水体细菌多样性研究

While the strong general effects of salinity on microbial diversity are well-known and described for marine and freshwater habitats, the impact of the specific composition of major inorganic ions remains largely unexplored. In this study, we assess how microbial community structure in inland saline aquatic habitats is influenced by ionic composition as compared to salinity, spatial factors, and other environmental parameters. We collected and analysed 16S rRNA gene V4 and V3-V4 amplicon datasets from freshwater to hypersaline aquatic environments worldwide (in total 375 samples from 130 lakes). With an emphasis on saline inland waters characterised by highly variable ionic composition, we demonstrated that the ionic composition of the major ions explained more variability in community composition than bulk salinity and that the geographic location of the sampling sites had only an ambiguous effect. We also identified the taxa contributing the most to the observed dissimilarity between communities from sites with different ionic composition and found mostly lineages known to be characteristic for a given habitat type, such as Actinobacteria acI in freshwater, Halomonadaceae in saline, or Nitriliruptorales in soda and soda-saline habitats. Many of these habitat type-specific indicator lineages were monophyletic, underpinning ionic composition as a crucial eco-evolutionary driver of aquatic microbial diversity.

Due to the recent decades of climate change and intensive human activities, endorheic lakes are threatened by both salinization and eutrophication. However, knowledge of the aquatic bacterial community’s response to simultaneous increasing salinity and trophic status is still poor. To address this knowledge gap, we collected 40 surface water samples from five lakes and six rivers on the semi-arid Inner Mongolia Plateau, and investigated their bacterial communities using 16S rRNA gene-targeted amplicon sequencing. We found that bacterial species diversity significantly decreased from the mesotrophic freshwater river habitat to the eutrophic high-brackish lake habitat; salinity was more important than trophic status in explaining this decreased diversity. Salinity was the most important environmental factor in shaping community composition, while increased nitrogen loading was more important in structuring predicted functional composition. Within the lake habitats, the impact of environmental filtering on bacterial community assembly increased with the increasing salinity. The results suggested that the elevated salinity and nutrients have combined effects on the aquatic bacterial community, resulting in dramatic declines in species diversity, and promoted the importance of deterministic processes in community assembly. Our findings provide new insights into bacterial communities’ responses to the intensified climate-driven and anthropogenic environmental changes in aquatic ecosystems.

Highlights • Bacterial diversity in disturbed conditions increased significantly.• Bacterial diversity in nutrient addition decreased significantly.• Bacterial community composition in disturbances and nutrient addition exhibited different variations.• Nutrient input enhance positive interactions among bacteria.• Disturbance indirectly influenced bacterial community composition by affecting algal community composition.

No abstract available

Microbial communities are vital components of freshwater ecosystems due to their role in nutrient cycling and energy flow; however, the mechanisms driving their variation are still being explored. In aquatic systems, water flow (hydrology) can impact microbial community composition through community connectivity; however, the details of hydrology’s effects on microbial connectivity remain unclear. To address this question, we used 16S rRNA metabarcoding to determine bacterial community composition and connectivity across flow transects in three connected Great Lakes waterbodies with very different water-flow regimes: the Little River (high flow), the Detroit River (moderate flow), and Lake Erie (low flow). Bacterial alpha diversity (Chao1) did not differ among the three locations or sample sites along the transects. Analyses of beta diversity using community dissimilarity matrices identified significant differences among the three locations and among sample sites within locations. Bacterial community connectivity varied among the three locations, with a significant distance–decay relationship observed only in the low-flow location, which is indicative of connectivity driven by spatial proximity. Directional analyses showed that the water-flow direction affected bacterial similarity, consistent with the expected hydrological effects on community connectivity and previous published work. Our results indicate that (1) microbial community composition varies within and among even geographically close sampling locations and (2) the specific water-flow regime appears to affect bacterial community connectivity. Including hydrology in models of bacterial community composition will improve our understanding of the relative roles of selection versus stochastic effects on bacterial community diversity and composition in freshwater ecosystems.

ABSTRACT Sponges serve as the natural cleaner in diverse aquatic ecosystems, harboring diverse microbial communities and forming a highly specialized holobiont. The present study provides the first insights into the bacterial communities associated with freshwater sponges of Sundarban, highlighting their distinct microbial community composition compared to the surrounding water using 16S rRNA gene-based metataxonomic analyses. The analysis encompassing six sponge species collected from Sagar Island and Ghoramara revealed distinct variations in microbial abundance and diversity compared to their ambient water, suggesting selective bacterial associations with the sponges. The sponge species displayed a varied abundance of bacterial taxa across different species and locations. Furthermore, significantly greater concentrations of potentially toxic elements (PTEs) were observed in sponges when compared with corresponding water samples, thereby suggesting the bioaccumulation capability of these sponges. Functional profiling of bacterial communities in sponge and water samples revealed enrichment of various metabolic pathways linked to metal ion transport and resistance, as well as antimicrobial resistance in the sponges, suggesting an adaptive response to environmental stressors. The abundance of diverse metal ion regulators and transporters underscores the ecologically significant function of sponge-associated bacterial communities in metal ion resistance, placing the sponges as promising bioindicators for monitoring polluted aquatic ecosystems. IMPORTANCE Freshwater sponges play an essential role as natural biofilters in aquatic ecosystems, effectively purifying water. These sponges harbor unique microbial communities, forming a holobiont that is key to their ecological function. This study offers new insights into the bacterial communities associated with freshwater sponges from the Sundarbans, a previously underexplored region. Using 16S rRNA gene-based metataxonomic analyses, we compared the bacterial diversity of six sponge species from Sagar Island and Ghoramara to that of surrounding water. Our results reveal distinct bacterial associations within sponges, different from the ambient water’s microbial composition. Notably, sponge concentrations of potentially toxic elements (PTEs) were much higher than in the surrounding water, highlighting their bioaccumulation capacity. Functional profiling of sponge-associated bacteria revealed genes related to metal ion transport and antimicrobial resistance, suggesting adaptive responses to environmental stress. This research enhances our understanding of sponge microbiomes and their potential for bioremediation, particularly for removing heavy metals from polluted water. Freshwater sponges play an essential role as natural biofilters in aquatic ecosystems, effectively purifying water. These sponges harbor unique microbial communities, forming a holobiont that is key to their ecological function. This study offers new insights into the bacterial communities associated with freshwater sponges from the Sundarbans, a previously underexplored region. Using 16S rRNA gene-based metataxonomic analyses, we compared the bacterial diversity of six sponge species from Sagar Island and Ghoramara to that of surrounding water. Our results reveal distinct bacterial associations within sponges, different from the ambient water’s microbial composition. Notably, sponge concentrations of potentially toxic elements (PTEs) were much higher than in the surrounding water, highlighting their bioaccumulation capacity. Functional profiling of sponge-associated bacteria revealed genes related to metal ion transport and antimicrobial resistance, suggesting adaptive responses to environmental stress. This research enhances our understanding of sponge microbiomes and their potential for bioremediation, particularly for removing heavy metals from polluted water.

Oligotrophy and hypereutrophy represent the two extremes of lake trophic states, and understanding the distribution of bacterial communities across these contrasting conditions is crucial for advancing aquatic microbial research. Despite the significance of these extreme trophic states, bacterial community characteristics and co-occurrence patterns in such environments have been scarcely interpreted. To bridge this knowledge gap, we collected 60 water samples from Lake Fuxian (oligotrophic) and Lake Xingyun (hypereutrophic) during different hydrological periods. Employing 16S rRNA gene sequencing, our findings revealed distinct community structures and metabolic potentials in bacterial communities of hypereutrophic and oligotrophic lake ecosystems. The hypereutrophic ecosystem exhibited higher bacterial α- and β-diversity compared to the oligotrophic ecosystem. Actinobacteria dominated the oligotrophic Lake Fuxian, while Cyanobacteria, Proteobacteria, and Bacteroidetes were more prevalent in the hypereutrophic Lake Xingyun. Functions associated with methanol oxidation, methylotrophy, fermentation, aromatic compound degradation, nitrogen/nitrate respiration, and nitrogen/nitrate denitrification were enriched in the oligotrophic lake, underscoring the vital role of bacteria in carbon and nitrogen cycling. In contrast, functions related to ureolysis, human pathogens, animal parasites or symbionts, and phototrophy were enriched in the hypereutrophic lake, highlighting human activity-related disturbances and potential pathogenic risks. Co-occurrence network analysis unveiled a more complex and stable bacterial network in the hypereutrophic lake compared to the oligotrophic lake. Our study provides insights into the intricate relationships between trophic states and bacterial community structure, emphasizing significant differences in diversity, community composition, and network characteristics between extreme states of oligotrophy and hypereutrophy. Additionally, it explores the nuanced responses of bacterial communities to environmental conditions in these two contrasting trophic states.

Abstract Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity–productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, the effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test the effects of diatom species/strain diversity on biomass production and bacterial diversity in algae–bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2–3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.

Tanjung Emas Port is the entry and exit point for trade commodities, both regional and international filled with many ships. This condition makes biofouling a very massive process in that place by various types of marine bacteria. The initial formation of a biofilm is relevant to bacterial diversity, colonization and adhesion. The objective of the study was assessing bacterial diversity in relation to with biofouling within Tanjung Mas Port Semarang, by using 16S rRNA eDNA metabarcoding Next-Generation Sequencing (NGS). Seawater samples from aquatic sites of Tanjung Mas harbor was used for DNA extraction and amplification of the 16S rRNA V-3-V4 hypervariable region, followed by sequencing and library construction of eDNA Metabarcoding. Sequence processing and analysis was performed in QIIME 2 and RStudio using DADA2 for advanced sequencing processing and Phyloseq. The results of this research showed that bacteria is the predominant taxon constituting 100% of the community. The taxon consists of Proteobacteria (49.38%), Bacteroidota (8.67%), and Firmicutes (8.88%). Alphaproteobacteria (20.92%) and Gammaproteobacteria (12.39%) dominate at the Class level, emphasizing their versatility and ecological influence. At the Order and Family levels reveals the prevalence of Rhodobacterales (10.04%), Chitinophagales (2.53%), Rhizobiales (3.61%), Rhodobacteraceae (5.67%), Saprospiraceae (3.63%), and Rhizobiaceae (2.15%). It was found that the unculturable taxa dominance in Tanjung Mas Port was 44.66%. These taxonomic entities contribute significantly to the taxonomic and functional diversity of the microbial community, influencing nutrient cycling, organic matter degradation, ecosystem stability and biofilm formation.

No abstract available

Highlights • The analysis of 16S rRNA sequences reveals a more diverse microbial habitat in the Sundarbans mangrove forest of Bangladesh.• The research found 872 bacterial species, 94 genera, 38 families, and 6 phyla. Out of these, 49.3% are typically harmless and non-pathogenic.• There is still a 24.9% uncertainty, with 13.4% showing pathogenic and non-pathogenic, and 8.4% being strictly pathogenic to other organisms.• There are varying levels of pathogenicity, with 2.6% potentially non-highly pathogenic, 1.3% occasionally pathogenic, and 0.1% pathogenic.• By establishing a genomic baseline for harmful bacterial communities in mangrove habitats, diseases in fish and shellfish may be reduced.

Simple Summary The number of arboviral diseases, such as dengue, that are transmitted in the Amazon basin has significantly increased during the last 3 years, with its control becoming more complex as the environmental plasticity and geographical distribution of vectors such as Aedes aegypti also increase. Likewise, bacterial communities have favored rapid adaptation to environmental changes at different developmental stages. This problem, from an ecological context, raises the need to generate new knowledge regarding the influence of physicochemical parameters of water and the microbial diversity that are related to the type of artificial breeding sites, and how these interactions can impact the life cycle of Ae. aegypti. In the present study, a high richness in bacteria genera from Ae. aegypti breeding sites and developmental stages was observed. Some of these genera have biotechnological, entomopathogenic, or antiviral potential. Additionally, we found a close relationship between the bacterial composition profile in the water body and the physicochemical characteristics of the different types of breeding sites. The information derived from this study allowed us to describe the dissolved oxygen, conductivity, and total dissolved solids as key ecological markers associated with the breeding sites from the Amazon basin and highlights the need to understand the microbiome of Ae. aegypti for the design of biological control strategies for insect vectors.

Fungi produce a variety of extracellular enzymes making recalcitrant substrates bioavailable. Thus, fungi are central for decomposition of dead organic matter such as leaf litter. Despite their ecological importance, our understanding of relationships between fungal species diversity and ecosystem functioning is limited, especially with regard to aquatic habitats. Moreover, fungal interactions with other groups of microorganisms such as bacteria are rarely investigated. This lack of information may be attributed to methodological limitations in tracking the biomass of individual fungal species in communities, impeding a detailed assessment of deviations from the overall performance expected from the sum of individual species' performances, so-called net diversity effects (NDEs). We used fungal species-specific biomolecular tools to target fungal-fungal and fungal-bacterial interactions on submerged leaves using four cosmopolitan aquatic fungal species and a stream microbial community dominated by bacteria. In microcosms, we experimentally manipulated fungal diversity and bacterial absence/presence and assessed functional performances and fungal community composition after 14 days of incubation. Fungal community data was used to evaluate NDEs on leaf colonization. The individual fungal species were functionally distinct and fungal cultures were on average more efficient than the bacterial culture. In absence of bacteria, NDEs correlated with growth rate (negatively) and genetic divergence (positively), but were predominantly negative, suggesting that higher fungal diversity led to a lower colonization success (niche overlap). In both absence and presence of bacteria, the overall functional performances of the communities were largely defined by their composition (i.e., no interactions at the functional level). In presence of bacteria, NDEs correlated with genetic divergence (positively) and were largely positive, suggesting higher fungal diversity stimulated colonization (niche complementarity). This stimulation may be driven by a bacteria-induced inhibition of fungal growth, alleviating competition among fungi. Resulting feedback loops eventually promote fungal coexistence and synergistic interactions. Nonetheless, overall functional performances are reduced compared to bacteria-free cultures. These findings highlight the necessity to conduct future studies, investigating biodiversity-ecosystem functioning relationships using artificial systems, without exclusion of key organisms naturally co-occurring in the compartment of interest. Otherwise, study outcomes might not reflect true ecological relationships and ultimately misguide conservation strategies.

The aquatic bacterial community (BC) plays a vital role in determining the nature and rate of ecosystem function. However, the biotic and abiotic factors influencing BC structure and function are largely unknown. Hence, the current study characterizes the impact of biotic and abiotic factors on aquatic bacterial biodiversity to determine whether the dominant effects are biotic or abiotic by partitioning their relative effects across temperate Canadian lakes. We collected water samples from sixty southern Ontario lakes and characterized their BC and microbial eukaryotic community (MEC) compositions using high throughput metabarcode sequencing of 16S and 18S rRNA gene fragments. The diversity and richness of aquatic BCs differed considerably among our study lakes, and those differences were explained by environmental, spatial, and biotic (MEC) factors (31%, 23%, and 23% of variance explained, respectively). The relatively large contribution from biotic and abiotic factors (54%), relative to spatial effects, shows deterministic processes prevail in shaping BC assembly in freshwater lakes. However, spatial effects also contributed significantly, highlighting the role of stochastic processes (ecological drift and coupled with limited dispersal) in shaping BC structure. Furthermore, our co-occurrence network analysis showed strong positive and negative interactions within and between the BCs and MECs, indicating mutualistic or antagonistic co-occurrence patterns relationships play important roles in driving the variation in BC composition among our sampled lakes. Considered together, our community analyses show that deterministic and stochastic processes combined contribute to determining the aquatic BC composition, and hence likely function as well, across a broad array of temperate freshwater lakes.

Environmental change coupled with alteration in human lifestyles are profoundly impact-ing the microbial communities that play critical roles in the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat changes respectively, we retrieved paired 16S and ITS rRNA amplicon sequence data from 1,580 host, soil, and aquatic samples and explored the ecological patterns of the thousands of detected bacterial and fungal genera. Through this large-scale analysis, we identified 48 bacterial and 4 fungal genera that were prevalent and abundant across the three biomes, demonstrating their fitness in diverse environmental conditions. The presence of generalists significantly contributed to the alpha diversity of their respective kingdom. Their distri-bution across samples explained a large percentage of the variation in the cross-kingdom community structure. We also found that the genomes of these generalists were larger and encoded more secondary metabolism and antimicrobial resistance genes, illuminating how they can dominate diverse microbial communities. Conversely, 30 bacterial and 19 fungal genera were only found in a single habitat, suggesting they cannot readily adapt to different and changing environments. These findings can contribute to our understanding of microbial niche breadth and its consequences for global diversity loss.

The Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. In this work, we aim to produce the first characterization of aquatic bacterial communities in the Rimac river using a 16S rRNA metabarcoding approach which would be useful to identify bacterial diversity and potential understudied pathogens. We report a lower diversity in bacterial communities from the Lower Rimac (Metropolitan zone) in comparison to other sub-basins. Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility and quorum sensing. Additional metabolomic analyses showed the presence of some insecticides and herbicides in the Parac-Upper Rimac and Santa Eulalia-Parac sub-basins. The dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

No abstract available

Abstract Container aquatic habitats host a community of aquatic insects, primarily mosquito larvae that browse on container surface microbial biofilm and filter-feed on microorganisms in the water column. We examined how the bacterial communities in these habitats respond to feeding by larvae of two container-dwelling mosquito species, Culex pipiens and Cx. restuans. We also investigated how the microbiota of these larvae is impacted by intra- and interspecific interactions. Microbial diversity and richness were significantly higher in water samples when mosquito larvae were present, and in Cx. restuans compared to Cx. pipiens larvae. Microbial communities of water samples clustered based on the presence or absence of mosquito larvae and were distinct from those of mosquito larvae. Culex pipiens and Cx. restuans larvae harbored distinct microbial communities when reared under intraspecific conditions and similar microbial communities when reared under interspecific conditions. These findings demonstrate that mosquito larvae play a major role in structuring the microbial communities in container habitats and that intra- and interspecific interactions in mosquito larvae may shape their microbiota. This has important ecological and public health implications since larvae of the two mosquito species are major occupants of container habitats while the adults are vectors of West Nile virus.

Anthropogenic disturbances, such as pollution discharge and damming, can lead to a global decline in biodiversity in aquatic ecosystems. However, how such disturbances affect microbial community composition and function remains poorly understood. In November 2019, we explored bacterial diversity, community composition and metabolic function in Lake Tianmuhu, China, and in its upstream dammed river, using Illumina MiSeq sequencing and Biolog EcoPlate method based on carbon source utilization. Our results revealed higher variations in bacterial α- and β-diversity in the dammed river ecosystem than in the lake ecosystem. In addition, the dammed river and lake ecosystems were significantly different in bacterial community compositions and metabolic structures. No significant relationship between species richness and functional (metabolic) diversity was observed in this study. The site that was most impacted by domestic wastewater had the lowest taxonomic diversity but highest metabolic capacity and activity, suggesting that community composition rather than species diversity is more important in determining ecosystem functioning. Overall, our findings indicate that anthropogenic disturbances can significantly alter bacterial community and function, and taxonomic diversity is a weak proxy for ecosystem functioning in a natural freshwater habitat.

