynthesis of bile acids (BAs), especially tauroursodeoxycholic acid (TUDCA), which has been identified as the signature BA during SJZD treatment. Cumulatively, our findings disclose that SJZD attenuates UC via orchestrating gut homeostasis in microbial modulation and intestinal barrier integrity, thus offering a promising alternative approach to the clinical management of UC.

Objective Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity. Methods We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity. Results Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (PWilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, PWilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, PWilcoxon = 0.006), both of which were positively associated with fecal thiamine. Conclusion Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.

Cancer cachexia, a debilitating syndrome characterized by muscle wasting and systemic inflammation, remains a major unmet clinical need. Qingjie Fuzheng granules (QFG), a traditional Chinese medicine formulation, have shown promise in cancer therapy, but their role in cachexia management is unclear. Here, we investigated the anti-cachectic effects of QFG in a murine model of colon adenocarcinoma-induced cachexia. 16S rRNA sequencing revealed gut dysbiosis in cachectic mice, with increased Enterobacteriaceae and decreased Lactobacillus. QFG treatment restored microbial balance, reduced pro-inflammatory cytokines TNF-α, IL-6, and enhanced intestinal barrier integrity by upregulating tight junction proteins ZO-1, Occludin, Calprotectin. Mechanistically, QFG rebalanced Th17/Treg cell ratios and suppressed IL-6/NF-κB signaling, a key driver of muscle atrophy. Combining QFG with glutamine (Gln) further amplified these effects, suggesting synergistic therapeutic potential. Our findings demonstrate that QFG ameliorates cancer cachexia through microbiota modulation and IL-6/NF-κB inhibition, providing a novel multi-targeted approach for cachexia treatment.

This study examined the regulatory effects of vitamin C (VitC) on intestinal microbial homeostasis in patients with sepsis complicated by gastrointestinal perforation (GIP). Ninety-six septic GIP patients were divided into two groups: the VitC group (VCG) (GIP repair + conventional sepsis treatment + VitC) and the non-VitC group (nVCG) (GIP repair + conventional sepsis treatment). A control group (Ctrl) of 96 non-septic GIP patients was also included. Faecal samples were analysed using 16S rRNA sequencing to assess bacterial community structure, alpha and beta diversity, and relative abundance (RA). Clinical parameters, including inflammatory markers, organ function, and coagulation indices, were evaluated before and after treatment. The RA of Firmicutes and Bacteroidetes was higher, while Actinobacteria and Proteobacteria were lower in the VCG compared to nVCG (p < 0.05). Chao1 and Faith pd indices indicated improved microbial diversity in the VCG. After treatment, the VCG showed distinct enrichment of beneficial gut flora, while nVCG exhibited

As obligate hematophagous parasites, ticks have evolved to cope with substantial amounts of iron and exogenous microorganisms present in host blood during feeding. In ticks, ferritin plays an important role in maintaining the oxidative balance of gut and the homeostasis of the microbial community structure, but its regulatory mechanism has not yet been clarified. This study successfully identified a ferritin gene from Haemaphysalis doenitzi, named Hd-fer, and further studied the function of Hd-fer. The results showed that rHd-fer had antioxidant properties and antibacterial activity. The expression of Hd-fer gene in the ovary and midgut was significantly higher than other organs, and the expression in adults was significantly higher than other stages. The Hd-fer gene knock-out significantly changed the abundance of the midgut microbial community, and the relative abundance decreased generally, while the relative abundance of Achromobacter increased. The knockout of Hd-fer gene also significantly changed the structural composition of the midgut microbial species, and pathogenic microorganisms showed a growing trend, producing their unique microbial genera, including Barnesiellaceae, Carnobacterium and Pediococcus. The RNA interference of Hd-fer led to prolonging the tick's blood sucking time and reducing engorged weight. The results of this study showed that Hd-fer may affect the stability of the midgut microbial community structure by regulating iron availability, which in turn plays an important role in the survival and reproduction of ticks. These findings provide novel insights into the role of ferritin in tick biology and highlight its potential as a target for controlling tick-borne diseases.