No abstract available

As a ubiquitous emerging pollutant, microplastics can interact with algal and bacterial communities in aquatic ecosystems. Currently, knowledge on how microplastics influence algae/bacteria is mostly limited to toxicity tests using either monocultures of algae/bacteria or specific algal-bacterial consortium. However, information on the effect of microplastics on algal and bacterial communities in natural habitats is not easily available. Here, we conducted a mesocosm experiment to test the effect of nanoplastics on algal and bacterial communities in aquatic ecosystems dominated by different submerged macrophytes. The community structure of algae and bacteria suspended in the water column (planktonic) and attached to the surface of submerged macrophytes (phyllospheric) were identified, respectively. Results showed that both planktonic and phyllospheric bacteria were more susceptible to nanoplastics, and these variations driven by decreased bacterial diversity and increased abundance of microplastic-degrading taxa, especially in aquatic systems dominated by V. natans. The community composition of both algae and bacteria were influenced to varying degrees by nanoplastics and/or plant types, but RDA results showed that only bacterial community composition was strongly correlated with environmental variables. Correlation network analysis showed that nanoplastics not only reduced the intensity of associations between planktonic algae and bacteria (average degree reduced from 4.88 to 3.24), but also reduced proportion of positive correlations (from 64% to 36%). Besides, nanoplastics also decreased the algal/bacterial connections between planktonic and phyllospheric habitats. Our study elucidates the potential interactions between nanoplastics and algal-bacterial community in natural aquatic ecosystems. These findings suggest that in aquatic ecosystems, bacterial community are more vulnerable to nanoplastics and may serve as a protective barrier for algae community. Further research is needed to reveal the protective mechanism of bacteria against algae at the community level.

No abstract available

Despite that the ballast water management (BWM) convention has come into force to prevent the spread of harmful aquatic organisms, to date, very few bacteria can be identified through microbial culture method. In this study, we explored a reduced-representation sequencing of 2b-RAD approach to investigate the bacterial diversity in ballast water and sediments (BWS). Our results indicated a large amount of bacteria species (1496) detected in BWS up to now, including 13 pathogens that are seriously concerning in marine environment and aquaculture like the most harmful Vibrio harveyi and Aurantimonas coralicida. We showed that the ballast water had relative lower species, which was dominated by Proteobacteria. In contrast, the sediments had richer species, which was dominated by Bacteroidetes. Although BWS differed significantly in species composition, sediments shared most of the concerned pathogens with ballast water, highlighting the importance of sediment management. In conclusion, 2b-RAD sequencing shows promise in future BWM.

The Yellow River Delta region is densely covered with saline-alkali land. Wild soybean (Glycine soja Siebold & Zucc.), as a typical plant in this area, exhibits notable salt tolerance. Consequently, understanding the composition and function of its rhizosphere microbiota is therefore crucial for deciphering the mechanisms underlying its environmental adaptation. This study focused on wild soybeans from the Yellow River Delta region as the research subject. Salt stress treatments of varying concentrations were established, and Illumina-based high-throughput 16 S rRNA gene sequencing was employed to investigate the effects of salt stress on the composition and diversity of bacterial communities in both the rhizosphere and surrounding aquatic environments of wild soybeans. The findings revealed that salt stress significantly decreased the diversity of bacterial communities in both the rhizosphere and aquatic environments and altered their bacterial community structures. At the phylum level, Proteobacteria predominated across all samples, with a notable upward trend in relative abundance as salinity increased. In the rhizosphere of wild soybeans, Cyanobacteria accumulated progressively with increasing salinity. At the genus level, the relative abundances of Pseudomonas and Acinetobacter significantly increased (p < 0.05) in response to elevated salinity levels. The roots of wild soybeans harbor Pseudomonas, Shewanella, and Rhizobium, which contribute to enhancing salt stress resistance. Research has found that under salt stress conditions, the dominant bacterial communities in the rhizosphere and surrounding environments of wild soybeans may shift toward more salt-tolerant species. These bacteria likely play a critical role in facilitating the adaptation of wild soybeans to saline environments. This study not only deepens our understanding of microbial-mediated salt tolerance mechanisms but also provides valuable technical insights for utilizing saline-alkali lands and breeding stress-tolerant crops.

The freshwater plastisphere, a unique ecological habitat formed on plastic surfaces in aquatic environments, has garnered increasing attention. Recent studies have primarily focused on its formation, composition, and responses to abiotic factors. However, the influence of biotic factors on the plastisphere has received comparatively less attention, particularly regarding its fate after ingestion and excretion by aquatic animals. Here, we conducted a microcosm experiment to investigate the effects of invasive snail Pomacea canaliculata on plastispheres formed on conventional polyethylene (PE) and biodegradable polylactic acid (PLA) microplastics (MPs). In the absence of snails, significant differences were observed in the structure, composition, diversity, function, and assembly of bacterial communities between PE and PLA plastispheres. Notably, the PLA plastisphere was enriched with more human pathogens. We found that P. canaliculata could directly ingest MPs or employ a behavior termed "pedal surface collecting" (PSC) to capture PE MPs for feeding. The gut of each tested snail was found to contain approximately 80 PE MPs (1 mm) or 26 PLA MPs (1 mm). The presence of snails significantly altered the bacterial community structure, composition, and function in both PE and PLA plastispheres, reducing α-diversity, phylogenetic diversity, dispersal limitation, and microbial network complexity. Meanwhile, in both plastispheres, the proportion of bacteria carrying mobile genetic elements increased, while bacteria associated with biofilm formation, denitrification, and plastic degradation decreased. These findings provide evidence that the plastisphere can carry microorganisms transferred from the snail gut, and highlight the potential risks of MPs as carriers of human pathogens for transmission from gut-to-gut or gut-to-environment.

The application of high-throughput sequencing of the 16S rRNA gene has increased the size of microbial diversity datasets by several orders of magnitude, providing improved access to the rare biosphere compared with cultivation-based approaches and more established cultivation-independent techniques. By contrast, cultivation-based approaches allow the retrieval of both common and uncommon bacteria that can grow in the conditions used and provide access to strains for biotechnological applications. We performed bidirectional pyrosequencing of the bacterial 16S rRNA gene diversity in two terrestrial and seven aquatic Antarctic microbial mat samples previously studied by heterotrophic cultivation. While, not unexpectedly, 77.5% of genera recovered by pyrosequencing were not among the isolates, 25.6% of the genera picked up by cultivation were not detected by pyrosequencing. To allow comparison between both techniques, we focused on the five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Deinococcus-Thermus) recovered by heterotrophic cultivation. Four of these phyla were among the most abundantly recovered by pyrosequencing. Strikingly, there was relatively little overlap between cultivation and the forward and reverse pyrosequencing-based datasets at the genus (17.1–22.2%) and OTU (3.5–3.6%) level (defined on a 97% similarity cut-off level). Comparison of the V1–V2 and V3–V2 datasets of the 16S rRNA gene revealed remarkable differences in number of OTUs and genera recovered. The forward dataset missed 33% of the genera from the reverse dataset despite comprising 50% more OTUs, while the reverse dataset did not contain 40% of the genera of the forward dataset. Similar observations were evident when comparing the forward and reverse cultivation datasets. Our results indicate that the region under consideration can have a large impact on perceived diversity, and should be considered when comparing different datasets. Finally, a high number of OTUs could not be classified using the RDP reference database, suggesting the presence of a large amount of novel diversity.

The unicellular green alga, Oophila amblystomatis, populates egg capsules of the spotted salamander Ambystoma maculatum. This nutrient-exchange mutualism is widely perceived as a bipartite interaction but the presence and contributing effects of bacteria to this symbiosis are unknown. We used standard cultivation techniques and amplicon sequencing of the V4/V5 region of 16S rRNA gene to identify and compare diversity of bacterial taxa in embryonic capsules to that in the aquatic breeding habitat. Our sampling regime allowed us to investigate diversity among individual capsules of an egg mass and between two ponds and sampling years. Capsules contain much lower diversity of bacteria than pond water and spatial and temporal variation in intracapsular and pond bacterial diversity was observed. Despite this variation, sequences corresponding to species in the orders Burkholderiales and Oligoflexales and were either prevalent, abundant, or both. Isolates most commonly recovered from capsules were closely related to species in the genus Herbaspirillum (Burkholderiaceae); other isolates were pseudomonads, but in all cases are closely related to known vascular plant-associated species. We conclude that, despite observed variation, there are bacterial taxa whose presence is held in common spatially and temporally among capsules and that the symbiosis between O. amblystomatis and A. maculatum may involve these taxa.

Disposed plastics in oceans provide a substrate to which microbes can adhere and structure the biofilm, namely the plastisphere. In this study, we showed that the mesoplastic density-based separation, routinely used in quantification assays, is detrimental to studying the microbiome diversity and ecology as it underestimates the real microbial diversity within these samples. Based on SEM and microbiome observations, we propose that chemically fixing samples before density separation preserves cellular diversity (2.32-fold change) and richness (1.12-fold change) that would be naturally lost due to the current methodology. OTUs assigned to Gram-negative bacterial species are the most negatively affected by omitting fixation and polymer composition was not decisive in shifting microbiome composition. Considering our findings, the formaldehyde-fixation step should be incorporated into the current methodology described in most studies as this is crucial to promote a deeper understanding of the microbial community in this ecosystem and biofilm-adhered scattering through aquatic ecosystems.

Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3–1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.

Understanding microbial roles in ecosystem function requires integrating microscopic processes into food webs. The carnivorous pitcher plant, Sarracenia purpurea, offers a tractable study system where diverse food webs of macroinvertebrates and microbes facilitate digestion of captured insect prey, releasing nutrients supporting the food web and host plant. However, how interactions between these macroinvertebrate and microbial communities contribute to ecosystem functions remains unclear. We examined the role of the pitcher plant mosquito, Wyeomyia smithii, in top‐down control of the composition and function of pitcher plant microbial communities. Mosquito larval abundance was enriched or depleted across a natural population of S. purpurea pitchers over a 74‐day field experiment. Bacterial community composition and microbial community function were characterized by 16S rRNA amplicon sequencing and profiling of carbon substrate use, bulk metabolic rate, hydrolytic enzyme activity, and macronutrient pools. Bacterial communities changed from pitcher opening to maturation, but larvae exerted minor effects on high‐level taxonomic composition. Higher larval abundance was associated with lower diversity communities with distinct functions and elevated nitrogen availability. Treatment‐independent clustering also supported roles for larvae in curating pitcher microbial communities through shifts in community diversity and function. These results demonstrate top‐down control of microbial functions in an aquatic microecosystem.

In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.

Bacterial microbiomes influence global carbon and nutrient cycling as the environment changes. Rain-fed rock basins are ephemeral aquatic systems, potentially subject to extreme environmental stress, that can host a wide variety of biological communities, including bacteria. However, bacterial communities are barely described in these habitats. Here we provide a detailed description on the occurrence, diversity and distribution patterns of the bacterial communities within and between rain-fed granite mountain rock basins located in the Sierra de Guadarrama National Park, Spain, using high-throughput sequencing of 16S RNA. We recovered a highly diverse community consisting of 3174 operational taxonomic units (OTUs) belonging to 32 phyla. In total, 50% of OTUs were shared among basins and 6–10% were basin-exclusive OTUs, suggesting a robust global bacterial metacommunity colonizes the basins. The existence of 6% replicate-exclusive OTUs and the fact that at least four replicates were required to catalogue 90% of the basin bacterial community emphasized the heterogeneity of these habitats. Both environmental filtering and random dispersal are likely to be involved in the arrangement of the bacterial communities. The taxa identified in this study are versatile in metabolism, and some have biotechnological potential. The taxonomic affiliation of many of the OTUs found suggests that rain-fed rock basins could be a resource for mining novel bacterial biocompounds.

Bacteria are diverse and play important roles in biogeochemical cycling of aquatic ecosystems, but the global distribution patterns of bacterial communities in lake sediments across different climate zones are still obscure. Here we integrated the high-throughput sequencing data of 750 sediment samples from published literature to investigate the distribution of bacterial communities in different climate zones and the potential driving mechanisms. The obtained results indicated that the diversity and richness of bacterial community were notably higher in temperate and cold zones than those in other climate zones. In addition, the bacterial community composition varied significantly in different climate zones, which further led to changes in bacterial functional groups. Specifically, the relative abundance of nitrogen cycling functional groups in polar zones was notably higher compared to other climate zones. Regression analysis revealed that climate (mean annual precipitation, MAP; and mean annual temperature, MAT), vegetation, and geography together determined the diversity pattern of sediment bacterial community on a global scale. The results of partial least squares path modeling further demonstrated that climate was the most significant factor affecting the composition and diversity of bacterial communities, and MAP was the most important climate factor affecting the composition of bacteria community (R2 = 0.443, P < 0.001). It is worth noting that a strong positive correlation was observed between the abundance of the dominant bacterial group uncultured_f_Anaerolineaceae and the normalized difference vegetation index (NDVI; P < 0.001), suggesting that vegetation could affect bacterial community diversity by influencing dominant bacterial taxa. This study enhances our understanding of the global diversity patterns and biogeography of sediment bacteria.

ABSTRACT The assembly of host-associated bacterial communities is influenced by a multitude of biotic and abiotic factors. It is essential to gain insight in the impact and relative strength of these factors if we want to be able to predict the effects of environmental change on the assembly of host-associated bacterial communities, or deliberately modify them. The environmental pool of bacteria, from which the host is colonized, and the genetic background of the host are both considered to be important in determining the composition of host-associated bacterial communities. We experimentally assessed the relative importance of these two factors and their interaction on the composition of Daphnia magna gut bacterial communities. Bacterioplankton originating from natural ponds or a laboratory culture were used to inoculate germ-free Daphnia of different genotypes. We found that the composition of the environmental bacterial community has a major influence on the Daphnia gut bacterial community, both reflected by the presence or absence of specific taxa as well as by a correlation between abundances in the environment and on the host. Our data also indicate a consistent effect of host genotype on the occurrence of specific bacterial taxa in the gut of Daphnia over different environments.

Amazonian floodplains form complex hydrological networks that play relevant roles in global biogeochemical cycles, and bacterial degradation of the organic matter in these systems is key for regional carbon budget. The Amazon undergoes extreme seasonal variations in water level, which produces changes in landscape and diversifies sources of organic inputs into floodplain systems. Although these changes should affect bacterioplankton community composition (BCC), little is known about which factors drive spatial and temporal patterns of bacterioplankton in these Amazonian floodplains. We used high-throughput sequencing (Illumina MiSeq) of the V3-V4 region of the 16S rRNA gene to investigate spatial and temporal patterns of BCC of two size fractions, and their correlation with environmental variables in an Amazon floodplain lake (Lago Grande do Curuai). We found a high degree of novelty in bacterioplankton, as more than half of operational taxonomic units (OTUs) could not be classified at genus level. Spatial habitat heterogeneity and the flood pulse were the main factors shaping free-living (FL) BCC. The gradient of organic matter from transition zone-lake-Amazon River was the main driver for particle-attached (PA) BCC. The BCC reflected the complexity of the system, with more variation in space than in time, although both factors were important drivers of the BCC in this Amazon floodplain system.

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The significance of salinity in shaping bacterial communities dwelling in estuarine areas has been well documented. However, the influences of other environmental factors such as dissolved oxygen and nutrients in determining distribution patterns of both individual taxa and bacterial communities inhabited local estuarine regions remain elusive. Here, bacterioplankton community structures of surface and bottom waters from eight sites along the Pearl Estuary were characterized with 16S rRNA gene pyrosequencing. The results showed significant differences of bacterioplankton community between freshwater and saltwater sites, and further between surface and bottom waters of saltwater sites. Synechococcus dominated the surface water of saltwater sites while Oceanospirillales, SAR11 and SAR406 were prevalent in the bottom water. Betaproteobacteria was abundant in freshwater sites, with no significant difference between water layers. Occurrence of phylogenetic shifts in taxa affiliated to the same clade was also detected. Dissolved oxygen explained most of the bacterial community variation in the redundancy analysis targeting only freshwater sites, whereas nutrients and salinity explained most of the variation across all samples in the Pearl Estuary. Methylophilales (mainly PE2 clade) was positively correlated to dissolved oxygen, whereas Rhodocyclales (mainly R.12up clade) was negatively correlated. Moreover, high nutrient inputs to the freshwater area of the Pearl Estuary have shifted the bacterial communities toward copiotrophic groups, such as Sphingomonadales. The present study demonstrated that the overall nutrients and freshwater hypoxia play important roles in determining bacterioplankton compositions and provided insights into the potential ecological roles of specific taxa in estuarine environments.

The bacterioplankton community composition’s (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao’an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria.

ABSTRACT In the Boreal region, extreme seasonal variations in day–night length expose communities to dynamic light and temperature fluctuations. Freshwater bacterioplankton, representing key ecosystem components, faces climate‐driven shifts; yet the fixed day‐length patterns determined by latitude underscore the importance of studying light's role in predicting ecosystem responses. We investigated bacterial community composition in a brown peat bog and a clear oligotrophic lake across seasons with contrasting light regimes: the summer solstice (> 20 h of daylight) and the autumn equinox (equal day‐night length). Using amplicon sequencing of 16S rRNA transcripts, alongside measurements of physicochemical parameters, organic matter characterisation and dissolved carbon dioxide and methane gas measurements, we found no diel cycling in the lake during either period or in the peat bog near the summer solstice. However, the structure of bacterial peat bog communities exhibited cyclic changes over diel cycles at the autumn equinox. Twelve amplicon sequence variants, including both phototrophic and heterotrophic taxa, increased in abundance at all measured morning sampling times. These findings provide valuable insights into the diel patterns of boreal lentic habitats and their bacterioplankton communities, highlighting the absence of diel fluctuations in some systems and seasons, while revealing cyclic dynamics in others, driven by conditionally rare taxa.

Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates.

With the rapid development of society and economy, most lakes in southwest China are in a state of eutrophication. As decomposers and producers in lake ecosystems, the overlying water bacterioplankton communities play an important role in maintaining material circulation and energy flow. However, the response mechanism of their composition to eutrophication remains unclear. This research sampled the overlying water of Sancha Lake, a typical sub-deep-water lake in Southwest China, at nine different sampling sites in April (spring) and November (autumn) 2017. High-throughput sequencing of 16S rRNA gene and molecular ecological network approach are used to analyze the structure and network topology of bacterioplankton community and the response mechanism of key species to eutrophication in the overlying water of Sancha Lake. The results show that the bacterial species diversity is abundant, belonging to 55 phyla, 64 classes and 732 genera. Pseudomonadota, Actinomycetota and Bacillota are the dominant phyla, while Pseudomonas and Bacillus are the dominant genera. The relative abundance of bacterial groups in the overlying water in spring and autumn has significant seasonal differences (P < 0.05 or P < 0.01). There are seasonal differences between spring and autumn in bacterioplankton community structure in the overlying water (P < 0.01). The bacterioplankton community structure is mainly influenced by phosphorus, permanganate index (CODMn), dissolved oxygen (DO) and pH. In spring and autumn, the overlying water bacterioplankton communities are mainly affected by deterministic processes and random processes, respectively. In spring and autumn, there are more positive interactions than negative interactions among bacterioplankton in the overlying water. The closeness of the overlying water bacterioplankton network is higher in spring than in autumn, and the interaction degree of the components of the overlying water bacterioplankton network is higher in autumn than in spring. The key species in the spring bacterioplankton molecular ecological network are Methylobacter, Candidatus Magnetoovum, Pseudomonas and Thiobacillus. In autumn, Methylacidimicrobium, Thiothrix and Clostridium are found. The relative abundance of key species is positively correlated with soluble reactive phosphate (SRP) content in spring, but negatively correlated with SRP content in autumn. The results of this research indicate that the bacterioplankton community in the overlying water of Sancha Lake is abundant in diversity, and its composition and structure changes are dynamic responses to the changes of eutrophication environmental factors, and the key species of bacterioplankton may play an important role in the phosphorus cycle of eutrophication.

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This study aimed to determine the environmental and ecological factors influencing the planktonic prokaryotic community profiles in the composite ecosystem comprising Taihu Lake, Taipu River, and Jinze Reservoir in the Taihu Watershed in China. A total of 42 water samples were intermittently collected from different sites in six months across four seasons. Physicochemical characteristics of the ecosystem, bacterioplankton diversity, and composition, the presence of co-occurrence patterns, and environmental predictors of ecological modules in the bacterioplankton network were determined. The central species played a more important role in regulating the structure and function of the bacterioplankton community and in responding to environmental contamination than the entire community. The relative abundance of the phylum Proteobacteria and the class Betaproteobacteria varied significantly between months and locations, which were identified as core functional taxa. A nonrandom co-occurrence pattern and function-driven modular structure were observed in the bacterioplankton co-occurrence network. Dissolved oxygen and ammonium nitrogen were the major and mutual environmental predictors of the bacterioplankton community composition, functional attributes, and relative abundance of ecological modules. The results improve our understanding of the impact of anthropogenic contamination on bacterioplankton diversity and biogeochemical cycles and the formulation of strategies for bioremediation of the Taihu Watershed.

To characterize the abundance and relative composition of seawater bacterioplankton communities in Changle city using Illumina MiSeq sequencing and bacterial culture techniques.

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Heterotrophic bacterioplankton communities play an important role in organic matter processing in the oceans worldwide. In order to investigate the significance of distinct phylogenetic bacterial groups it is not only important to assess their quantitative abundance but also their growth dynamics in relation to the entire bacterioplankton. Therefore bacterial abundance, biomass production and the composition of the entire and cell-proliferating bacterioplankton community were assessed in North Sea surface waters between the German Bight and 58°N in early summer by applying catalyzed reporter deposition (CARD-FISH) and bromodeoxyuridine fluorescence in situ hybridization (BrdU-FISH). Bacteroidetes and the Roseobacter group dominated the cell-proliferating fraction with 10–55 and 8–31% of total BrdU-positive cells, respectively. While Bacteroidetes also showed high abundances in the total bacterial fraction, roseobacters constituted only 1–9% of all cells. Despite abundances of up to 55% of total bacterial cells, the SAR11 clade constituted <6% of BrdU-positive cells. Gammaproteobacteria accounted for 2–16% of the total and 2–13% of the cell-proliferating cells. Within the two most active groups, BrdU-positive cells made up 28% of Bacteroidetes as an overall mean and 36% of roseobacters. Estimated mean growth rates of Bacteroidetes and the Roseobacter group were 1.2 and 1.5 day-1, respectively, and much higher than bulk growth rates of the bacterioplankton whereas those of the SAR11 clade and Gammaproteobacteria were 0.04 and 0.21 day-1, respectively, and much lower than bulk growth rates. Only numbers of total and cell-proliferating roseobacters but not those of Bacteroidetes and the other groups were significantly correlated to chlorophyll fluorescence and bacterioplankton biomass production. The Roseobacter group, besides Bacteroidetes, appeared to be a major player in processing phytoplankton derived organic matter despite its low partitioning in the total bacterioplankton community.

Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance.

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Toxic cyanobacterial blooms present a substantial risk to public health due to the production of secondary metabolites, notably microcystins (MCs). Microcystin-LR (MC-LR) is the most prevalent and toxic variant in freshwater. MCs resist conventional water treatment methods, persistently impacting water quality. This study focused on an oligohaline shallow lagoon historically affected by MC-producing cyanobacteria, aiming to identify bacteria capable of degrading MC and investigating the influence of environmental factors on this process. While isolated strains did not exhibit MC degradation, microbial assemblages directly sourced from lagoon water removed MC-LR within seven days at 25 ºC and pH 8.0. The associated bacterial community demonstrated an increased abundance of bacterial taxa assigned to Methylophilales, and also Rhodospirillales and Rhodocyclales to a lesser extent. However, elevated atmospheric temperatures (45 ºC) and acidification (pH 5.0 and 3.0) hindered MC-LR removal, indicating that extreme environmental changes could contribute to prolonged MC persistence in the water column. This study highlights the importance of considering environmental conditions in order to develop strategies to mitigate cyanotoxin contamination in aquatic ecosystems.

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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.

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The composition of bacterial communities in freshwater ecosystems is influenced by numerous factors including environmental conditions and biological interactions. In grassland inland closed lakes, factors affecting lake ecosystems are either exogenous or endogenous, contributing to the formation of distinct habitats in the surface and bottom waters of the bacterial communities. However, the extent to which environmental factors selectively shape the bacterial communities in aquatic systems remains unclear. Therefore, we sampled the surface, middle, and bottom waters at 13 sampling points in each layer. High-throughput sequencing techniques were employed to examine the spatial heterogeneity of the bacterial community structure during summer in Hulun Lake, the largest grassland-type lake in Inner Mongolia, China, to determine the microbial community dynamics and symbiosis patterns under different habitat conditions. Our results revealed a decrease in the diversity and heterogeneity of the bacterioplankton community, influenced by changes in the environment from exogenous inputs to endogenous releases. Furthermore, this alteration in community structure was concomitant with enhanced co-occurrences among microorganisms in the bottom water layers. This finding suggests that endogenous release promotes heightened symbiotic interactions, thereby facilitating the development of more complex modular structures. Symbiotic networks in different layers were differentiated by key species, with the ecological clustering modules of these species demonstrating dissimilar environmental preferences. The microbial communities were highly habitat-specific, mimicking responses to total nitrogen (TN) in the surface layer, pH in the middle layer, and chemical oxygen demand (COD) in the bottom layer. Bacterioplankton functions were assessed using Tax4Fun, indicating exogenous inputs and endogenous release increased the relative abundance of genes with nitrogen-fixing and nitrification potential nitrogen metabolism functions in surface and bottom waters, respectively. With Planctomycetota and Proteobacteria phyla as potential key groups for regulating nitrogen metabolic processes, Proteobacteria may facilitate the depletion of nitrate in surface and bottom waters, while the close contact of surface waters with the atmosphere accelerated Planctomycetota-dominated nitrogen fixation into the lake. Our findings contribute to the understanding of vertical microbial diversity and its network patterns in grassland type lakes, underscoring the potential role of environmental factors (exogenous inputs and endogenous releases) in bacterioplankton community formation.

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Aquaculture environments harbor complex bacterial communities that are critical for the growth and health of culture species. Apex predators are frequently added to aquaculture ponds to improve ecosystem stability. However, limited research has explored the effects of apex predators on the composition and function of bacterioplankton communities, as well as the underlying mechanisms of community assembly. Using 16S ribosomal RNA (rRNA) high-throughput sequencing, we investigated bacterioplankton communities of crustacean aquaculture ponds with and without apex predators (mandarin fish, Siniperca chuatsi) throughout the culture process. In addition to investigating differences in bacterioplankton communities, we also explored variations in environmental adaptation, functional redundancy, and community stability. Significant differences were observed in bacterioplankton composition among different cultural stages; there was an increase in Bacteriobota and fermentation-related bacteria, but a decrease in Firmicutes and pathogens in the middle stages of aquaculture. Apex predators increased the abundance of organic matter degradation bacteria and decreased pathogens. Bacterioplankton communities under apex predator disturbances had a wider environmental breadth, indicating broader environmental adaptation. Moreover, functional prediction and network analyses revealed that communities under apex predator disturbances were less functionally redundant and unstable. Based on the null model, stochastic processes drove community assembly during aquaculture, whereas apex predators elevated the contribution of deterministic processes. Greater changes in nitrate in culture ponds caused by apex predator disturbances were decisive in controlling the balance between stochasticity and determinism in community assembly. Our study provided insight into the mechanisms underlying bacterioplankton community assembly in aquaculture systems in response to apex predator disturbances.

Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO4. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.

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Rivers make vital contributions to the transport of water, sediment and nutrients from terrestrial to marine ecosystems. However, many large rivers worldwide are suffering from dam regulation. Increasing attention has been paid to bacterioplankton communities since they are highly responsive to river alterations and may influence biogeochemical processes. Here, a comprehensive study was conducted in the highly regulated Lancang–Mekong River Basin to address the question of how bacterioplankton communities respond to cascade damming. The results showed that dam constructions increased nutrient concentrations and threatened water quality in cascade reservoirs. Bacterioplankton cell abundance was reduced by damming, and α‐diversity was inhibited in cascade reservoirs. Fortunately, however, river ecosystems were resilient after the remarkable disturbance caused by damming. Moreover, bacterioplankton community composition was significantly altered by cascade dams, including a shift in the dominant phylum from r‐strategists to k‐strategists. Meanwhile, according to GeoChip analysis, the functional composition of bacterioplankton was less affected than taxonomic composition. In addition, geographic and environmental features both followed a distance–decay relationship with community and functional composition, but the local environment condition was the dominant driver in the Lancang River. Therefore, the impoundments of cascade dams had significant impacts on bacterioplankton communities and more attention should be paid to the potential ecological consequences of river regulation.

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Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer, and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production. pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. Our work adds to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.

The impact of salinization on freshwater ecosystems became apparent during the 2022 ecological disaster in the Oder River, located in Poland and Germany, which was caused by salt discharge from mining activities. How bacterial communities respond to salinization caused by industrial salt discharge, or climate change-driven events, depends on the sensitivity of these complex bacterial communities. To investigate the sensitivity of bacterial communities to pulse salinization, we performed an experiment in the salinity range from 0.2 to 6.0. In addition, we sampled similar salinities in the littoral zone of the Baltic Sea where the bacterial communities are permanently exposed to the aforementioned salinities. To simulate a major disturbance, we included an ampicillin/streptomycin treatment in the experiment. Although the addition of antibiotics and increase in salinity had a significant impact on the water bacterial richness and community composition, only antibiotics affected the sediment bacterial community in the experiment. In contrast, sediment bacterial communities from the Baltic Sea littoral zone clustered according to salinity. Hence, sediment bacterial communities are more resistant to pulse changes in salinity than water bacteria but are able to adapt to a permanent change without loss in species richness. Our results indicate that moderate pulse salinization events such as industrial salt discharge or heavy storms will cause changes in the water bacterial communities with unknown consequences for ecosystem functioning. Sediment bacterial communities, however, will probably be unaffected in their ecosystem functions depending on the disturbance strength. Long-term disturbances, such as sea level rise or constant salt discharge, will cause permanent changes in the sediment bacterial community composition.

Limited data exists on the simultaneous impact of bottom-up (nutrients) and top-down (viruses and heterotrophic nanoflagellates) forces in shaping freshwater bacterial communities. In our laboratory microcosms, nutrient additions (organic and inorganic) and viral reduction approach led to the proliferation of high nucleic acid (HNA) bacterial subpopulation without an increase in phage abundance. High viral-mediated bacterial lysis in the presence of nanoflagellates yielded high proportion of low nucleic acid bacterial subpopulation. 16S rRNA gene sequence analysis indicated that members of class Proteobacteria and Bacteroidetes evoked differential responses to nutrients and mortality forces thereby resulting in differences (p < 0.001) in bacterial community composition and diversity, as observed from ANOSIM and UniFrac analysis. Bacterial species richness (Chao) and diversity (Shannon) index was significantly higher (p < 0.001) in the presence of both the top-down factors and viruses alone, whereas lower host diversity was observed under nutrient relaxation of growth limiting substrates due to the explosive growth of opportunistic HNA bacterial subpopulation. Our results are in agreement with the theoretical model of 'Killing the Winner' where the availability of growth limiting substrates can act as a stimulating factor for host community composition while top-down forces can operate in the control of host diversity.

The study aimed to evaluate the safety of copper ion sterilization based on copper ion residues in zebrafish ( Brachydanio rerio ), as well as bacterial community structure and diversity in recirculating aquaculture systems (RASs). The copper ion content was determined using national food safety standard GB 5009.13-2017. Bacterial community structures and alpha and beta diversity indexes were examined using the 16S rRNA gene sequences produced by Illumina HiSeq sequencing. The results revealed no significant copper ion enrichment in B. rerio when the copper ion concentration was 0.15 mg/L. The relative abundances of Erythrobacter , nitrite bacteria, and Flavanobacteria were clearly higher in the treatment group than in the control and differences in bacterial species richness and diversity were obvious. In addition, there was no sharp decrease in the microflora at the outflow of the copper ion generator. In conjunction with the changes in ammonia nitrogen, nitrate, and nitrite concentrations during the experiment, the results indicated that there were no significant effects on the purification efficacy of the biological filter, but the abundances of beneficial bacteria increased significantly. This is of great relevance in order to understand the response of bacterial communities affected by changing environmental conditions, such as copper ion sterilization.

Start-up of biofilters plays crucial roles in the successful operation of recirculating aquaculture system, and the nature is bacterial community succession. We explored the pattern of bacterial temporal succession during the start-up process of biofilters in a commercial cold-freshwater recirculating aquaculture system (RAS). The whole succession process was divided into three distinct phases: incubation, growth and stability. Phylogenetic diversity and evenness of the bacterial community increased during the start-up process, whereas richness reached its peak at the growth phase. Seven biomarkers were identified, namely Cytophagales, Gemmatimonadales, Sphingomonadales, Sphingobacteriales, Rhizobiales, Clostridiales and Nitrospirales. The relative abundances of these functional bacteria increased, while those with a competitive growth advantage declined. The network interactions were dramatically altered from fairly simple to most complex, and then decreased in complexity during start-up. Positive relationships decreased, while competition increased. The shift in predicted function exhibited a trend from simple to diverse, and converged to idiosyncratic configuration.

Legionella pneumophila is one of the most tracked waterborne pathogens and remains an important threat to human health. Despite the use of biocides, L. pneumophila is able to persist in engineered water systems with the help of multispecies biofilms and phagocytic protists. For few years now, high-throughput sequencing methods have enabled a better understanding of microbial communities in freshwater environments. Those unexplored and complex communities compete for nutrients using antagonistic molecules as war weapons. Up to now, few of these molecules were characterized in regards of L. pneumophila sensitivity. In this context, we established, from five freshwater environments, a vast collection of culturable bacteria and investigated their ability to inhibit the growth of L. pneumophila. All bacterial isolates were classified within 4 phyla, namely Proteobacteria (179/273), Bacteroidetes (48/273), Firmicutes (43/273), and Actinobacteria (3/273) according to 16S rRNA coding sequences. Aeromonas, Bacillus, Flavobacterium, and Pseudomonas were the most abundant genera (154/273). Among the 273 isolates, 178 (65.2%) were shown to be active against L. pneumophila including 137 isolates of the four previously cited main genera. Additionally, other less represented genera depicted anti-Legionella activity such as Acinetobacter, Kluyvera, Rahnella, or Sphingobacterium. Furthermore, various inhibition diameters were observed among active isolates, ranging from 0.4 to 9 cm. Such variability suggests the presence of numerous and diverse natural compounds in the microenvironment of L. pneumophila. These molecules include both diffusible secreted compounds and volatile organic compounds, the latter being mainly produced by Pseudomonas strains. Altogether, this work sheds light on unexplored freshwater bacterial communities that could be relevant for the biological control of L. pneumophila in manmade water systems.

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The freshwater microbiome harbours numerous copiotrophic bacteria that rapidly respond to elevated substrate concentrations. We hypothesized that their high centimetre-scale beta diversity in lake water translates into pronounced metabolic variability, and that a large fraction of microbial 'metabolic potential' originates from point sources such as fragile organic aggregates. Three experiments were conducted in pre-alpine Lake Zurich over the course of a harmful cyanobacterial bloom: Spatially explicit 9 ml 'syringe' samples were collected in situ at centimetre distances along with equally sized 'mixed' samples drawn from pre-homogenized lake water and incubated in BIOLOG EcoPlate substrate arrays. Fewer compounds promoted bacterial growth in the syringe than in the mixed samples, in particular during the pre- and late bloom periods. Community analysis of enrichments on three frequently utilized substrates revealed both pronounced heterogeneity and functional redundancy. Bacterial consortia had higher richness in mixed than in syringe samples and differed in composition. Members of the Enterobacter cloacae complex dominated the EcoPlate assemblages during the mid-bloom period irrespective of treatment or substrate. We conclude that small-scale functional dispersal limitation among free-living copiotrophs in lake water reduces local biotransformation potential, and that lacustrine blooms of harmful cyanobacteria can be environmental reservoirs for metabolically versatile potential pathogens.

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The bacteriome profile was studied in freshwater ecosystems within the Yonghwasil pond, situated at the National Institute of Ecology, Seocheon-gun, Chungcheongnam-do, central western Korea. Six samples from water, mud, and soil niches were assessed, specifically from lake water, bottom mud (sediment), and root-soil samples of Bulrush, wild rice, Reed, and Korean Willow. Notably, the phylum Actinobacteria exhibited an upward trend moving from water to mud to soil samples, whereas Chloroflexi showed a contrasting decrease. Across the board, Proteobacteria emerged as the reigning phylum, and subsequent dominance was attributed to Firmicutes and Actinobacteria. The water samples were characterized by an enriched presence of Cyanobacteria and Bacteroidetes, whereas the mud samples distinctly housed a higher concentration of Chloroflexi. Assessing biodiversity through OTU and ACE indices revealed a subdued species richness in the water samples. On the contrary, mud samples stood out with the highest OTU and ACE metrics, signifying a microbially diverse habitat. Bulrush, wild rice, Reed, and Willow samples showed intermediate microbial diversity. The Shannon index further corroborated the pronounced microbial diversity in mud and Bulrush habitats with others. This research elucidates the microbial intricacies across different habitats within Yonghwasil Pond, emphasizing the pivotal role of environmental matrices in shaping bacterial communities.