Objective This study aimed to investigate the effect of selenium on gut microbiota in mice with breast cancer under a high-fat diet. Methods A total of 12 female BALB/c mice were randomly divided into two groups: 4 T1 + selenium+ high-fat diet group and 4 T1 + high-fat diet group. Mice were injected with 4 T1 cells on the right 4th mammary fat pad and kept on a high-fat diet. Fecal samples were collected, and DNA was extracted for metagenomic sequencing and bioinformatics analysis. Relevant target genes and pathways were annotated and metabolically analyzed to explore the intervention effect of selenium on breast cancer in the high-fat diet state. Results Selenium supplementation in the high-fat diet altered the composition and diversity of gut microbiota in mice with breast cancer. The gut microbial composition was significantly different in the selenium intervention group, with an increased abundance of Proteobacteria, Actinobacteria, and Verrucomicrobia phyla and species such as Helicobacter ganmani, Helicobacter japonicus, and Akkermansia muciniphila, while phyla, such as Bacteroidetes, Firmicutes, Deferribacteres, and Spirochaetes, and species, such as Prevotella sp. MGM2, Muribaculum intestinale, Lactobacillus murinus, and Prevotella sp. MGM1, were decreased. Functional analysis revealed differential expression of genes related to carbohydrate-active enzymes, pathogen–host interactions, cell communication, cell auto-induction, membrane transporters, and virulence factors. Furthermore, 37 COGs and 48 metabolites with rising metabolic potential in the selenium intervention group were predicted. Conclusion Selenium alters the homeostasis of gut microbiota in mice with breast cancer on a high-fat diet, affecting their composition, abundance, and associated metabolism. These findings suggest that the mechanism involves interfering with gut microbiota homeostasis, leading to altered synthesis of tumor-associated proteins and fatty acids and inducing tumor cell apoptosis and pyroptosis.

The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.

Curcumin is widely used as a traditional drug in Asia. Interestingly, curcumin and its metabolites have been demonstrated to influence the microbiota. However, the effect of curcumin on the gut microbiota in patients with myasthenia gravis (MG) remains unclear. This study aimed to investigate the effects of curcumin on the gut microbiota community, short-chain fatty acids (SCFAs) levels, intestinal permeability, and Th17/Treg balance in a Torpedo acetylcholine receptor (T-AChR)-induced MG mouse model. The results showed that curcumin significantly alleviated the clinical symptoms of MG mice induced by T-AChR. Curcumin modified the gut microbiota composition, increased microbial diversity, and, in particular, reduced endotoxin-producing Proteobacteria and Desulfovibrio levels in T-AChR-induced gut dysbiosis. Moreover, we found that curcumin significantly increased fecal butyrate levels in mice with T-AChR-induced gut dysbiosis. Butyrate levels increased in conjunction with the increase in butyrate-producing species such as Oscillospira, Akkermansia, and Allobaculum in the curcumin-treated group. In addition, curcumin repressed the increased levels of lipopolysaccharide (LPS), zonulin, and FD4 in plasma. It enhanced Occludin expression in the colons of MG mice induced with T-AChR, indicating dramatically alleviated gut permeability. Furthermore, curcumin treatment corrected T-AChR-induced imbalances in Th17/Treg cells. In summary, curcumin may protect mice against myasthenia gravis by modulating both the gut microbiota and SCFAs, improving gut permeability, and regulating the Th17/Treg balance. This study provides novel insights into curcumin's clinical value in MG therapy.

Acute lung injury (ALI) is a life-threatening disease characterized by severe lung inflammation and intestinal microbiota disorder. The GPR18 receptor has been demonstrated to be a potential therapeutic target against ALI. Extracting Naringin dihydrochalcone (NDC) from the life-sustaining orange peel is known for its diverse anti-inflammatory properties, yet the specific action target remains uncertain. In the present study, we identified NDC as a potential agonist of the GPR18 receptor using virtual screening and investigated the pharmacological effects of NDC on sepsis-induced acute lung injury in rats and explored underlying mechanisms. In in vivo experiments, CLP-induced ALI model was established by cecum puncture and treated with NDC gavage one hour prior to drug administration, lung histopathology and inflammatory cytokines were evaluated, and feces were subjected to 16s rRNA sequencing and untargeted metabolomics analysis. In in vitro experiments, the anti-inflammatory properties were exerted by evaluating NDC targeting the GPR18 receptor to inhibit lipopolysaccharide (LPS)-induced secretion of TNF-α, IL-6, IL-1β and activation of inflammatory signaling pathways in MH-S cells. Our findings showed that NDC significantly ameliorated lung damage and pro-inflammatory cytokine levels (TNF-α, IL-6, IL-1β) in both cells and lung tissues via inhibiting the activation of STAT3, NF-κB, and NLRP3 inflammatory signaling pathways through GRP18 receptor activation. In addition, NDC can also partly reverse the imbalance of gut microbiota composition caused by CLP via increasing the proportion of Firmicutes/Bacteroidetes and Lactobacillus and decreasing the relative abundance of Proteobacteria. Meanwhile, the fecal metabolites in the NDC treatment group also significantly were changed, including decreased secretion of Phenylalanin, Glycine, and bile secretion, and increased secretion of Lysine. In conclusion, these findings suggest that NDC can alleviate sepsis-induced ALI via improving gut microbial homeostasis and metabolism and mitigate inflammation via activating GPR18 receptor. In conclusion, the results indicate that NDC, derived from the typical orange peel of food, could significantly contribute to development by enhancing intestinal microbial balance and metabolic processes, and reducing inflammation by activating the GPR18 receptor, thus mitigating sepsis-induced ALI and expanding the range of functional foods.

Mine tailing dumps are arguably one of the leading sources of environmental degradation with often both public health and ecologically consequences. The present study investigated the concentration of heavy metals in gold mine tailings, and used high throughput sequencing techniques to determine the microbial community diversity of these tailings using 16S rRNA gene based amplicon sequence analysis. The concentration of detected metals and metalloids followed the order Si > Al > Fe > K > Ca > Mg. The 16S rRNA gene based sequence analysis resulted in a total of 273,398 reads across the five samples, represented among 7 major phyla, 41 classes, 77 orders, 142 families and 247 major genera. Phylum Actinobacteria was the most dominant, followed by Proteobacteria, Firmicutes, Chloroflexi, Cyanobacteria, Bacteroidetes, Acidobacteria and Planctomycetes. Redundancy analysis (RDA) and pairwise correlation analysis positively correlated the distribution of Alphaproteobacteria and Gammaproteobacteria to Al and K; Actinobacteria to Cr and Chloroflexi to Si. Negative correlations were observed in the distribution of Bacteroidetes with respect to As concentrations, Actinobacteria to Al, and Alphaproteobacteria and Gammaproteobacteria to high As and Te content of the soils. Predictive functional analysis showed the presence of putative biosynthetic and degradative pathways across the five sample sites. The study concludes that mine tailing sites harbour diverse and unique microbial assemblages with potentially biotechnologically important genes for biosynthesis and biodegradation.

More attention has been paid to the abundance and diversity of antibiotic resistance genes (ARGs) in aquatic environments. However, few studies have investigated the persistence and spatial variation of ARGs in aquatic organisms. This study investigated the occurrence and abundance of ARGs and the bacterial populations in shrimp intestinal tracts during the rearing period in different regions of Guangdong, South China. The results showed that sul1, sul2, qnrD, and floR were the predominant ARGs. Compared with those of juvenile shrimp, the total concentrations of ARGs in the intestinal tract of adult shrimp in three shrimp farms were 2.45-3.92 times higher (p < 0.05), and the bacterial populations in the adult shrimp intestinal tract changed considerably. Redundancy analysis (RDA) showed that the abundance of Proteobacteria, Firmicutes, and Verrucomicrobia in Farms A, B, and C, respectively, were strongly positively correlated with the most abundant and predominant genes (sul1 and qnrD for Farm A; floR and sul2 for Farm B; floR and sul2 for Farm C) in the shrimp intestinal tract. The results of this study indicated that ARGs gained persistence in the developmental stages of the reared shrimp. Different phyla of predominant bacteria were responsible for the increase of ARGs abundance in the shrimp intestinal tract in different regions. This study represents a case study of the persistence and spatial variation of ARGs in aquaculture and can be a reference for the determination of harmful impacts of ARGs on food safety and human health.