Bloom-forming phytoplankton dynamics are still unpredictable, even though it is known that several abiotic factors, such as nutrient availability and temperature, are key factors for bloom development. We investigated whether biotic factors, i.e. the bacterioplankton composition (via 16SrDNA metabarcoding), were correlated with phytoplankton dynamics, through a weekly monitoring of a shallow lake known to host recurrent cyanobacterial blooms. We detected concomitant changes in both bacterial and phytoplankton community biomass and diversity. During the bloom event, a significant decrease in phytoplankton diversity, was detected, with a first co-dominance of Ceratium, Microcystis and Aphanizomenon, followed by a co-dominance of the two cyanobacterial genera. In the same time, we observed a decrease of the particle-associated (PA) bacterial richness and the emergence of a specific bacterial consortium that was potentially better adapted to the new nutritional niche. Unexpectedly, changes in PA bacterial communities occurred just before the development the emergence of the phytoplanktonic bloom and the associated modification of the phytoplanktonic community composition, suggesting that changes in environmental conditions leading to the bloom, were first sensed by the bacterial PA community. This last was quite stable throughout the bloom event, even though there were changes in the blooming species, suggesting that the association between cyanobacterial species and bacterial communities may not be as tight as previously described for monospecific blooming communities. Finally, the dynamics of the free-living (FL) bacterial communities displayed a different trajectory from those of the PA and phytoplankton communities. This FL communities can be viewed as a reservoir for bacterial recruitment for the PA fraction. Altogether, these data also highlight s that the spatial organization within these different microenvironments in the water column is a relevant factor in the structuring of these communities.

Submerged aquatic macrophytes and their microbiomes can help mitigate eutrophication, yet how microbial communities and functions differ across specific plant-associated and surrounding niches remains unclear. Here, we profiled bacterial community composition (16S rRNA gene sequencing) and quantified nitrogen and phosphorus cycling genes (narG, nirK, nirS, nosZ, phoD by qPCR) across eight distinct compartments associated with the submerged macrophyte Hydrilla verticillata in a eutrophic freshwater wetland. The niches spanned open water, bulk sediment, rhizosphere, and plant phyllosphere (leaf/stem surfaces) and endosphere (leaf/stem/root interiors). Alpha diversity differed significantly among niches: sediments (non-rhizosphere and rhizosphere) exhibited the highest Operational Taxonomic Unit (OTU) richness and diversity, whereas leaf-associated niches (phyllosphere and endosphere) had the lowest. Beta diversity showed clear separation by niche, indicating strong habitat filtering. Community composition also varied markedly: the water column was dominated by Bacteroidota (~51% of sequences), plant-associated communities were enriched in Pseudomonadota (43-90%), and sediment niches were dominated by Firmicutes (23~48%). Functional gene abundances showed pronounced niche partitioning. Nitrate/nitrite reduction genes (narG, nirK, nirS) were most enriched on leaf phyllosphere, with narG abundance equally high in the water, whereas the N2O reductase gene nosZ peaked in sediment niches. The alkaline phosphatase gene phoD had its highest copy numbers in leaf biofilms, with significantly lower levels in internal plant tissues. Overall, neutral processes explained ~61% of community variation, but deterministic assembly was evident in the well-connected water and leaf surface niches. These findings reveal strong niche differentiation in plant-associated microbiomes and suggest that compartmentalized microbial functional capacity within the H. verticillata holobiont enhances nitrogen removal and phosphorus cycling in eutrophic waters.

Epiphytic bacterial communities play a regulatory role in biogeochemical carbon (C) and nitrogen (N) cycling and host plant growth. Although their biogeography has been well studied in terrestrial ecosystems, the latitudinal diversity patterns of epiphytic bacterial communities and their implications for cosmopolitan macrophyte production in freshwater ecosystems remain unclear. Here, we conducted a field survey to investigate the latitudinal patterns of bacterial communities colonising the leaf and root surfaces of Myriophyllum spicatum and a surface microbe sterilisation experiment using sediments from high and low latitude regions to verify their causal effects on plant biomass. Distinct diversity patterns were observed across plant compartments. Leaf bacterial community richness increased significantly and linearly with latitude, whereas root bacterial community richness exhibited no significant pattern. Leaf and root bacterial community β diversity significantly decreased with latitude. Mean annual precipitation and temperature emerged as the primary factors influencing the leaf and root community compositions, respectively. The total network edges, total network nodes, and node degree of the leaf bacterial community significantly increased with latitude. Moreover, the network stability peaked at mid-latitudes. The field survey revealed a significant unimodal pattern in host plant biomass along the latitudinal gradient. Significant pathways linking environmental nutrient and leaf bacterial N cycling to host biomass were observed. In the sterilisation experiment, epiphytic bacterial communities significantly increased host biomass in sediment from low latitudes, whereas an opposite pattern was observed in sediment from high latitudes. Sediment source and root bacterial N cycling were identified as significant direct drivers of host biomass. These findings demonstrate the biogeographic patterns of multifaceted epiphytic bacterial matrices (taxonomy, function, and network) of a cosmopolitan macrophyte and highlight the key roles of environmental nutrients and epiphytic bacterial communities in shaping primary production in freshwater ecosystems.

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Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater–freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche.

Bacterial community composition of different sized aggregates within the Microcystis cyanobacterial phycosphere were determined during summer and fall in Lake Taihu, a eutrophic lake in eastern China. Bloom samples taken in August and September represent healthy bloom biomass, whereas samples from October represent decomposing bloom biomass. To improve our understanding of the complex interior structure in the phycosphere, bloom samples were separated into large (>100 µm), medium (10–100 µm) and small (0.2–10 µm) size aggregates. Species richness and library coverage indicated that pyrosequencing recovered a large bacterial diversity. The community of each size aggregate was highly organized, indicating highly specific conditions within the Microcystis phycosphere. While the communities of medium and small-size aggregates clustered together in August and September samples, large- and medium-size aggregate communities in the October sample were grouped together and distinct from small-size aggregate community. Pronounced changes in the absolute and relative percentages of the dominant genus from the two most important phyla Proteobacteria and Bacteroidetes were observed among the various size aggregates. Bacterial species on large and small-size aggregates likely have the ability to degrade high and low molecular weight compounds, respectively. Thus, there exists a spatial differentiation of bacterial taxa within the phycosphere, possibly operating in sequence and synergy to catalyze the turnover of complex organic matters.

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The application of Biolog EcoPlate™ for community-level physiological profiling of soils is well documented; however, the functional diversity of aquatic bacterial communities has been hardly studied. The objective of this study was to investigate the applicability of the Biolog EcoPlate™ technique and evaluate comparatively the applied endpoints, for the characterisation of the effects of metal oxide nanoparticles (MONPs) on freshwater microbial communities. Microcosm experiments were run to assess the effect of nano ZnO and nano TiO2 in freshwater at 0.8–100 mg/L concentration range. The average well colour development, substrate average well colour development, substrate richness, Shannon index and evenness, Simpson index, McIntosh index and Gini coefficient were determined to quantify the metabolic capabilities and functional diversity. Comprehensive analysis of the experimental data demonstrated that short-term exposure to TiO2 and ZnO NPs affected the metabolic activity at different extent and through different mechanisms of action. TiO2 NPs displayed lower impact on the metabolic profile showing up to 30% inhibition. However, the inhibitory effect of ZnO NPs reached 99% with clearly concentration-dependent responses. This study demonstrated that the McIntosh and Gini coefficients were well applicable and sensitive diversity indices. The parallel use of general metabolic capabilities and functional diversity indices may improve the output information of the ecological studies on microbial communities.

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Summary To reduce the reliance on fishmeal (FM), other protein sources have been evaluated on cultured animals. In a 60‐days feeding trial, marrons (Cherax cainii) were fed a FM diet and five test diets containing 100% of plant‐based protein sources such as soybean, lupin and valorised animal‐based proteins such as poultry‐by‐product, black soldier fly and tuna hydrolysate. At the end of the trial, DNA samples from marron gut and rearing water were investigated through DNA‐based 16S rRNA gene sequencing. Plant‐based diets increased abundance for Aeromonas, Flavobacterium and Vogesella, whereas animal and insect proteins influenced diverse bacterial groups in the gut linked to various metabolic activities. Insect meal in the water favoured the growth of Firmicutes and lactic acid bacteria, beneficial for the marron health. Aeromonas richness in the gut and reared water signified the ubiquitous nature of the genus in the environment. The higher bacterial diversity in the gut and water with PBP and BSF was further supported by qPCR quantification of the bacterial single‐copy gene, rpoB. The overall results suggested that PBP and BSF can exhibit positive and influential effects on the gut and water microbial communities, hence can be used as sustainable ingredients for the crayfish aquaculture.

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This study investigated bacterial diversities in surface water and sediment of the East Lake located in Wuhan, China. Bacterial community of lake water was mainly composed of Proteobacteria (31.1%), Actinobacteria (25.0%), Bacteroidetes (18.6%), Cyanobacteria (18.9%), Planctomycetes (2.4%) and Verrucomicrobia (1.4%), while more abundant and richer bacterial community was found in the sediments, e.g. 46.1% for Proteobacteria, 10.1% for Bacteroidetes, 8.7% for Chloroflexi, 8.4% for Acidobacteria, 5.0% for Cyanobacteria, 3.6% for Firmicutes, 3.1% for Planctomycetes, 2.8% for Actinobacteria and 2.3% for Nitrospirae. The decreased bacterial community richness and abundance was found in poor-quality water. Moreover, Bacterial Eutrophic Index (BEI) was firstly put forward to quantitatively describe the water quality of a freshwater ecosystem, which was defined as the ratio of abundance of Cyanobacteria and Actinobacteria in water. It was demonstrated BEI was well correlated to Carlson's Trophic State Index (TSI) (Spearman's ρ = 0.848, p < 0.01). The average TSI and BEI were determined to be 64 and 0.81, suggesting that East Lake could be classified as a medium eutrophic level.

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The microbial communities in freshwater have raised concerns about the ecosystem and human health. Many ecological environmental problems have been found in urban river because of the unreasonable use and long-term wastewater discharge. In this study, we explored the bacterial community composition, abundance of 14 antibiotics and 21 antibiotic resistance genes (ARGs), and water environment features in seven water samples and seven sediment samples from Ba River in Xi’an, China. Results showed Proteobacteria and Bacteroidetes were the dominant phyla in all samples, and sediment samples had a higher bacterial diversity and richness than it in water. Bacterial communities of site 5 and 6 were clustered in discrepant patterns compared to those at remaining sites from other samples. It might be influenced by nutrients, heavy metals and antibiotics. Antibiotics concentrations ranged from 1.26 to 1.61 × 103 ng L-1 in water samples and 1.55 to 4.05 × 102 μg kg-1 in sediment samples. Sulfamerazine (SM1) and erythromycin (ERY) were the chief antibiotics in water samples, while the level of oxytetracycline (OTC) and cefazolin (CFZ) were higher in sediment samples. Canonical correspondence analysis showed that trimethoprim (TMP) was significantly related to Acinetobacter in W6, and that SM1 and OTC had positive correlation with Arcobacter in W5. The tetC, blaTEM, ermF and sul1 had higher pollution abundance ranging from 10-4 to 100 copies/16S rRNA gene copies in all samples. Significant correlations were observed between ARGs and matching antibiotics, suggesting that antibiotics can pose the selective pressure on ARGs in this river. In summary, these finding might provide some new data to the limited information available on the bacterial community characteristics, abundance of antibiotics and ARGs in urban river of China.

The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR–Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR–Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine. Analysis of 43,191 genomes obtained from publicly available marine bacterial and archaeal metagenome data provides insights into marine bacterial evolution, CRISPR–Cas defence and antibiotic resistance genes, and demonstrates the potential of marine metagenomes for biotechnological applications.

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Three replicate seawater samples were collected on three different days, filtered immediately and preserved with one of two guanidinium thiocyanate-based preservatives (DNAzol™ or RNA Lysis Buffer™ plus β-mercaptoethanol (RLA+)) and were kept frozen while being shipped to a lab. In parallel, a carboy of seawater was collected on each of the three days and maintained at ambient temperature while being shipped to a lab. Upon receipt the samples were filtered and treated in the same manner as for immediate preservation. Significantly more DNA was obtained from samples immediately preserved with DNAzol than the corresponding shipped samples for 2 of the 3 days. More DNA was extracted from DNAzol preserved samples but more RNA was obtained from RLA+ preserved samples. A protocol was designed to extract both DNA and RNA from split samples preserved with RLA+ and cDNA was synthesized from the RNA. Three high-throughput 16S rRNA gene libraries were constructed, one from DNA preserved with DNAzol, one from DNA preserved with RLA+ and one from cDNA (RLA+ preserved). Greater alpha diversity was found for libraries constructed from immediately preserved vs. shipped samples for both preservation types, with immediate preservation with DNAzol obtaining the highest level of diversity. Libraries constructed from immediately preserved (RLA+) DNA had greater alpha diversity than libraries constructed from shipped preserved (RLA+) DNA or cDNA. Unifrac measures of beta diversity showed clearer separation of sample types and a greater % variance explained for weighted than for unweighted principal coordinate analysis (PCoA) plots, indicating sample types varied more in their relative abundance of taxa than the presence/absence of particular taxa. We recommend immediate preservation of seawater samples, with DNAzol as the preferred preservative if quantification via qPCR will be performed or the highest alpha diversity is desired but preservation with RLA+ if RNA will be extracted.

Recent big data analyses have illuminated marine microbial diversity from a global perspective, focusing on planktonic microorganisms. Here, we analyze 2.5 terabases of newly sequenced datasets and the Tara Oceans metagenomes to study the diversity of biofilm-forming marine microorganisms. We identify more than 7,300 biofilm-forming ‘species’ that are undetected in seawater analyses, increasing the known microbial diversity in the oceans by more than 20%, and provide evidence for differentiation across oceanic niches. Generation of a gene distribution profile reveals a functional core across the biofilms, comprised of genes from a variety of microbial phyla that may play roles in stress responses and microbe-microbe interactions. Analysis of 479 genomes reconstructed from the biofilm metagenomes reveals novel biosynthetic gene clusters and CRISPR-Cas systems. Our data highlight the previously underestimated ocean microbial diversity, and allow mining novel microbial lineages and gene resources.Previous surveys of global ocean microbial diversity have focused on planktonic microbes. Here, Zhang et al. use metagenomics to study biofilm-forming marine microbes, increasing the known microbial diversity in the oceans by more than 20% and revealing new biosynthetic gene clusters and CRISPR-Cas systems.

The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) approaches capture the broadest perspective on community composition, culture-dependent (CD) methods can capture low abundance taxa that are missed using CI approaches. The aim of this study was to assess microbial diversity in tropical marine sediments collected from five shallow water sites in Belize using both CD and CI approaches. CD methods captured approximately 3% of the >800 genera detected across the five sites. Additionally, 39 genera were only detected using CD approaches revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in the delineation of sediment communities. This study provides important baseline data describing shallow water sediment microbial communities and evidence that standard cultivation techniques may be more effective than previously recognized. Originality-Significance Statement Marine sediments host some of the most diverse microbial communities on the planet. While these communities are critical for global nutrient cycling, the oceanic food web, and the maintenance of ecosystem dynamics, they remain poorly studied. Studies that have assessed sediment communities typically use culture-independent approaches, which have known biases and can miss ecologically important taxa. Here we describe microbial diversity in marine sediments using both culture-dependent and culture-independent approaches. Our culturing approach, sequencing communities as opposed to individual colonies, revealed an additional 39 genera that were not detected with culture-independent methods. Additionally, we cultured numerous, as-yet undescribed species, suggesting that traditional culturing practices can be more efficient than commonly thought. Moreover, our results indicate rare taxa play an important role in distinguishing microbial communities at different sites, thus highlighting the importance of deep sequencing and incorporating culture-dependent approaches for diversity assessments.

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ABSTRACT Marine microbes play essential roles in global energy and nutrient cycles. A primary method of determining their diversity and distribution is through sequencing of 16S ribosomal RNA genes from environmental samples. However, the perceived community composition may vary significantly based on differences in methodology, including choice of 16S variable region(s). This study investigated the influence of 16S variable region selection (V4-V5 or V6-V8) on perceived community composition and diversity for bacteria, Archaea and chloroplasts by tag-Illumina sequencing. We used 24 samples from the photic zone of the Scotian Shelf, northwest Atlantic, collected during a spring phytoplankton bloom. Taxonomic assignment and community composition varied greatly depending on the choice of variable regions while observed patterns of beta diversity were reproducible between variable regions. V4-V5 was considered the preferred variable region for future studies based on its superior recognition of Archaea, which has received little attention in bloom dynamics. The V6-V8 region captured more of the bacterial diversity, including the abundant SAR11 clades and, to a lesser extent, that of chloroplasts. However, the magnitude of difference between variable regions for bacteria and chloroplast was less than for Archaea.

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The cyanobacteria Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; heterotrophs grow on organic carbon supplied by the photolithoautotrophs. For examining the selective pressures shaping autotroph/heterotroph interactions, we have made use of unialgal enrichment cultures of Prochlorococcus and Synechococcus maintained for hundreds to thousands of generations in the lab. We examine the diversity of heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans. Heterotroph community composition differed between clades and ecotypes of the autotrophic ‘hosts’ but there was significant overlap in heterotroph community composition across these cultures. Collectively, the cultures were comprised of many shared taxa, even at the genus level. Yet, observed differences in community composition were associated with time since isolation, location, depth, and methods of isolation. The majority of heterotrophs in the cultures are rare in the global ocean, but enrichment conditions favor the opportunistic outgrowth of these rare bacteria. However, we found a few examples, such as bacteria in the family Rhodobacteraceae, of heterotrophs that were ubiquitous and abundant in cultures and in the global oceans. We found their abundance in the wild is also positively correlated with that of picocyanobacteria. Particular conditions surrounding isolation have a persistent effect on long-term culture composition, likely from bottlenecking and selection that happen during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans.

The ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments. The current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts. This finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation. DRyDF7ykR-XALqAtu34uZt Video Abstract Video Abstract

Offshore coastal marine ranching ecosystems are one of the most productive ecosystems. The results showed that the composition and structure of the microbial communities varied considerably with the season. Co-occurrence network analysis demonstrated that the microbial network was more complex in summer and positively correlated links (cooperative or symbiotic) were dominated in autumn and winter. Null model indicated that the ecological processes of the bacterial communities were mainly governed by deterministic processes (mainly homogeneous selection) in summer. For microeukaryotic communities, assembly processes were more regulated by stochastic processes in all seasons. For rare taxa, assembly processes were regulated by stochastic processes and were not affected by seasonality. Changes in water temperature due to seasonal variations were the main, but not the only, environmental factor driving changes in microbial communities. This study will improve the understanding of offshore coastal ecosystems through the perspective of microbial ecology.