Robinia pseudoacacia (R. pseudoacacia) is a well reported plant species for heavy metal phytoremediation, and it was capable to improve Cd uptake efficiency after inoculated with plant growth promoting endophytes. However, the knowledge on R. pseudoacacia associated endophytes in field condition and the relationship between these microbial communities and heavy metal uptake capacities are still scarce. In this study, the characteristics of heavy metal bioaccumulation and translocation in R. pseudoacacia, and the structure and function of its endophytic bacterial communities were revealed. The results showed that heavy metal pollution made microbes more sensitive to the environment as the diversity (Shannon) of endophyte community decreased but the abundance (Chao) increased. Redundancy analysis (RDA) also showed that heavy metals were the key factor affecting the composition of endophyte. In the co-occurrence network, 27 keystone taxa mainly from Actinobacteria, Proteobacteria and Firmicutes occupied the dominant niches, among which 16 OTUs mainly from lactobacillus, bacteroides, staphylococcus, methylorubrum and bifidobacterium were positively related to bioaccumulation and translocation of Cd, Cu, Pb and Zn. Besides, heavy metal stress enhanced the functional adaptability of endophytic bacteria community. Related predicted genes were enriched in immune response, physiological metabolism pathway and stress-resistant enzyme synthesis. This study showed that heavy metal stress enhanced the structural and functional adaptability of endophyte community and keystone taxa played significant role in improving the efficiency of phytoremediation.

Astragalus is a medicinal plant with obvious rhizosphere effects. At present, there are many Astragalus plants with high application value but low recognition and resource reserves in the northwestern area of Yunnan province, China. In this study, metagenomics was used to analyze the microbial diversity and community structure of rhizosphere soil of A. forrestii, A. acaulis, and A. ernestii plants grown in a special high-cold environment of northwestern Yunnan, China, at different altitudes ranging from 3225 to 4353 m. These microbes were taxonomically annotated to obtain 24 phyla and 501 genera for A. forrestii, 30 phyla and 504 genera for A. acaulis, as well as 39 phyla and 533 genera for A. ernestii. Overall, the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Acidobacteria, while the dominant fungal ones were Ascomycota and Basidiomycota. At the genus level, Bradyrhizobium, Afipia, and Paraburkholderia were the most prevalent bacteria, and Hyaloscypha, Pseudogymnoascus, and Russula were the dominant fungal genera. Some of them are considered biocontrol microbes that could sustain the growth and health of host Astragalus plants. Redundancy analysis revealed that pH, TN, and SOM had a significant impact on the microbial community structures (p < 0.05). Finally, triterpene, flavonoid, polysaccharide, and amino acid metabolisms accounted for a high proportion of the enriched KEGG pathways, which possibly contributed to the synthesis of bioactive constituents in the Astragalus plants.

The Chinese alligator (Alligator sinensis) is currently an endangered species due to a combination of factors, including climate change, anthropogenic activities, and habitat fragmentation. Captivity plays a crucial role in mitigating the decline of the Chinese alligator population. Currently, there is a lack of clarity regarding the influence of host development and captive conditions on the gut microbiota of Chinese alligators. The aim of the study was to investigate the gut bacterial communities of Chinese alligators and their surrounding environmental bacterial communities using 16S rRNA sequencing. The primary gut flora of Chinese alligators consists of Proteobacteria, Bacteroidetes, and Firmicutes. Proteobacteria is the most abundant and efficient settler in the gut, water, and sediment. PCoA and Adonis test revealed significant differences in bacterial communities across these habitats. Venn analysis revealed overlap in OTUs among the gut, water, and sediment, varying with growth stage and density stress. Different growth stages of Chinese alligator guts harbor distinct pathogenic bacteria, requiring attention. Density stress leads to an increase in pathogenic bacteria, a decrease in gut absorption efficiency. PICRUst2 predicts more abundant metabolic pathways related to gut function during high‐density stress, possibly linked to Roseburia. SourceTracker Analysis indicated that water bacteria have a greater impact on Chinese alligator gut bacteria than sediment, and density stress significantly affects the contribution of environmental microorganisms to the gut microbes of Chinese alligator. BugBase analysis identified water body microbes as the main source of “potentially pathogenic” phenotypes in the gut microbiota. RDA analysis found dissolved oxygen (DO) in water to be the most significant factor influencing water microorganisms, positively correlated with certain pathogenic strains. These findings enhance our understanding of the significance of microbial communities in the gut and surrounding aquatic environment of the Chinese alligator. Furthermore, they provide theoretical support for environmental regulation, disease control, and healthy breeding.

While human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that obscure differences in gene abundance between individuals. To account for these biases, we developed a powerful test of gene variability called CCoDA, which is applicable to shotgun metagenomes from any environment and can integrate data from multiple studies. Our analysis of healthy human fecal metagenomes from three separate cohorts revealed thousands of genes whose abundance differs significantly and consistently between people, including glycolytic enzymes, lipopolysaccharide biosynthetic genes, and secretion systems. Even housekeeping pathways contain a mix of variable and invariable genes, though most highly conserved genes are significantly invariable. Variable genes tend to be associated with Proteobacteria, as opposed to taxa used to define enterotypes or the dominant phyla Bacteroidetes and Firmicutes. These results establish limits on functional redundancy and predict specific genes and taxa that may explain physiological differences between gut microbiomes.

As a crucial plateau freshwater lake in Yunnan Province, China, Erhai Lake exhibits distinct environmental heterogeneity driven by its unique watershed characteristics and human activities, significantly influencing sediment microbial communities. This study investigated the spatial relationships between environmental factors and microbial community structures in surface sediments from the eastern, western, and northern shores using redundancy analysis (RDA) and Spearman correlation analysis. Results revealed that pH, total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), and redox potential (Eh) were key drivers of microbial community divergence. The western shore, with the highest TP, TOC, and nitrogen levels, displayed elevated microbial diversity dominated by Proteobacteria and Bacteroidetes, reflecting higher pollution loads. The northern shore exhibited severe nitrogen pollution, marked by the highest TN content and enrichment of Thiobacillus, potentially enhancing water self-purification. The eastern shore, with minimal anthropogenic disturbance, showed the highest bacterial diversity but the lowest nutrient concentrations. Fungal community structure was significantly influenced by pH, Eh, and TOC, while ecological restoration measures on the western shore enhanced fungal community stability. This study highlights how spatial heterogeneity in environmental factors regulates microbial community structure and function, ultimately affecting the stability of lake ecosystems. These findings provide a scientific basis for ecological restoration and sustainable management of plateau lakes.

Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from ‘omics’ approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g . , C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.

Phytoplankton-bacterioplankton interactions critically influence aquatic ecosystem stability, yet their dynamics remain poorly understood in eutrophic plateau lakes. This study employed environmental DNA (eDNA) metagenomics to investigate these cross-kingdom relationships in Caohai Plateau Lake, a vulnerable wetland undergoing macrophyte-to-algae regime shifts, integrating correlation analysis, niche overlap, redundancy analysis (RDA), co-occurrence networks, and neutral community model (NCM). A total of 331 phytoplankton species across 10 phyla were characterized in the phytoplankton community, dominated by Cyanophyta with Microcystis as the representative genus, while bacterioplankton communities were primarily structured by Proteobacteria and Sphingomonas. The assembly of phytoplankton community was primarily driven by stochastic processes (R²>0.90). Co-occurrence network analysis showed phytoplankton interactions were dominated by positive effects (84.25%), whereas bacterioplankton networks exhibited balanced positive and negative effects. Metabolic specialization emerged through LEfSe analysis: phytoplankton specialized in photosynthesis and carbon storage, while bacterioplankton dominated anaerobic respiration (propanoate metabolism). The positive interactions were more prevalent than negative ones; combined with the metabolic complementarity of phytoplankton and bacterioplankton, this suggests that mutualism is more dominant than competition in cross-kingdom interactions. High niche overlap under sufficient nutrients (TP) facilitated species coexistence of phytoplankton and bacterioplankton by minimizing resource competition, thereby promoting stochastic community assembly, while keystone taxa (Cyanothece, Sphingobium) mediated ecosystem stability. This work demonstrates that nutrient enrichment promote stochastic assembly in eutrophic plateau lakes.