Anaerobic biotechnology using sulfate-reducing bacteria (SRB) is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG), an acidic (pH ~3) by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate) and sulfate sources (i.e., sodium sulfate or PG) as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia). Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures) was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB.

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Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts.

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Objectives The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Spatio-Temporal Patterns of the Microbial Communities Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Macrofauna, Microbes and the Benthic N-Cycle Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment.

Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication—human-derived nutrient pollution—on the marine microbial biosphere. Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants. Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.

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Industrial waste, agricultural runoff and untreated sewage contaminate the Nile, leaving a toxic legacy in its sediments. Organohalides-polluted sediment in particular poses serious public health risks and detrimental effects on aquatic life. Sediment microbiomes may harbor bacterial strains that could be utilized in bioremediation of such toxic pollutants. Two microbiomes from polluted River Nile sediments were analyzed by using 16S rRNA gene amplicon sequencing. In addition, PICRUSt analysis based on 16S rRNA data was used to explore the organohalide respiring bacteria (OHRB) genera and their corresponding organohalide respiration (OHR) activity. Microcosm studies were performed to validate the potential for dechlorination activity of River Nile sediment. Dechlorination of the parent chloroethenes into daughter end product were detected by gas chromatography coupled with flame ionization detection analysis. Analysis of 16S rRNA gene amplicon sequences using the EZ-biocloud server identified Proteobacteria as the dominant phylum in both microbiomes, with Bacteroidetes and Chloroflexi prevalent in RNS1 sediment and Chlorobi in RNS2 sediment. EZ-biocloud and PCR analyses detected several potential OHRB genera, including Dehalococcoides, Dehalogenimonas, Desulfomonile, Desulfovibrio, and Geobacter, suggesting potential OHR activity. Further evidence for potential OHR activity was provided by PICRUSt functional prediction analysis, which suggested the presence of reductive dehalogenases as functional biomarkers associated with OHR in the sediment samples. Specifically, PICRUSt analysis predicted the presence of potential genes of tetrachloroethene reductive dehalogenase and 3-chloro-4-hydroxyphenylacetate reductive dehalogenase, previously linked to OHR. Microcosm studies confirmed the dechlorination potential of tetrachloroethene to dichloroethene. This study demonstrates that River Nile sediment in industrialized area harbors distinct microbiomes enclosing various OHRB genera, providing substantial evidence for potential reductive dechlorination activity. It also provides potential functional biomarkers for OHR activity.

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j . Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe, playing critical roles in many of Earth's biogeochemical cycles both in both aquatic and terrestrial systems. Despite their well‐known significance, their taxonomy remains problematic and is the subject of much research. Taxonomic issues of Cyanobacteria have consequently led to inaccurate curation within known reference databases, ultimately leading to problematic taxonomic assignment during diversity studies. Recent advances in sequencing technologies have increased our ability to characterize and understand microbial communities, leading to the generation of thousands of sequences that require taxonomic assignment. We herein propose CyanoSeq (https://zenodo.org/record/7569105), a database of cyanobacterial 16S rRNA gene sequences with curated taxonomy. The taxonomy of CyanoSeq is based on the current state of cyanobacterial taxonomy, with ranks from the domain to genus level. Files are provided for use with common naive Bayes taxonomic classifiers, such as those included in DADA2 or the QIIME2 platform. Additionally, FASTA files are provided for creation of de novo phylogenetic trees with (near) full‐length 16S rRNA gene sequences to determine the phylogenetic relationship of cyanobacterial strains and/or ASV/OTUs. The database currently consists of 5410 cyanobacterial 16S rRNA gene sequences along with 123 Chloroplast, Bacterial, and Vampirovibrionia (formally Melainabacteria) sequences.

Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.

Understanding the complex microbiota of agricultural irrigation water is vital to multiple sectors of sustainable agriculture and public health. To date, microbiome characterization methods have provided comprehensive profiles of aquatic microbiotas, but have not described which taxa are likely metabolically-active. Here, we combined 5‑bromo‑2'-deoxyuridine (BrdU) labeling with 16S rRNA and shotgun sequencing to identify metabolically-active bacteria in reclaimed and agricultural pond water samples (n = 28) recovered from the Mid-Atlantic United States between March 2017 and January 2018. BrdU-treated samples were significantly less diverse (alpha diversity) compared to non-BrdU-treated samples. The most abundant taxa in the metabolically-active fraction of water samples (BrdU-treated samples) were unclassified Actinobacteria, Flavobacterium spp., Pseudomonas spp. and Aeromonas spp. Interestingly, we also observed that antimicrobial resistance and virulence gene profiles seemed to be more diverse and more abundant in non-BrdU-treated water samples compared to BrdU-treated samples. These findings raise the possibility that these genes may be associated more with relic (inactive) DNA present in the tested water types rather than viable, metabolically-active microorganisms. Our study demonstrates that the coupled use of BrdU labeling and sequencing can enhance understanding of the metabolically-active fraction of bacterial communities in alternative irrigation water sources. Agricultural pond and reclaimed waters are vital to the future of sustainable agriculture, and thus, the full understanding of the pathogenic potential of these waters is important to guide mitigation strategies that ensure appropriate water quality for intended purposes.

Unused feed containing protein in the water affects the fish survivability under the recirculating aquaculture systems. Microbial communities play important roles in nutrient cycling in the aquatic ecosystems, however, bacteria that may help in protein degradation remains underexplored. This study aimed to identify the proteolytic bacteria obtained from aquaculture system based on 16S rRNA genes. Bacteria were isolated using non-selective medium and then assayed for proteolytic activity on skim milk agar. Characterizations were conducted for selected proteolytic bacteria before subjected to Sanger dideoxy DNA sequencing. The results of BLAST show that five representative isolates are closely related to Flavobacterium nitratireducens, Micrococcus aloeverae, Acinetobacter baumannii, and Exiguobacteríum indicum at the level similarity of 99%. The nucleotides of collected proteolytic bacterial strains have been deposited in NCBI Genbank. Finding of those proteolytic bacteria in the recirculating aquaculture system may lead the further ecological studies about their roles in the ecosystem.

The microbial characteristics of water bodies located in the outflow of hot springs may affect the water quality parameters of the associated river ecosystem. Using 16S rRNA amplicon sequencing, we investigated the bacterial diversity and functional profiles of the Huang Gang (HG) Creek, located in the trace metal-rich, acid-sulfate thermal springs zone of the Tatun Volcano Group (TVG). Biofilms and water samples were collected from the upstream, midstream, and geothermal valleys and downstream of the creek. The results showed that the biofilm and water samples had distinct bacterial diversity and abundance profiles. Acidophilic sulfur-oxidizing bacteria were found to be more abundant in water samples, whereas aquatic photosynthetic bacterial communities were dominant in biofilms. The water samples were contaminated with Legionella and Chlamydiae, which could contaminate the nearby river and cause clinical infections in humans. The upstream samples were highly unique and displayed higher diversity than the other sites. Moderate thermo-acidophiles were dominant in the upstream and midstream regions, whereas the geothermal valley and downstream samples were abundant in thermo-acidophiles. In addition, functional profiling revealed higher expression of sulfur, arsenic, and iron-related functions in water and lead-related functions in the biofilms of the creek. As described in previous studies, the hydrochemical properties of the HG Creek were influenced by the TVG hot springs. Our findings indicated that the hydrochemical properties of the HG Creek were highly correlated with the bacterial diversity and functional potential of running water as compared to biofilms.

The interaction between the fish gill and surrounding bacteria-rich water provides an intriguing model for examining the interaction between the fish, free-floating bacteria, and the bacterial microbiome on the gill surface. Samples that are inherently low in bacteria, or that have components that inhibit the ability to produce libraries that identify the components of microbial communities, present significant challenges. ABSTRACT The major aquatic interface between host and environment in teleost finfish species is the gill. The diversity of this infraclass, high complexity of the organ, and its direct exposure to the surrounding environment make it an ideal candidate for furthering our understanding of the intertwined relationships between host and microbiome. Capturing the structure and diversity of bacterial communities from this low-biomass, inhibitor-rich tissue can, however, prove challenging. Lessons learned in doing so are directly applicable to similar sample types in other areas of microbiology. Through the development of a quantitative PCR assay for both host material and 16S rRNA genes, we tested and developed a robust method for low-biomass sample collection which minimized host DNA contamination. Quantification of 16S rRNA facilitated not only the screening of samples prior to costly library construction and sequencing but also the production of equicopy libraries based on 16S rRNA gene copies. A significant increase in diversity of bacteria captured was achieved, providing greater information on the true structure of the microbial community. Such findings offer important information for determining functional processes. Results were confirmed across fresh, brackish, and marine environs with four different fish species, with results showing broad homology between samples, demonstrating the robustness of the approach. Evidence presented is widely applicable to samples similar in composition, such as sputum or mucus, or those that are challenging due to the inherent inclusion of inhibitors. IMPORTANCE The interaction between the fish gill and surrounding bacteria-rich water provides an intriguing model for examining the interaction between the fish, free-floating bacteria, and the bacterial microbiome on the gill surface. Samples that are inherently low in bacteria, or that have components that inhibit the ability to produce libraries that identify the components of microbial communities, present significant challenges. Gill samples present both of these types of challenges. We developed methods for quantifying both the bacterial and host DNA material and established a sampling method which both reduced inhibitor content and maximized bacterial diversity. By quantifying and normalizing bacteria prior to library construction, we showed significant improvements with regards to the fidelity of the final data. Our results support wide-ranging applications for analyzing samples of similar composition, such as mucus and sputum, in other microbiological spheres.

Abstract Premise Within a broader study on leaf fossilization in freshwater environments, a long‐term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, water lily leaves are employed as a study model to investigate the relationship between bacterial microbiomes, biodegradation, and fossilization. We compare four DNA extraction kits to reduce biases in interpretation and to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis. Methods We extracted surface‐associated DNA from Nymphaea leaves in early stages of decay at two water depth levels using four commercially available kits to identify the most suitable protocol for bacterial extraction, applying a mock microbial community standard to enable a reliable comparison of the kits. Results Kit 4, the FastDNA Spin Kit for Soil, resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition. Discussion The success of Kit 4 may be attributed to its use of bead beating with a homogenizer, which was more efficient in the lysis of Gram‐positive bacteria than the manual vortexing protocols used by the other kits. Our results show that microbial composition on leaves during early decay remains comparable and may change only in later stages of decomposition.

Microcystins (MCs) are the most toxic and abundant cyanotoxins found in natural waters during harmful cyanobacterial blooms. These toxins pose a significant threat to plant, animal, and human health due to their toxicity. Degradation of MCs by MC-degrading bacteria is a promising method for controlling these toxins, demonstrating safety, high efficiency, and cost-effectiveness. In this study, we isolated potential MC-degrading bacteria (strains TA13, TA14, and TA19) from Lake Kasumigaura in Japan and found that they possess a high capacity for MC degradation. Based on 16S rRNA gene sequencing, all three isolated strains were identified as belonging to the Klebsiella species. These bacteria effectively degraded MC-RR, MC-YR, and MC-LR under various temperature and pH conditions within 10 h, with the highest degrading activity and degradation rate observed at 40 °C. Furthermore, the isolated strains efficiently degraded MCs not only under neutral pH conditions, but also in alkaline environments. Additionally, we detected the MC-degrading gene (mlrA) in all three isolated strains, marking the first report of the mlrA gene in Klebsiella species. The copy number of the mlrA gene in the strains increased after exposure to MCs. These findings indicate that strains TA13, TA14, and TA19 significantly contribute of MC bioremediation in Lake Kasumigaura during cyanobacterial blooms.

Restoration of degraded aquatic habitats is critical to preserve and maintain ecosystem processes and economic viability. Effective restoration requires contaminant sources identification. Microbial communities are increasingly used to characterize fecal contamination sources. The objective was to determine whether nearshore and adjacent beach bacterial contamination originated from the Grand Calumet River, a highly urbanized aquatic ecosystem, and to determine if there were correlations between pathogens/feces associated bacteria in any of the samples to counts of the pathogen indicator species Escherichia coli. Water samples were collected from the river, river mouth, nearshore, and offshore sites along southern Lake Michigan. Comparisons among communities were made using beta diversity distances (weighted and unweighted Unifrac, and Bray Curtis) and Principal Coordinate Analysis of 16S rRNA gene Illumina sequence data that indicated river bacterial communities differed significantly from the river mouth, nearshore lake, and offshore lake samples. These differences were further supported using Source Tracker software that indicated nearshore lake communities differed significantly from river and offshore samples. Among locations, there was separation by sampling date that was associated with environmental factors (e.g., water and air temperature, water turbidity). Although about half the genera (48.1%) were common to all sampling sites, linear discriminant analysis effect size indicated there were several taxa that differed significantly among sites; there were significant positive correlations of feces-associated genera with E. coli most probable numbers. Results collectively highlight that understanding microbial communities, rather than relying solely on select fecal indicators with uncertain origin, are more useful for developing strategies to restore degraded aquatic habitats.

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Appropriate use and specific primers are important in assessing the diversity and abundance of microbial groups of interest. Bdellovibrio and like organisms (BALOs), that refer to obligate Gram-negative bacterial predators of other Gram-negative bacteria, evolved in terms of taxonomy and classification over the past two decades. Hence, some former primers have become inadequate while others are yet to be designed, for both PCR (especially with the advent of NGS) and qPCR approaches. Thus, to study BALOs' abundance and diversity in a variety of aquatic ecosystems, we designed in silico specific primer sets for each BALO genera and tested them in vitro on a variety of cultures and environmental samples. Also, we performed Sanger and Nano Miseq sequencing to reveal the exact degree of specificity of the most promising primers set. Here we report our success in designing specific primers for some BALOs genera, i.e. Bdellovibrio PCR primers, Bacteriovorax qPCR, Peredibacter PCR set of primers.

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The immigration history of communities can profoundly affect community composition. For instance, early‐arriving species can have a lasting effect on community structure by reducing the invasion success of late‐arriving ones through priority effects. This can be particularly important when early‐arriving communities coalesce with another community during dispersal (mixing) events. However, the outcome of such community coalescence is unknown as we lack knowledge on how different factors influence the persistence of early‐arriving communities and the invasion success of late‐arriving taxa. Therefore, we implemented a full‐factorial experiment with aquatic bacteria where temperature and dispersal rate of a better adapted community were manipulated to test their joint effects on the resistance of early‐arriving communities to invasion, both at community and population level. Our 16S rRNA gene sequencing‐based results showed that invasion success of better adapted late‐arriving bacteria equaled or even exceeded what we expected based on the dispersal ratios of the recipient and invading communities suggesting limited priority effects on the community level. Patterns detected at the population level, however, showed that resistance of aquatic bacteria to invasion might be strengthened by warming as higher temperatures (a) increased the sum of relative abundances of persistent bacteria in the recipient communities, and (b) restricted the total relative abundance of successfully established late‐arriving bacteria. Warming‐enhanced resistance, however, was not always found and its strengths differed between recipient communities and dispersal rates. Nevertheless, our findings highlight the potential role of warming in mitigating the effects of invasion at the population level.

Glacier-fed aquatic ecosystems provide habitats for diverse and active bacterial communities. However, the environmental vulnerabilities of co-existing water and sediment bacterial communities in these ecosystems remain unclear. Here, 16S rRNA gene sequencing was used to investigate co-existing bacterial communities in paired water and sediment samples from multiple rivers and lakes that are mainly fed by glaciers from the southeast Tibetan Plateau. Overall, the bacterial communities were dissimilar between the water and sediment, which indicated that there were limited interactions between them. Bacterial diversity was greatest in the sediments, where it was mainly driven by changes in nitrogen compounds and pH. Meanwhile water bacterial diversity was more susceptible to evapotranspiration, elevation, and mean annual temperature. Water samples contained higher proportions of Proteobacteria and Bacteroidetes, while sediment harbored higher proportions of Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Cyanobacteria, and Gemmatimonadetes. Bacterial community composition was significantly correlated with mean annual precipitation in water, but with nitrogen compounds in sediment. The co-occurrence network of water included more keystone species (e.g., CL500-29 marine group, Nocardioides spp., and Bacillus spp.) than the sediment network. These keystone species showed stronger phylogenetic signals than the species in the modular structures. Further, ecological clusters within the networks suggested that there were contrasting environmental vulnerabilities and preferences between water and sediment communities. These findings demonstrated that co-existing water and sediment bacterial communities and ecological clusters were shaped by contrasting environmental factors. This work provides a basis for understanding the importance of bacterial communities in maintaining glacier-fed aquatic ecosystems. Further, the results provide new perspectives for water resource management and water conservation in changing environments.

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Summary Cable bacteria are sulfide‐oxidising, filamentous bacteria that reduce toxic sulfide levels, suppress methane emissions and drive nutrient and carbon cycling in sediments. Recently, cable bacteria have been found associated with roots of aquatic plants and rice (Oryza sativa). However, the extent to which cable bacteria are associated with aquatic plants in nature remains unexplored. Using newly generated and public 16S rRNA gene sequence datasets combined with fluorescence in situ hybridisation, we investigated the distribution of cable bacteria around the roots of aquatic plants, encompassing seagrass (including seagrass seedlings), rice, freshwater and saltmarsh plants. Diverse cable bacteria were found associated with roots of 16 out of 28 plant species and at 36 out of 55 investigated sites, across four continents. Plant‐associated cable bacteria were confirmed across a variety of ecosystems, including marine coastal environments, estuaries, freshwater streams, isolated pristine lakes and intensive agricultural systems. This pattern indicates that this plant–microbe relationship is globally widespread and neither obligate nor species specific. The occurrence of cable bacteria in plant rhizospheres may be of general importance to vegetation vitality, primary productivity, coastal restoration practices and greenhouse gas balance of rice fields and wetlands.

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BACKGROUND Immature anophelines inhabit aquatic environments with diverse physicochemical properties and microorganisms. In insectary settings, ammonia accumulation in larval rearing trays can lead to high larval mortality. Bacterial communities in these trays may influence ammonia levels through nitrification and denitrification. While symbiotic bacteria are known to be crucial for nutrition, digestion, reproduction, and immune responses in anophelines, the microbial communities specifically associated with Anopheles coluzzii larvae have not been characterised. METHODS AND RESULTS Building on a study examining ammonia-capturing zeolite and water changes for rearing Anopheles coluzzii, this research characterised the bacterial communities using 16S rRNA gene sequencing to identify species linked to larval survival and phenotypic quality. Functional filters were applied to identify bacteria related to ammonia nitrification and their impact on larval development. qPCR was used to validate the sequencing data for the ten most significant bacteria. Water changes significantly reduced bacterial diversity and abundance, improving adult mosquito development and quality. In contrast, untreated trays showed a higher abundance of potentially harmful bacteria, adversely affecting development. Applying zeolite increased nitrifying bacteria presence, benefiting mosquito growth while lowering toxic bacteria levels-trends confirmed by qPCR. CONCLUSIONS This study offers insights into the bacterial communities in mosquito larval-rearing water, highlighting species that could enhance ammonia nitrification and overall rearing success.