No abstract available

Organic fertilizers are critically important to soil fertility, microbial communities, and sustainable agricultural strategies. We compared the effect of two fertilizer groups (organic+chemical fertilizer: OM, chemical fertilizer: CK) on sugarcane growth, by observing the difference in microbial communities and functions, soil nutrient status, and agronomic characters of sugarcane. The results showed that the sugar content and yield of sugarcane increased significantly under organic fertilizer treatment. We believe that the increased soil nutrient status and soil microorganisms are the reasons for this phenomenon. In addition, redundancy analysis (RDA) shows that the soil nutrient condition has a major impact on the soil microbial community. In comparison with CK, the species richness of Acidobacteria, Proteobacteria, Chloroflexi, and Gemmatimonadetes as well as the functional abundance of nucleotide metabolism and energy metabolism increased significantly in the OM field. Moreover, compared with CK, genes related to the absorption and biosynthesis of sulfate were more prominent in OM. Therefore, consecutive organic fertilizer application could be an effective method in reference to sustainable production of sugarcane.

Abstract Microbial diversity plays a crucial role within the plant rhizosphere ecosystem, serving as a pivotal indicator of plant health and stability. In order to explore the correlation between the growth of mycorrhizal seedlings and the nutrition and microbial diversity of the ectomycorrhizosphere, the soil of the ectomycorrhizosphere with different growth conditions was used as the research object, and the ITS1 region and 16S rRNA high-throughput sequencing technology were used to explore the inter-relationship. The findings indicated that the primary phyla within the rhizosphere soil microbial communities of various mycorrhizal seedlings were comparable, although their relative abundances varied. The relative abundance of Tuberaceae in good-growing mycorrhizal seedlings (CHTG) was 17.87% and 15.58% higher than in medium-growing (CHTM) and bad-growing (CHTB), respectively. Comparing the diversity indexes Chao1, Shannon and Simpson, it was found that CHTG had the lowest richness. Redundancy analysis (RDA)/canonical correspondence analysis (CCA) analysis revealed that Tuber was positively correlated with soil pH and negatively correlated with available nitrogen, organic matter, total nitrogen, total phosphorus, total potassium, available potassium, and available phosphorus. Rhizosphere core species analysis showed that symbiotic Ascomycota dominated the rhizosphere soil fungi, and the bacterial community was composed mainly of Proteobacteria. There was a positive correlation between most genera of bacteria and fungi. This study proved that in the bionic cultivation of Tuber himalayense-Corylus heterophylla, the growth of mycorrhizal seedlings can be promoted by adjusting the pH to weakly alkaline and enhancing the advantages of Plectosphaerella in the soil flora, without adding other nutrients, which provides a theoretical basis for the establishment of truffle plantations, soil improvement and ecosystem stability.