The long co-existence of bacteria and protozoa has led to the development of bacterial protozoa resistance strategies, which are suggested to serve as drivers for the evolution of pathogenic bacteria. However, the ecological mechanisms underpinning selection for protozoa-resistance in aquatic bacteria are poorly known. To assess the role of nutrient availability and predation-pressure on selection for protozoa-resisting bacteria (PRB), an enrichment-dilution experiment was designed using laboratory microcosms containing natural lake water. PRB was monitored by screening 16S rRNA amplicon sequence data for reads assigned to bacteria that previously has been shown to resist degradation by amoebae. To estimate the effects of the microbial food web dynamics (microscopy of; heterotrophic bacteria, phytoplankton, protozoa and rotifers) and physicochemical variables on the PRB abundance in the study system, a joint species distribution modelling approach was used. The predation-pressure (ratio between predator and bacterial biomass) had a positive effect on the abundance of the PRB genus Mycobacterium, while perturbation (enrichment and dilution) favored the PRB genus Pseudomonas that dominated the bacterial community in the disturbed systems. Our results show that PRB with different ecological strategies can be expected in water of high and intermediate nutrient levels and after major disturbances of an aquatic system.

Duckweeds are small, fast-growing aquatic plants with high starch and protein content, making them promising candidates for next-generation plant biomass resources. Despite their importance, little is known about their interactions with microorganisms, particularly plant growth-promoting bacteria (PGPB), which play key roles in enhancing plant productivity. In this study, we report the plant growth-promoting effects of strain LA-C6, a member of the phylum Armatimonadota, isolated from duckweed fronds. Based on 16S rRNA gene analysis, this strain represents a novel genus-level lineage, and is referred to as Fimbriimonadaceae bacterium strain LA-C6. In axenic co-culture experiments, strain LA-C6 promoted duckweed growth, increasing the frond proliferation of four duckweed species (Lemna minor, Lemna aequinoctialis, Spirodela polyrhiza, and Landoltia punctata) by 1.8- to 4.0-fold compared with uninoculated controls. Importantly, three other phylogenetically distinct Armatimonadota species also exhibited significant plant growth-promoting effects on L. minor, increasing frond number by up to 2.3-fold and dry weight by up to 2.4-fold. This finding highlights the broader potential of diverse Armatimonadota members as PGP bacteria. A survey of the IMNGS database showed that strain LA-C6 and other Armatimonadota species are widely distributed across diverse plant-associated environments. Biochemical assays and gene prediction analyses revealed that strain LA-C6 produces indole-3-acetic acid (IAA) as a representative PGP trait, whereas no additional PGP-associated traits were detected. These results suggest that diverse bacterial lineages within the phylum Armatimonadota exert growth-promoting effects on aquatic plants, potentially through yet-to-be-identified mechanisms.

Microbial communities consist of bacteria, archaea, fungi, and viruses, and are critical to the health, resiliency, and ecological balance in both marine and freshwater systems. They help maintain environmental equilibrium. There is increasing curiosity about the differences, at a gross level, in the structure and function of freshwater and marine microbiomes, although comparative studies remain limited. This study analyzes the compositional and functional diversity of the microbial consortia in different aquatic systems within the spectrum of their contributions to enhanced immunity, nutrient cycling, and possible disease antagonism... An integrated framework of Metagenomic-Host Interaction Profiling (MHIP) is introduced, where community structure is determined by 16S rRNA gene sequencing and shotgun metagenomic sequencing, and metagenomic analysis is followed by machine learning correlation mapping to enable the understanding of community dynamics and their impact on specific host physiological attributes. Sampling was performed to capture spatial variability and the impact of anthropogenic activities, ranging from the freshwater environments (lakes, rivers) to the marine environments (estuaries, coastal zones). Preliminary analysis shows marine microbiomes to be taxonomically more complex with functional redundancy than freshwater systems, where more specialized symbiotic relationships are encountered and driven by environmental factors. The MHIP framework can be described as an exceptional diagnostic tool in species health evaluation based on microbial signatures and can aid targeted aquaculture and biodiversity maintenance.

Harmful Algal Blooms (HABs) are outbreaks of aquatic toxic microalgae emerging as a global problem driven by nutrient enrichment, global climate change and invasive species. We uniquely describe a HAB of unprecedented duration, extent and magnitude during 2023 in Lough Neagh; the UK and Ireland's largest freshwater lake, using an unparalleled combination of satellite imagery, nutrient analysis, 16S rRNA gene sequencing and cyanotoxin profiling. The causative agent Microcystis aeruginosa accounted for over a third of DNA in water samples though common bacterioplankton species also bloomed. Water phosphate levels were hypertrophic and drove local algal biomass. The HAB pervaded the entire ecosystem with algal mats accumulating around jetties, marinas and lock gates. Over 80 % of bacterial DNA isolated from algal mat samples consisted of species associated with wildfowl or livestock faeces and human-effluent wastewater including 13 potential pathogens that can cause serious human illness including: E. coli, Salmonella, Enterobacter and Clostridium among others. Ten microcystins, nodularin and two anabaenopeptin toxins were confirmed as present (with a further microcystin and four anabaenopeptins suspected), with MC-RR and -LR in high concentrations at some locations (1,137-18,493 μg/L) with MC-LR exceeding World Health Organisation (WHO) recreational exposure guidelines in all algal mats sampled. This is the first detection of anabaenopeptins in any waterbody on the island of Ireland. Notwithstanding the ecological impacts, this HAB represented an environmental and public health risk, curtailing recreational activities in-and-around the lake and damaging local businesses. Reducing agricultural runoff and discharge from human-effluent wastewater treatment to manage nutrient loading, and the public health risk, should be the top priority of stakeholders, especially government. Key recommendations include Nature-based Solutions that avoid conflict with the productivity and profitability of the farming sector enhancing sustainability. We hope this stimulates real-world action to resolve the problems besetting this internationally important ecosystem.

ABSTRACT Phytoplankton-bacteria interactions underpin primary production and nutrient cycling in both oligotrophic and eutrophic aquatic environments, profoundly influencing marine biogeochemical cycles. Despite their importance, how these interactions vary under simultaneous environmental stressors such as warming and iron (Fe) limitation remains largely unexplored, especially across differing ecotypes. Here, we compared the responses of oligotrophic (strain YX04-1) and eutrophic (strain XM-24) ecotype Synechococcus-heterotrophic bacteria interactions to concurrent warming and Fe limitation, using the 16S rRNA gene amplicon sequencing alongside metagenomic and metatranscriptomic analyses. Our results revealed that community composition and gene expression in the oceanic Synechococcus sp. YX04-1 co-culture were more sensitive to warming, whereas the coastal Synechococcus sp. XM-24 co-culture responded more strongly to Fe limitation. The resilience of oligotrophic YX04-1 and its bacterial partners to iron deficiency may result from potential mutualistic triangular dynamics, involving complex carbohydrate decomposition, low-molecular-weight organic substrate transfer, and feedback of public goods. In contrast, the eutrophic XM-24 co-culture experienced intensified competition and opportunistic exploitation of organic resources by dominant mixotrophic bacteria under concurrent warming and Fe limitation conditions. These findings reveal contrasting survival strategies of oligotrophic and eutrophic Synechococcus-bacteria co-cultures, highlighting the tighter and mutually beneficial interactions in the oligotrophic co-culture that may assist oligotrophic species in adapting to changing ocean conditions. IMPORTANCE Phytoplankton-bacteria interactions serve as a crucial biological network linking primary production and nutrient cycling in marine ecosystems. In the context of global change, the upper ocean inevitably faces increased warming and iron limitation, which will shift primary producer composition toward Synechococcus and impact its nutrient exchanges with co-existing bacteria. The changes in this fundamental and widespread microbial interaction may affect the stability of nutrient cycling, yet its universal response under warming and iron limitation remains poorly understood. Our research reveals contrasting responses of oligotrophic and eutrophic Synechococcus-bacteria interactions under the same stress, driven by stronger metabolic dependencies in the oligotrophic co-culture but greater individual competitiveness in the eutrophic one. These findings emphasize the importance of cooperative heterotrophic bacteria for host survival and imply a non-uniform co-evolution of in situ microbial interactions across different marine ecosystems in the future. Phytoplankton-bacteria interactions serve as a crucial biological network linking primary production and nutrient cycling in marine ecosystems. In the context of global change, the upper ocean inevitably faces increased warming and iron limitation, which will shift primary producer composition toward Synechococcus and impact its nutrient exchanges with co-existing bacteria. The changes in this fundamental and widespread microbial interaction may affect the stability of nutrient cycling, yet its universal response under warming and iron limitation remains poorly understood. Our research reveals contrasting responses of oligotrophic and eutrophic Synechococcus-bacteria interactions under the same stress, driven by stronger metabolic dependencies in the oligotrophic co-culture but greater individual competitiveness in the eutrophic one. These findings emphasize the importance of cooperative heterotrophic bacteria for host survival and imply a non-uniform co-evolution of in situ microbial interactions across different marine ecosystems in the future.

ABSTRACT Beaver ponds create unique aquatic ecosystems. The activities of beavers promote the growth of biodiversity and enhance water purification but can also lead to the accumulation of harmful pollutants. Water retention in beaver ponds leads to the growth of bacteria and other microorganisms that play a key role in biogeochemical cycling. Stagnation of water can lead to anaerobic conditions and the formation of toxic substances that can limit benthic diversity. Beavers play an important role in shaping these environments, and the study of bacteria in beaver ponds helps to better understand their impact on aquatic ecosystems. A 16S rRNA sequencing revealed the presence of 365 bacterial species in water and sediments, identified in 174 genera and 83 families, 62 of which are present in water and sediments. The main indicator family for the bacteria identified in water samples was the family Xantonomodaceae, while for the sediments, it was the family Planococcaceae. The occurrence of bacterial families was similar in both substrates, but sediments showed greater variability compared to water. The statistical differences in the distribution of families between water and sediments were confirmed by a paired sample T test. IMPORTANCE This study helps us to understand how beavers shape their environment and influence water quality. By building dams, beavers create wetlands that change the flow of water and influence which bacteria thrive there. Some of these bacteria contribute to the natural purification of water, while others can pose a threat to biodiversity. Knowing how the activities of beavers affect microbial life is important to protect ecosystems and ensure water safety. The results can help scientists, conservationists, and policy makers make better decisions about beaver conservation and water management. By understanding the role of bacteria in these wetlands, we can predict both the benefits—such as improved natural filtration and potential risks—such as the spread of harmful bacteria. This research also provides insights into how nature itself filters and purifies water, which could lead to sustainable water management strategies in the future. This study helps us to understand how beavers shape their environment and influence water quality. By building dams, beavers create wetlands that change the flow of water and influence which bacteria thrive there. Some of these bacteria contribute to the natural purification of water, while others can pose a threat to biodiversity. Knowing how the activities of beavers affect microbial life is important to protect ecosystems and ensure water safety. The results can help scientists, conservationists, and policy makers make better decisions about beaver conservation and water management. By understanding the role of bacteria in these wetlands, we can predict both the benefits—such as improved natural filtration and potential risks—such as the spread of harmful bacteria. This research also provides insights into how nature itself filters and purifies water, which could lead to sustainable water management strategies in the future.

Globally, P. vannamei is the vital species in aquaculture production. Beneficial bacterial exploration of gut, sediment and water were investigated in P. vannamei culture using Illumina Miseq sequencing of 16S RNA V3-V4 hypervariable regions. Predominant phyla identified were Proteobacteria, Tenericutes, Bacteroidetes in gut; Proteobacteria, Bacteroidetes, Planctomycetes in sediment and Cyanobacteria, Proteobacteria and Planctomycetes in water. In total, 46 phyla, 509 families and 902 genera; 70 phyla, 735 families and 1255 genera; 55 phyla, 580 families and 996 genera were observed in gut, sediment and water, respectively. Diversity of microbial communities in respect of observed Operational Taxonomic Units, diversity indices (Shannon and Simpson), richness index (Chao1) were significantly high P(<0.05) in 60 DoC in gut and 30 DoC in sediment. Beta diversity indicated separate clusters for bacterial communities in gut, sediment and water samples and formation of distinct community profiles. Core microbiome in P. vannamei rearing ponds over a time consisted of 9, 21 and 20 OTUs in gut, rearing water and sediment, respectively. This study helps to intervene with suitable beneficial microbes to establish aquaculture system thereby contributes to enhance the productivity, improve water quality and pond bottom condition and control the pathogenic agents at each stage of the culture.

Private wells are used daily worldwide as convenient household water sources. In Japan, where water supply coverage is high, well water is occasionally used for non-potable purposes, such as irrigation and watering. Currently, the main microbiological test of well water is designed to detect Escherichia coli, which is an indicator of fecal contamination, using culture methods. Water use such as watering generates bioaerosols, which may cause airborne infection. However, many causative bacteria of aerosol-derived infections, such as Legionella spp., are difficult to detect using culture methods. Thus, more comprehensive modern assessment is desirable for securing the microbiological quality of well water. Here, the bacterial community structure of five private wells located in different environments was examined using the rapid and portable MinION sequencer, which enabled us to identify bacteria to the species level based on full-length 16S ribosomal RNA (rRNA) gene sequences. The results revealed the differences in the bacterial community structures of water samples from the five wells and detected Legionella pneumophila and Aeromonas hydrophila as new candidate microbial indicators. The comprehensive analysis method used in this study successfully detected bacteria causing opportunistic infections, which are difficult to detect by conventional methods. This approach is expected to be routinely applied in the future as a highly accurate method for assessing the microbiological quality of private well water.

In recent years, 16S rRNA gene amplicon sequencing has been widely adopted for analyzing the microbial communities in drinking water (DW). However, no comprehensive attempts have been made to illuminate the inherent method biases specifically relating to DW communities. In this study, we investigated the impact of DNA extraction and primer choice on the observed microbial community, and furthermore estimated the detection limit of the 16S rRNA gene amplicon sequencing in these experimental settings. Of the two DNA extraction kits investigated, the PowerWater DNA Isolation Kit resulted in higher yield, better reproducibility and more OTUs identified compared to the FastDNA SPIN Kit for Soil, which is also commonly used within DW microbiome research. The use of three separate primer-sets targeting the V1-3, V3-4, and V4 region of the 16S rRNA gene revealed large differences in OTU abundances, with some of the primers unable to detect entire phyla. Estimations of the detection limit were based on bacteria-free water samples (1 L) spiked with Escherichia coli cells in different concentrations [101–106 cells/ml]. E. coli could be detected in all samples, however, samples with ∼101 cells/ml had several contaminating OTUs constituting approximately 8% of the read abundances. Based on our findings, we recommend using the PowerWater DNA Isolation Kit for DNA extraction in combination with PCR amplification of the V3-4 or V4 region for DW samples if a broad overview of the microbial community is to be obtained.

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Amplicon sequencing using next‐generation technology (bTEFAP®) has been utilized in describing the diversity of Dead Sea microbiota. The investigated area is a well‐known salt lake in the western part of Jordan found in the lowest geographical location in the world (more than 420 m below sea level) and characterized by extreme salinity (approximately, 34%) in addition to other extreme conditions (low pH, unique ionic composition different from sea water). DNA was extracted from Dead Sea water. A total of 314,310 small subunit RNA (SSU rRNA) sequences were parsed, and 288,452 sequences were then clustered. For alpha diversity analysis, sample was rarefied to 3,000 sequences. The Shannon–Wiener index curve plot reached a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. Archaea was found to be dominating the sequences (52%), whereas Bacteria constitute 45% of the sequences. Altogether, prokaryotic sequences (which constitute 97% of all sequences) were found to predominate. The findings expand on previous studies by using high‐throughput amplicon sequencing to describe the microbial community in an environment which in recent years has been shown to hide some interesting diversity.

No abstract available

Bacteria are primarily responsible for biological water treatment processes in constructed wetland systems. Gravel in constructed wetlands serves as an essential substrate onto which complex bacterial biofilms may successfully grow and evolve. To fully understand the bacterial community in these systems it is crucial to properly isolate biofilms and process DNA from such substrates. This study looked at how best to isolate bacterial biofilms from gravel substrates in terms of bacterial richness. It considered factors including the duration of agitation during extraction, extraction temperature, and enzyme usage. Further, the 16S taxonomy data subsequently produced from Illumina MiSeq reads (using the SILVA 132 ribosomal RNA (rRNA) database on the DADA2 pipeline) were compared with the 16S data produced from Oxford Nanopore Technologies (ONT) MinION reads (using the NCBI 16S database on the EPI2ME pipeline). Finally, performance was tested by comparing the taxonomy data generated from the Illumina MiSeq and ONT MinION reads using the same (SILVA 132) database. We found no significant differences in the effective number of species observed when using different bacterial biofilm detachment techniques. However, enzyme treatment enhanced the total concentration of DNA. In terms of wetland community profiles, relative abundance differences within each sample type were clearer at the genus level. For genus-level taxonomic classification, MinION sequencing with the EPI2ME pipeline (NCBI database) produced bacterial abundance information that was poorly correlated with that from the Illumina MiSeq and DADA2 pipelines (SILVA132 database). When using the same database for each sequencing technology (SILVA132), the correlation between relative abundances at genus-level improved from negligible to moderate. This study provides detailed information of value to researchers working on constructed wetlands regarding efficient biofilm detachment techniques for DNA isolation and 16 s metabarcoding platforms for sequencing and data analysis.

The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum , Vibrio tapetis , and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.

DNA-based monitoring of microbial communities that are responsible for the performance of anaerobic digestion of sewage wastes has the potential to improve resource recoveries for wastewater treatment facilities. By treating sludge with propidium monoazide (PMA) prior to amplicon sequencing, this study explored how the presence of DNA from dead microbial biomass carried over with feed sludge may mislead process-relevant biomarkers, and whether primer choice impacts such assessments. Four common primers were selected for amplicon preparation, also to determine if universal primers have sufficient taxonomic or functional coverage for monitoring ecological performance; or whether two domain-specific primers for Bacteria and Archaea are necessary. Anaerobic sludges of three municipal continuously stirred-tank reactors in Victoria, Australia, were sampled at one time-point. A total of 240 amplicon libraries were sequenced on a Miseq using two universal and two domain-specific primer pairs. Untargeted metabolomics was chosen to complement biological interpretation of amplicon gene-based functional predictions. Diversity, taxonomy, phylogeny and functional potentials were systematically assessed using PICRUSt2, which can predict community wide pathway abundance. The two chosen universal primers provided similar diversity profiles of abundant Bacteria and Archaea, compared to the domain-specific primers. About 16 % of all detected prokaryotic genera covering 30 % of total abundances and 6 % of PICRUSt2-estimated pathway abundances were affected by PMA. This showed that dead biomass in the anaerobic digesters impacted DNA-based assessments, with implications for predicting active processes, such as methanogenesis, denitrification or the identification of organisms associated with biological foams. Hence, instead of running two sequencing runs with two different domain-specific primers, we propose conducting PMA-seq with universal primer pairs for routine performance monitoring. However, dead sludge biomass may have some predictive value. In principal component analysis the compositional variation of 239 sludge metabolites resembled that of 'dead-plus-alive' biomass, suggesting that dead organisms contributed to the potentially process-relevant sludge metabolome.

The Chinese mitten crab (CMC, Eriocheir sinensi) culture in ponds is a unique aquaculture system. Probiotics are commonly used in the maintenance of the health of pond-cultured CMCs. However, the effects of probiotics on the bacterial community of CMC-culturing water remain unclear. This study utilized 16S rRNA gene amplicon sequencing to assess changes in the bacterial community composition, diversity, assembly, and co-occurrence patterns in CMC-culturing water following probiotic application. The results indicate that the α-diversity of the bacterial community in CMC-culturing water varied with time following probiotic application. The addition of probiotics to the water resulted in an increase in the occurrence of new OTUs. The bacterial community assembly in the CMC-culturing water was shaped by a balance between deterministic and stochastic processes, while commercial probiotics enhanced the proportion of heterogeneous selection. In addition, including OTU2953 (Burkholderiaceae) and OTU3005 (Lactobacillaceae), from the commercial probiotics served as keystone species in the bacterial network of CMC-culturing water. Overall, probiotic application had a significant impact on the bacterial ecology of CMC-culturing water.

Wastewater has become one of the most important and least expensive water for the agriculture sector, as well as an alternative to the overexploitation of water resources. However, inappropriate treatment before its reuse can result in a negative impact on the environment, such as the presence of pathogens. This poses an increased risk for environmental safety, which can subsequently lead to an increased risk for human health. Among all the emerging wastewater pathogens, bacteria of the genus Helicobacter are some of the most disturbing ones, since they are directly related to gastric illness and hepatobiliary and gastric cancer. Therefore, the aim of this study was to determine the presence of potentially pathogenic Helicobacter spp. in treated wastewater intended for irrigation. We used a next generation sequencing approach, based on Illumina sequencing in combination with culture and other molecular techniques (qPCR, FISH and DVC-FISH), to analyze 16 wastewater samples, with and without an enrichment step. By culture, one of the direct samples was positive for H. pylori. FISH and DVC-FISH techniques allowed for detecting viable Helicobacter spp., including H. pylori, in seven out of eight samples of wastewater from the tertiary effluents, while qPCR analysis yielded only three positive results. When wastewater microbiome was analyzed, Helicobacter genus was detected in 7 samples. The different molecular techniques used in the present study provided evidence, for the first time, of the presence of species belonging to the genus Helicobacter such as H. pylori, H. hepaticus, H. pullorum and H. suis in wastewater samples, even after disinfection treatment.

For microbiological management of water quality, it is important to identify bacteria and to understand the community structure. To analyze the community structure during water purification and distribution, we selected a distribution system in which water from other water treatment facilities was not mixed with the target water. Changes in the bacterial community structure during treatment and distribution processes in a slow filtration water treatment facility were analyzed using 16S rRNA gene amplicon sequencing with a portable sequencer MinION. The microbial diversity was reduced by chlorination. The genus level diversity increased during distribution and this diversity was maintained through to the terminal tap water. Yersinia and Aeromonas were dominant in the intake water, and Legionella was dominant in the slow sand filtered water. Chlorination greatly reduced the relative abundance of Yersinia, Aeromonas, and Legionella, and these bacteria were not detected in the terminal tap water. Sphingomonas, Starkeya and Methylobacterium became dominant in the water after chlorination. These bacteria could be used as important indicator bacteria to provide useful information for microbiological control in drinking water distribution systems.

Mixed-culture biotechnologies are widely used to capture nutrients from wastewater. Purple non-sulfur bacteria (PNSB), a guild of anoxygenic photomixotrophic organisms, rise interest for their ability to directly assimilate nutrients in the biomass. One challenge targets the aggregation and accumulation of PNSB biomass to separate it from the treated water. Our aim was to enrich and produce a concentrated, fast-settling PNSB biomass with high nutrient removal capacity in a 1.5-L, stirred-tank, anaerobic sequencing-batch photobioreactor (SBR). PNSB were rapidly enriched after inoculation with activated sludge at 0.1 gVSS L–1 in a first batch of 24 h under continuous irradiance of infrared (IR) light (>700 nm) at 375 W m–2, with Rhodobacter reaching 54% of amplicon sequencing read counts. SBR operations with decreasing hydraulic retention times (48 to 16 h, i.e., 1–3 cycles d–1) and increasing volumetric organic loading rates (0.2–1.3 kg COD d–1 m–3) stimulated biomass aggregation, settling, and accumulation in the system, reaching as high as 3.8 g VSS L–1. The sludge retention time (SRT) increased freely from 2.5 to 11 days. Acetate, ammonium, and orthophosphate were removed up to 96% at a rate of 1.1 kg COD d–1 m–3, 77% at 113 g N d–1 m–3, and 73% at 15 g P d–1 m–3, respectively, with COD:N:P assimilation ratio of 100:6.7:0.9 m/m/m. SBR regime shifts sequentially selected for Rhodobacter (90%) under shorter SRT and non-limiting concentration of acetate during reaction phases, for Rhodopseudomonas (70%) under longer SRT and acetate limitation during reaction, and Blastochloris (10%) under higher biomass concentrations, underlying competition for substrate and photons in the PNSB guild. With SBR operations we produced a fast-settling biomass, highly (>90%) enriched in PNSB. A high nutrient removal was achieved by biomass assimilation, reaching the European nutrient discharge limits. We opened further insights on the microbial ecology of PNSB-based processes for water resource recovery. Graphical Abstract Sequencing batch reactor enrichment and aggregation of purple non-sulfur bacteria.

Free-living amoebae (FLA) are ubiquitous protozoa commonly found in water. FLA are well-established hosts for amoeba-resistant bacteria, most of which are pathogenic, and offer them shelter from adverse environmental conditions or water treatments. Since there is very little knowledge about the complete bacterial microbiome of FLA, in this work the bacterial microbiome of FLA isolated from wastewater both after secondary and tertiary treatments was studied by amplicon-based sequencing. FLA were detected in 87.5% and 50.0% of wastewater samples taken after secondary and tertiary disinfection treatments, respectively. The most abundant bacterial phyla were Proteobacteria, Planctomycetes, Bacteroidetes and Firmicutes, which represented 83.77% of the total bacterial FLA microbiome. The most abundant class of bacteria was Gammaproteobacteria, which contains an important number of relevant pathogenic bacteria. The bacteria of public health concern Aeromonas, Arcobacter, Campylobacter, Helicobacter, Klebsiella, Legionella, Mycobacterium, Pseudomonas and Salmonella were detected as part of the FLA microbiome. Although different microbial communities were identified in each sample, there is no correlation between the microbiome of FLA and the extent of wastewater treatment. To our knowledge, this is the first work in which the bacterial microbiome of FLA isolated from wastewater is studied. Obtained results indicate that FLA are hosts of potentially pathogenic bacteria in treated wastewater used for irrigation, which may pose a public health threat.

No abstract available

No abstract available

Fine-scale analysis of ocean microbes provides insights into the dynamics and functions of the ocean microbiome community. Here, using amplicon and metagenome sequencing methods, we found that diatoms in the northern South China Sea displayed a potential water-depth pattern in species richness and community composition, which may be related to their biological characteristics. The potential effects of the differences in geographic sites mainly occurred in the diatom and bacterial communities. ABSTRACT Ocean microbiomes provide insightful details about the condition of water and the global impact of marine ecosystems. A fine-scale analysis of ocean microbes may shed light on the dynamics and function of the ocean microbiome community. In this study, we evaluated the changes in the community and function of marine bacteria, protists, and diatoms corresponding to different ocean depths using next-generation sequencing methods. We found that diatoms displayed a potential water-depth pattern in species richness (alpha diversity) and community composition (beta diversity). However, for bacteria and protists, there was no significant relationship between water depth and species richness. This may be related to the biological characteristics of diatoms. The photosynthesis of diatoms and their distribution may be associated with the fluctuating light regime in the underwater climate. Moreover, salinity displayed negative effects on the abundance of some diatom and bacterial groups, which indicates that salinity may be one of the factors restricting ocean microorganism diversity. In addition, compared to the global ocean microbiome composition, function, and antibiotic resistance genes, a water depth pattern due to the fine-scale region was not observed in this study. IMPORTANCE Fine-scale analysis of ocean microbes provides insights into the dynamics and functions of the ocean microbiome community. Here, using amplicon and metagenome sequencing methods, we found that diatoms in the northern South China Sea displayed a potential water-depth pattern in species richness and community composition, which may be related to their biological characteristics. The potential effects of the differences in geographic sites mainly occurred in the diatom and bacterial communities. Moreover, given the correlation between the environmental factors and relative abundance of antibiotic resistance genes (ARGs), the study of ocean ARG distribution patterns should integrate the potential effects of environmental factors.

The complex and highly diverse microbial environment of drinking water, consisting mainly of bacteria at different metabolic states, is still underexplored. The aim of this work was to characterize the bacterial communities in tap water and bottled mineral water, the two predominant sources of drinking water in modern societies. A total of 11 tap water samples from a range of locations and distribution networks and 10 brands of bottled natural mineral water were analysed using two approaches: a) heterotrophic plate counts by matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) for the culturable heterotrophic communities, and b) Illumina amplicon sequencing for total bacteria including non-culturable bacteria. Culturable heterotrophic bacteria were isolated in WPCA (ISO) agar at 22 ± 2 °C for 72 h and 2046 isolates were identified using MALDI-TOF MS. The Bruker Daltonics Library and a previously customized library (Drinking Water Library) were used as reference databases. For the total bacteria fraction, DNA was extracted from 6 L of water and submitted to Illumina 16S rRNA sequencing of the v4 region. Significant differences were observed between mineral and tap water, with a general dominance of Alphaproteobacteria (mainly the genus Blastomonas) in tap water and Gammaproteobacteria in mineral water with Acidovorax being the dominant genus in 3 out of 7 mineral water brands. The bacterial communities in the different brands of mineral water were highly diverse and characteristic of each one. Moreover, the season in which the water was bottled also affected the species distribution, with some of them identified in only one season. Among the culturable bacteria, the most abundant phylum was Proteobacteria (around 85% of the isolates), followed by Actinobacteria, Firmicutes and Bacteroidetes. Proteobacteria was also the most abundant phylum detected with Illumina sequencing (>99% of the reads). The two methods gave distinct results at the different taxonomic levels and could therefore have a complimentary application in the study of microbiota in mineral water environments. MALDI-TOF MS is a promising method for the rapid identification of heterotrophic bacteria in routine water analysis in the bottling industry. SIGNIFICANCE AND IMPACT OF THE STUDY: The complementarity of MALDI-TOF MS and NGS in the assessment of bacterial community diversity has been demonstrated in water intended for human consumption. The two methods are suitable for routine use in the water industry for water quality management.

Urban marine estuaries are often impacted by microbiological contamination that impairs use and affects human health acutely, while limited is known about microbiological water quality in urban marine estuaries in the absence of reported sewage spills. This study used a tropical urban marine estuary, the Ala Wai Canal in Honolulu, Hawaii, as the model system to compare fecal indicator bacteria (FIB) concentrations, bacterial pathogen profiles, and microbial community structures. The FIB Escherichia coli exhibited higher geometric mean 132 CFU/100mL (n=28) than those of enterococci (18 CFU/100mL) and Clostridium perfringens (21 CFU/100mL). Amongst the four pathogens targeted by cultivation methods (Salmonella, Campylobacter, Listeria monocytogenes and Vibrio parahaemolyticus), only was V. parahaemolyticus detected and was detected at high frequency. Microbial community analysis through 16S rRNA gene amplicon sequencing also indicated the high prevalence of Vibrio in the water. The pathogen detection patterns and microbial community structure showed no significant correlation with FIB concentration profiles. Together, the results highlight the limitation of using traditional FIB in assessing water microbiological quality in the tropical urban marine estuary environment, indicating the need for more comprehensive microbial risk assessment approaches such as direct detection of pathogens.

The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.

Extensive research has provided a wealth of data on prokaryotes in caves and their role in biogeochemical cycles. Ice caves in carbonate rocks, however, remain enigmatic environments with limited knowledge of their microbial taxonomic composition. In this study, bacterial and archaeal communities of the Obstans Ice Cave (Carnic Alps, Southern Austria) were analyzed by next-generation amplicon sequencing and by cultivation of bacterial strains at 10 °C and studying their metabolism. The most abundant bacterial taxa were uncultured Burkholderiaceae and Brevundimonas spp. in the drip water, Flavobacterium, Alkanindiges and Polaromonas spp. in the ice, Pseudonocardia, Blastocatella spp., uncultured Pyrinomonadaceae and Sphingomonadaceae in carbonate precipitates, and uncultured Gemmatimonadaceae and Longimicrobiaceae in clastic cave sediments. These taxa are psychrotolerant/psychrophilic and chemoorganotrophic bacteria. On a medium with Mg2+/Ca2+ = 1 at 21 °C and 10 °C, 65% and 35% of the cultivated strains precipitated carbonates, respectively. The first ~ 200 µm-size crystals appeared 2 and 6 weeks after the start of the cultivation experiments at 21 °C and 10 °C, respectively. The crystal structure of these microbially induced carbonate precipitates and their Mg-content are strongly influenced by the Mg2+/Ca2+ ratio of the culture medium. These results suggest that the high diversity of prokaryotic communities detected in cryogenic subsurface environments actively contributes to carbonate precipitation, despite living at the physical limit of the presence of liquid water.

Aim To determine major sources of microbially produced geosmin in the commercially important aquaculture fish species tilapia. Methods and Results Abundance and composition of geosmin-producing bacteria in water and fish biosphere (intestine, digesta, and fins) of Nile tilapia (Oreachromis niloticus) raised in net cages in Brazilian freshwater farms were examined. By combining qPCR of the geosmin synthase geoA gene and 16S rRNA gene amplicon sequencing to identify potential geosmin-producing organisms, we observed that the proportion and composition of geosmin producers appeared to be rather similar in the water, digesta, intestinal mucous, and on skin, making up about 0.1–0.2% of the total bacterial densities. A high proportion of Cyanobacteria and other putative geosmin producers affiliated to the Actinomycetales were identified in the intestinal mucous layer. The main uptake site for geosmin in fish is traditionally assumed to be through the gill surface, but the present results suggest that uptake by the intestinal tract may represent a major source of geosmin uptake in fish. Conclusion The high abundance of geosmin-producing bacteria in the intestinal mucous layer and digesta may indicate that the digestive system in fish is an important, but hitherto overlooked, source of geosmin and likely other off-flavors in fish. Significance and Impact of Study Tainting of fish by microbially produced off-flavors spoils fish quality and lowers consumer preferences for aquaculture-produced freshwater fish. Our results highlight the potential for the application of probiotic microorganisms for management of the intestinal microflora to improve the fish quality. HIGHLIGHTS- Off-flavor producing bacteria are widely abundant in aquaculture.- Off-flavor producers found on skin surface of fish.- Off-flavor producing bacteria accumulate in the digestive system.- Off-flavor producers might release significant amounts of off-flavor during lysis in the gut.- Off-flavor uptake through the digestive system might be quantitatively significant.

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Soil Aquifer Treatment (SAT) is a robust technology to increase groundwater recharge and to improve reclaimed water quality. SAT reduces dissolved organic carbon, contaminants of emerging concern, nutrients, and colloidal matter, including pathogen indicators, but little is known about its ability to reduce loads of antibiotic resistance genes (ARGs) from reclaimed waters. Here we test six pilot SAT systems to eliminate various biological hazards from the secondary effluents of a wastewater treatment plant (WWTP), equipped with reactive barriers (RBs) including different sorptive materials. Using flow cytometry, qPCR and 16S rRNA gene amplicon sequencing methods, we determined that all six SAT systems reduced total loads of bacteria by 80 to 95 % and of clinically relevant ARGs by 85 to 99.9 %. These efficiencies are similar to those reported for UV/oxidation or membrane-based tertiary treatments, which require much more energy and resources. The presence and composition of reactive barriers, the season of sampling (June 2020, October 2020, and September 2021), or the flow regime (continuous versus pulsating) did not affect ARG removal efficiency, although they did alter the microbial community composition. This suggests that an adequate design of the SAT reactive barriers may significantly increase their performance. Under a mechanistic point of view, we observed an ecological succession of bacterial groups, linked to the changing physical-chemical conditions along the SAT, and likely correlated to the removal of ARGs. We concluded that SAT is as cost-efficient technology able to dramatically reduce ARG loads and other biological hazards from WWTP secondary effluents.

Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ~3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.

Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic compounds carried by drip water on the microbial community, two limestone caves were selected in Brazil. Drip-water-saturated and unsaturated sediment, and dripping water itself, were collected from each cave and bacterial 16S rDNA amplicon sequencing and denaturing gradient gel electrophoresis (DGGE) of naphthalene dioxygenase (ndo) genes were performed. Energy-dispersive X-ray spectroscopy (EDX) and atomic absorption spectroscopy (AAS) were performed to evaluate inorganic nutrients, and GC was performed to estimate aromatic compounds in the samples. The high frequency of Sphingomonadaceae in drip water samples indicates the presence of aromatic hydrocarbon-degrading bacteria. This finding was consistent with the detection of naphthalene and acenaphthene and the presence of ndo genes in drip-water-related samples. The aromatic compounds, aromatic hydrocarbon-degrading bacteria and 16S rDNA sequencing indicate that aromatic compounds may be one of the sources of energy and carbon to the system and the drip-water-associated bacterial community contains several potentially aromatic hydrocarbon-degrading bacteria. To the best of our knowledge, this is the first work to present compelling evidence for the presence of aromatic hydrocarbon-degrading bacteria in cave drip water.

Amid growing concerns over water pollution, the secondary effluent from wastewater treatment plants poses significant threats to aquatic ecosystems with limited self-purification capacity. Secondary effluent-constructed wetlands (SECWs) offer a sustainable solution for advanced nitrogen removal from this low-ammonia effluent, yet the functional role of comammox bacteria remains largely unexplored in such habitats. This study investigated the abundance, activity, kinetics, and ecological adaptations of comammox in typical SECWs. Quantitative PCR and amplicon sequencing revealed that comammox Nitrospira ubiquitously presented across all samples, even numerically dominated over ammonia-oxidizing bacteria/archaea (AOB/AOA). Consistent results from double-inhibition assays and DNA-stable isotope probing microcosm experiments indicated that comammox actively participated in nitrification, contributing 2.03-3.89 times those of canonical nitrifiers. Substrate kinetic and metagenomic analyses identified the Nitrospira nitrosa cluster as the sole active comammox population in SECWs, which exhibited relatively lower ammonia affinity (Km(app) = 0.055 ± 0.007 mg N/L) than other comammox species and distinct genomic adaptations to SECW-specific stressors, potentially explaining its dominance. Compared to AOB, comammox combines high substrate affinity with environmental resilience, aligning with K-strategist traits that enable it to outperform r-strategist AOB in SECWs. Overall, it is within this niche differentiation among comammox species and nitrifiers that the N. nitrosa cluster numerically and functionally dominated the nitrification process in SECWs, positioning comammox Nitrospira as pivotal biocatalysts for advanced nitrogen removal in engineered ecosystems.