Soil heavy metal pollution poses a significant threat to soil biodiversity. While extensive research has examined heavy metal impacts on soil communities and organismal health, their effects on soil fauna gut microbiota remain less explored. Here, we characterize gut microbial communities of soil nematodes across heavy metal gradients using high-throughput sequencing. The gut microbiota of soil nematodes was predominantly composed of Proteobacteria (75.97 %), Firmicutes (6.62 %), Actinobacteriota (3.79 %), etc. Remarkably, core microbial taxa (shared ASVs) represented 89.77 % of total sequences, indicating high compositional similarity across nematodes. Heavy metal pollution significantly reduced gut microbiota diversity and compositional stability (p < 0.05). RDA analysis identified cadmium (Cd), copper (Cu), chromium (Cr), soil properties (TN, TP, TOC), and soil bacterial diversity as key determinants of community structure, with Cd emerging as the primary driver through Mantel tests and random forest analysis. A significant negative correlation existed between Cd levels and microbial diversity (p < 0.05). Structural equation model further delineated that Cd impacts nematode gut microbiota via both direct and indirect pathways mediated by soil properties and bacterial diversity. Network analysis demonstrated increasing complexity (interactions) and stability under pollution escalation, evidenced by rising network density (0.053→0.093→0.100) and declining modularity (0.579→0.480→0.464). Core microbiota in heavily polluted soils exhibited enhanced disturbance resistance, underscoring their role in maintaining stability under metal stress. Collectively, heavy metals drive a dual response: diminishing diversity and stability while simultaneously selecting for adaptive microbial network restructuring. This study elucidates the variations in nematode gut microbiota under heavy metal stress, advancing understanding over adaptive response of gut microbiota to contaminated environments.

The combined effects of imidacloprid (ICD) and glufosinate-ammonium (GLAM) on submerged plants and epiphytic microbial community remains unclear, despite the frequent co-occurrence of these pesticides in aquatic environments. In this study, a 24-day experiment was conducted to examine changes in water quality, plant physiology, and epiphytic microbial communities in Hydrilla verticillate-dominated wetlands under ICD alone or together with GLAM. Results showed that GLAM+ICD induced greater oxidative stress and a stronger antioxidant response in H. verticillata compared ICD alone, demonstrating that the mixtures exacerbated ecotoxicological effects on plant. Compared to ICD, many micro-biomarkers were obtained in ICD+GLAM, including Bacteroidota, Comamonadaceae, Proteobacteria and Cocconeis. Redundancy analysis indicated that the ICD concentration was correlated positively to Stigeoclonium, Closterium and Cocconeis, but negatively related with Oedogonium and Chloromonas, GLAM is opposite to ICD. More complex interkingdom interactions among bacteria and eukaryotes were observed in high concentration MIX treatment group compared to others. Co-occurrence networks analysis further demonstrated that GLAM and ICD changed microbial interactions within epiphytic biofilm, and impaired the stability and function of the microbial communities. These results underscore that the combined presence of ICD and GLAM poses a significant ecological risk to Hydrilla verticillate-biofilm system in agricultural regions.

As the aquaculture capacity of S. paramamosain in southern China nears saturation, northern coastal regions, which are characterized by abundant water resources, ample feed availability, and favorable climatic conditions, have emerged as ideal areas for aquaculture expansion. This study investigates the aquatic environment of S. paramamosain cultured in seawater and saline-alkali ponds in northern China. Over the course of a five-month aquaculture experiment, water samples were collected from seawater and saline-alkali ponds and subsequently analyzed using 16S rRNA gene sequencing technology to examine the bacterial community composition and its relationship with physicochemical water quality parameters. Sensitive bacterial species were identified as well. The results revealed that seawater ponds exhibited higher salinity and dissolved oxygen levels, but lower pH, ammonia nitrogen, and nitrite nitrogen concentrations. In contrast, saline-alkali ponds exhibited elevated pH, ammonia nitrogen, and nitrite nitrogen levels, accompanied by reduced salinity and dissolved oxygen. Bacterial communities in seawater ponds demonstrated greater species richness, evenness, and diversity indices, whereas those in saline-alkali ponds were characterized by reduced diversity and distinct dominant bacterial groups. Redundancy analysis (RDA) identified salinity, pH, and dissolved oxygen as the principal environmental factors influencing bacterial community structure. Using the IndVal method, we identified strong associations between specific bacterial species and pond types, such as Sphingoaurantiacus and Cobetia in seawater ponds, and Roseivivax, Tropicimonas, and Thiobacillus in saline-alkali ponds. Environmental factors exerted distinct effects on bacterial communities in the two pond types, with sensitive bacterial species demonstrating significant specificity and strong correlations with water quality parameters. Functional predictions indicated that microbes in saline-alkali ponds prioritized resource acquisition and stress resistance, whereas those in seawater ponds emphasized nitrogen metabolism and protein synthesis. This study demonstrated significant differences in bacterial community characteristics between seawater and saline-alkali ponds, which were strongly influenced by water quality parameters. These findings are crucial for optimizing the growth environment of S. paramamosain, providing essential data for improving aquaculture conditions and promoting the development of northern S. paramamosain farming.

Environmental selection of antibiotic resistance genes (ARGs) is considered to be caused by antibiotic or metal residues, frequently used in livestock. In this study we examined three commercial poultry farms to correlate the co-occurrence patterns of antibiotic and metal residues to the presence of ARGs. We quantified 283 ARGs, 12 mobile genetic elements (MGEs), 49 targeted antibiotics, 7 heavy metals and sequenced 16S rRNA genes. The abundance and type of ARG were significantly enriched in manure while soil harbored the most diverse bacterial community. Procrustes analysis displayed significant correlations between ARGs/MGEs and the microbiome. Cadmium (Cd), arsenic (As), zinc (Zn), copper (Cu) and lead (Pb) were responsible for a majority of positive correlations to ARGs when compared to antibiotics. Integrons and transposons co-occurred with ARGs corresponding to 9 classes of antibiotics, especially Class1 integrase intI-1LC. Redundancy analysis (RDA) and Variance partitioning analysis (VPA) showed that antibiotics, metals, MGEs and bacteria explain solely 0.7%, 5.7%, 12.4%, and 21.9% of variances of ARGs in the microbial community, respectively. These results suggested that bacterial composition and horizontal gene transfer were the major factors shaping the composition of ARGs; Metals had a bigger effect on ARG profile than detected antibiotics in this study.

No abstract available

Salinization is a severe threat to agriculture and the environment in many areas, and the same in Qaidam Basin, Qinghai Province, Northwestern China. Microorganisms have an important influence on regulating the biochemical cycles of ecosystems; however, systematic research exploring microbial diversity and interactions with saline-soil ecosystems' environmental variables remains scarce. Thus, 16 S rRNA high-throughput sequencing was performed in this paper to characterize microbial diversity under different levels of salinized soils: non-salinized (NS, 2.25 g/L), moderately salinized (MS, 6.14 g/L) and highly salinized (HS, 9.82 g/L). The alpha diversity results showed that the HS soil was significantly different from the NS and MS soils. An analysis of similarity (ANOSIM) and a principal co-ordinates analysis (PCoA) indicated that NS and MS clustered closely while HS separated from the other two. Significant differences in microbial composition were observed at the taxonomic level. Proteobacteria (42.29-79.23 %) were the most abundant phyla in the studied soils. Gammaproteobacteria (52.49 and 66.61 %) had higher abundance in the MS and HS soils at the class level; Methylophaga and Pseudomonas were the predominant bacteria in the HS soil; and Azotobacter and Methylobacillus were abundant in the MS soil. Most genera belonging to Proteobacteria and Actinobacteria were detected via a linear discriminate analysis (LDA) effect size (LEfSe) analysis, which indicated that microbes with the ability to degrade organic matter and accomplish nutrient cycling can be well-adapted to salt conditions. Further analyses (redundancy analysis and Mantel test) showed that the microbial communities were mainly related to the soil salinity, electrical conductivity (EC1:5), total phosphorus (TP) and ammonia nitrogen (NH4+-N). Overall, the findings of the study can provide insights for better understanding the dominant indigenous microbes and their roles in biochemical cycles in different saline soils in the Qaidam Basin, Qinghai Province, China. The researches related to microbial community under typical poplar species should further clarify the mechanism of plant-microbial interaction and benefit for microbial utilization in salt soil remediation.