Environmental conditions influence species composition, including the microbial communities that associate with benthic organisms such as corals. In this study we identified and compared bacteria that associate with three common deep-water corals Lophelia pertusa, Madrepora oculata and Paragorgia arborea from a reef habitat on the mid-Norwegian shelf. The 16S rRNA gene amplicon sequencing data obtained revealed that greater than 50% of sequences were represented by only five OTUs. Three were host-specific and unclassified below class level, belonging to Alphaproteobacteria with affiliation to members of the Rhizobiales order (L. pertusa), Flavobacteria affiliated with members of the Elisabethkingia genus (M. oculata) and Mollicutes sequences affiliated with the Mycoplasma genus (P. arborea). In addition gammaproteobacterial sequences within the genera Sulfitobacter and Oleispira were found across all three deep-water coral taxa. Although highly abundant in the coral microbiomes, these sequences accounted for less than 0.1% of the surrounding bacterioplankton, supporting specific relationships. We combined this information with previous studies, undertaking a meta-data analysis of 165 widespread samples across coral hosts and habitats. Patterns in bacterial diversity indicated enrichment of distinct uncultured species in coral microbiomes that differed among deep (>200 m), mesophotic (30-200 m) and shallow (<30 m) water reefs.

Amplicon sequencing has revolutionized our ability to study DNA collected from environmental samples by providing a rapid and sensitive technique for microbial community analysis that eliminates the challenges associated with lab cultivation and taxonomic identification through microscopy. In water resources management, it can be especially useful to evaluate ecosystem shifts in response to natural and anthropogenic landscape disturbances to signal potential water quality concerns, such as the detection of toxic cyanobacteria or pathogenic bacteria. Amplicon sequencing data consist of discrete counts of sequence reads, the sum of which is the library size. Groups of samples typically have different library sizes that are not representative of biological variation; library size normalization is required to meaningfully compare diversity between them. Rarefaction is a widely used normalization technique that involves the random subsampling of sequences from the initial sample library to a selected normalized library size. This process is often dismissed as statistically invalid because subsampling effectively discards a portion of the observed sequences, yet it remains prevalent in practice and the suitability of rarefying, relative to many other normalization approaches, for diversity analysis has been argued. Here, repeated rarefying is proposed as a tool to normalize library sizes for diversity analyses. This enables (i) proportionate representation of all observed sequences and (ii) characterization of the random variation introduced to diversity analyses by rarefying to a smaller library size shared by all samples. While many deterministic data transformations are not tailored to produce equal library sizes, repeatedly rarefying reflects the probabilistic process by which amplicon sequencing data are obtained as a representation of the amplified source microbial community. Specifically, it evaluates which data might have been obtained if a particular sample’s library size had been smaller and allows graphical representation of the effects of this library size normalization process upon diversity analysis results.

Oil recovery decreased with prolonged waterflood development in the main reservoirs in the Ordos Basin, and the extraction of the remaining oil was gradually difficult. To exploit oil-producing potential through microbial enhanced oil recovery (MEOR), bacterial communities of 26 samples from Yan 9, 10 layers, and 15 samples from Chang 6 layers were analyzed based on high-throughput sequencing. 1578 and 3581 amplicon sequence variants were obtained from Jurassic and Triassic samples, and α diversity analysis showed that dominant bacterial genera existed distinctly in both study areas. The distribution of the Jurassic bacteria community differed from that of the Triassic, revealed by a principal coordinate analysis. Pseudomonas (15.74%) and Sulfurospirillum (9.94%) were identified as the dominant bacteria in the Jurassic study areas, as well as Pseudomonas (33.54%) and Acinetobacter (11.41%) were the main bacteria in the Triassic reservoirs. Co-occurrence network analysis indicated that the Jurassic and Triassic study areas had both complex and unstable bacterial consortiums, which were closely connected with Proteobacteria and Firmicutes, respectively. The different development strategies and reservoir properties led to the discrepancy in indigenous bacteria distribution between the Jurassic and Triassic study areas. However, some bacteria that have been reported to have oil-displacing ability, such as Pseudomonas, Halomonas, Acinetobacter, Marinobacterium, and Marinobacter, were found in both regions, suggesting that these bacteria had extensive adaptability. Among them, the utilization of functional bacteria of Proteobacteria and Firmicutes might be conducive to enhancing oil recovery stably. Based on this, Pseudomonas aeruginosa PA2 was isolated from study areas and enhanced oil recovery by 17.85 and 11.89% during Jurassic and Triassic core flooding tests, respectively.

Understanding characteristic variation in aquatic bacterial community composition (BCC) across space and time can inform us about processes driving community assembly and the ability of bacterial communities to respond to perturbations. In this study, we synthesize BCC data from north temperate lakes to evaluate our current understanding of how BCC varies across multiple scales in time and space. A hierarchy of average similarity emerged with the highest similarity found among samples collected within the same lake, especially within the same basin, followed by similarity among samples collected through time within the same lake, and finally similarity among samples collected from different lakes. Using decay of similarity across time and space, we identified equivalent temporal (1 day) and spatial (10 m) scales of BCC variation. Finally, we identify an intriguing pattern of contrasting patterns of intra- and inter-annual BCC variation in two lakes. We argue our synthesis of spatio-temporal variation of aquatic BCC informs expectations for the response of aquatic bacterial communities to perturbation and environmental change. However, further long-term temporal observations will be needed to develop a general understanding of inter-annual BCC variation and our ability to use aquatic BCC as a sensitive metric of environmental change.

Concern about biodiversity loss has yielded a surge of studies on temporal change in α-diversity, whereas temporal β-diversity has gained less interest. We sampled bacterioplankton, biofilm, and riparian soil bacteria repeatedly across the open-water season in a pristine stream network to determine the level of temporal β-diversity in relation to stream network position and environmental variability. We tested the hypothesis that aquatic bacterial communities in isolated and environmentally heterogenous headwaters exhibit high temporal β-diversity while the better-connected and environmentally more stable mainstem sections support more stable communities, and soil communities bear no relationship to network position. As expected, temporal β-diversity decreased from headwaters toward mainstems for bacterioplankton. Against expectations, an opposite pattern was observed for biofilm. For bacterioplankton, temporal β-diversity was positively related to temporal variability in water chemistry. For biofilm bacteria, temporal variability was negatively related to variability in temperature. Temporal β-diversity of soil communities did not show any response to stream network position, but was strongly related to variability in the soil environment. The two aquatic habitats and riparian soils supported distinctly different bacterial communities. The number of ASVs shared between the soil and the aquatic communities decreased along the network, and more so for bacterioplankton. The higher temporal variability of bacterial communities in the headwaters likely results from temporally variable input of propagules from riparian soil, emphasizing the role of land–water connection and network position to bacterioplankton community composition. Overall, bacterial communities exhibited high temporal variability, highlighting the importance of temporal replication to fully capture their network-scale biodiversity.

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The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.

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Fish diversity in rivers is critical for aquatic ecosystem sustainability, with multitrophic microbial communities (bacteria, fungi, phytoplankton, zooplankton) playing key roles in energy transfer. This study in the upper Yangtze River's Fish National Nature Reserve (FNNR) used environmental DNA (eDNA) to investigate microbial succession and its relationship with fish diversity. Bacteria showed the highest alpha‐diversity, while zooplankton has the lowest beta‐diversity. Geographic location and total nitrogen emerged as primary drivers of microbial community succession. Bacteria and phytoplankton demonstrated stronger environmental adaptability but lower community turnover compared to fungi and zooplankton. Null model analysis revealed homogenizing processes dominated bacterial and fungal assembly, whereas heterogeneous processes shaped phytoplankton and zooplankton communities. Microbial association networks indicated distinct community structures in different river systems. Path modeling showed that multitrophic microbial communities negatively impacted fish diversity, but cross‐trophic interactions among microorganisms has positive effects. These findings highlight how microbial diversity supports fish communities and provide conservation insights by linking microbial processes to ecosystem health. The study emphasizes the importance of understanding microbial dynamics for adaptive management strategies in biodiversity preservation.

This study aimed to induce a shift in a bacterial community by adding substrate into a biofloc system to characterize this shift and estimate its benefits in improving water quality and aquatic animal growth. We compared the bacterial communities between two biofloc systems, either with (sB treatment) or without (nB treatment) the addition of substrate (elastic solid packing filler), and we also analyzed the effects of the shift on the water quality and growth performance of shrimp (Litopenaeus vannamei). Beta diversity analysis indicated that the bacterial communities in the two treatments were significantly different (Jaccard index 0.94 ± 0.01, pseudo-F = 3.96, p = 0.001). The addition of substrate showed significant positive effects on bacterial alpha diversity indices (Shannon, Heip, Pielou, and Simpson; p < 0.05) and the abundances of beneficial genera (e.g., Arenimonas, Arthrobacter, Exiguobacterium, Leadbetterella, Luteolibacter, Marinobacter, Nitratireductor, Novosphingobium, Thermomonas, Plesiocystis, and Rubrivivax; p < 0.05). In addition, the substrate also showed significant positive effects on water quality parameters (TAN, TSS, turbidity, biofloc volume, pH, and carbonate alkalinity; p < 0.05), and it also significantly improved shrimp zootechnical performance indices (survival rate, feed conversion ratio, and productivity; p < 0.05). Redundancy analysis revealed that 94.25–98.58% of the variation in the water quality and the shrimp growth performance between the two treatments could be attributed to the shift in bacterial composition and diversity induced by the addition of substrate. These findings characterize the shift in the microbial community in the biofloc system induced by the substrate, and demonstrate how this shift could be beneficial to the water quality and the growth performance of shrimp.

Freshwater systems are shaped by hydrological connectivity, yet distinct microbial communities persist between lotic and lentic habitats. While bacterial biogeography across aquatic habitats has been widely explored, less is known about the spatiotemporal links of microeukaryotes to bacterial communities. Here, we investigated microbial diversity, rRNA-based activity and community assembly within a stream-lake network in Sweden under contrasting hydrological regimes. Using amplicon sequencing of both rRNA genes and transcripts, we found parallel patterns in bacterial and microeukaryotic alpha and beta diversity, with lower richness in lakes than in inlet streams. Bacterial phenotypic diversity, assessed by flow cytometry, captured biogeographic trends comparable to sequencing-based methods. Bacteria and microeukaryotes also appeared to be structured by similar assembly mechanisms, with environmental selection having a higher relative importance in lakes compared to streams. During low-flow periods, the catchment outlet became increasingly distinct from upstream communities, demonstrating dispersal limitation from lakes. Finally, phantom taxa, undetected in rRNA genes, were predominantly rare and exhibited disproportionately high RNA:DNA ratios compared to active taxa, underscoring the need for their careful handling. Our findings revealed habitat-driven microbial dynamics, despite pronounced seasonal shifts in hydrology.

Bacterial community play an essential role in regulating water quality and the global biogeochemical cycle in aquatic ecosystems. However, how trophic interactions (i.e., biotic factors) regulate the diversity and composition of bacterial community in lake ecosystems remains unknown. Here, we employed DNA meta-barcoding of water samples to explore the impact of bacterivorous protozoans on the bacterial community. The results showed significant seasonal variations in the diversity and composition of both bacterial and protist communities. The composition of bacterivorous protozoans was identified as the primary predictor for the bacterial community alpha diversity in spring and summer, and for beta diversity in spring and autumn, indicating that biotic interactions play a greater role in driving the diversity of bacterial community across different seasons. Biological factors were more important than environmental factors for explaining the variations in the relative abundance of several bacterial genera (i.e., Pseudoxanthomonas, hgcI_clade, and Pseudorhodobacter). Network analyses showed that bacterial networks differed among seasons, and the autumn network exhibited the highest stability. Our findings indicated that the bacterial community stability was significantly affected by environmental factors, specifically SO42–and PO43–, rather than bacterivorous protozoans. Overall, our findings provide new perspectives on the role of trophic interactions in maintaining the structure of bacterial community in different seasons, and enhance our understanding of the bacterial community assembly in lake ecosystems.

Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.

Despite the importance of bacteria in aquatic ecosystems and their predictable diversity patterns across space and time, biomonitoring tools for status assessment relying on these organisms are widely lacking. This is partly due to insufficient data and models to identify reliable microbial predictors. Here, we show metabarcoding in combination with multivariate statistics and machine learning allows to identify bacterial bioindicators for existing biological status classification systems. Bacterial beta-diversity dynamics follow environmental gradients and the observed associations highlight potential bioindicators for ecological outcomes. Spatio-temporal links spanning the microbial communities along the river allow accurate prediction of downstream biological status from upstream information. Network analysis on amplicon sequence veariants identify as good indicators genera Fluviicola, Acinetobacter, Flavobacterium , and Rhodoluna , and reveal informational redundancy among taxa, which coincides with taxonomic relatedness. The redundancy among bacterial bioindicators reveals mutually exclusive taxa, which allow accurate biological status modeling using as few as 2–3 amplicon sequence variants. As such our models show that using a few bacterial amplicon sequence variants from globally distributed genera allows for biological status assessment along river systems. Bacterial communities sampled over 2,600 km of the River Danube revealed the predictability of downstream river conditions from upstream microbiota, with variance and prevalence of dominant taxa linked to environmental gradients, unveiling potential bioindicators.

The lactate-based polyester poly[lactate (LA)-co-3-hydroxybutyrate (3HB)], termed LAHB, is a highly transparent and flexible bio-based polymeric material. There are many unknowns regarding its degradation process in riverine environments, especially the changes in bacterial flora that might result from its degradation and the identities of any LAHB-degrading bacteria. LAHB were immersed in the river water samples (A and B), and LAHB degradation was observed in terms of the weight change of the polymer and the microscopic changes on the polymer surfaces. A metagenomic analysis of microorganisms was conducted to determine the effect of LAHB degradation on the aquatic environment. The bacterial flora obtained from beta diversity analysis differed between the two river samples. The river A water sample showed the simultaneous degradation of LA and 3HB even though the copolymer was LA-enriched, suggesting preferable hydrolysis of the LA-enriched segments. In contrast, only 3HB degraded for the LAHB in the river B water sample. The linear discriminant analysis effect size (LEfSe) analysis revealed 14 bacteria that were significantly increased in the river A water sample during LAHB degradation, suggesting that these bacteria preferentially degraded and assimilated LA-clustering polymers. Our metagenomic analysis provides useful insights into the dynamic changes in microbial communities and LA-clustering polymer-degrading bacteria.

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Comparison of the spatial distribution and assembly processes between bulk and rhizosphere bacterial communities at multiple spatial scales is vital for understanding the generation and maintenance of microbial diversity under the influence of plants. However, biogeographical patterns and the underlying mechanisms of microbial communities in bulk and rhizosphere sediments of aquatic ecosystems remain unclear. Here, we collected 140 bulk and rhizosphere sediment samples of Phragmites australis from 14 lakeshore zones across a 510‐km transect in the Middle–Lower Yangtze plain. We performed high‐throughput sequencing to investigate the bacterial diversity, composition, spatial distribution and assembly processes of these samples. Bacterial communities in the rhizosphere sediment exhibited higher alpha diversity but lower beta diversity than those in the bulk sediment. Both bulk and rhizosphere sediment bacterial communities had significant distance–decay relationships, but spatial turnover of the rhizosphere sediment bacterial community was strikingly lower than that of bulk sediment. Despite variable selection dominating the assembly processes of bacterial communities in bulk sediment, the rhizosphere of P. australis enhanced the role of dispersal limitation in governing bacterial communities. The relative importance of different ecological processes in determining bacterial assembly presented distinct patterns of increasing or decreasing linearly with an increase of scale. This investigation highlights the convergent selection of the aquatic plant rhizosphere for surrounding bacterial communities and emphasizes the importance of different ecological processes on bacterial community assembly in sediment environments over different scales. Furthermore, we provide a preliminary framework for exploring the scale dependence of microbial community assembly in aquatic ecosystems.

Microorganisms play a pivotal role in nutrient cycling in aquatic ecosystems. Understanding bacterial diversity and its functional composition are crucial for aquatic ecology and protection. We investigated the bacterial community structure using 16S rRNA gene amplicons high-throughput sequencing in this study. Results showed that 105 amplicon sequence variants (ASVs) account for 43.8% of the total sequences shared by the Nandu River’s lower, middle, and upper reach and the Songtao Reservoir. The dominant bacterial phylum in the Nandu River and its connected Songtao Reservoir were Proteobacteria and Actinobacteriota, respectively. The highest Chao1 and Shannon index values were found in the lower reach of the Nandu River. Beta diversity analysis showed the divergence in bacterial communities in the Nandu River and Songtao Reservoir, but not in different reaches. Among the water properties, based on the Mantel test, dissolved oxygen, total nitrogen, and nitrite significantly affected the bacterial communities. The functional profiles predicted by Tax4Fun2 showed that metabolism was the most abundant function group. The relative abundance of genetic information processing was significantly higher in the Songtao Reservoir than in the Nandu River, while the relative abundance of human diseases was significantly lower in the Songtao Reservoir than in the Nandu River. The appearance of the xenobiotics biodegradation and metabolism function group requires us to pay more attention to possible water pollution, especially at the upper reach of the Nandu River.

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Eutrophication substantially influences the community structure of aquatic organisms and has become a major threat to biodiversity. However, whether eutrophication is linked to homogenization of microbial communities and the possible underlying mechanisms are poorly understood. Here, we studied bacterial and fungal communities from water and sediments of 40 shallow lakes in the Yangtze-Huaihe River basin, a representative area characterized by intensifying eutrophication in China, and further examined the beta diversity patterns and underlying mechanisms under eutrophication conditions. Our results indicate that eutrophication generally caused biotic homogenization of bacterial and fungal communities in both habitats showing decreased community variations for the sites with a higher trophic state index (TSI). In the two habitats, community dissimilarities were positively correlated with TSI changes for both taxonomic groups, while the local contribution to beta diversity (LCBD) remarkably declined with increasing TSI for the fungal community. These phenomena were consistent with the pivotal importance of the TSI in statistically accounting for beta diversity of bacterial and fungal communities in both habitats. In addition, we found that physicochemical factors such as water temperature and pH were also important for bacterial and fungal communities in water, while heavy metal elements were important for the communities in sediments. Interestingly, generalist species, rather than specialist species, were revealed to more dominantly affect the variations in beta diversity along the trophic gradient, which were quantified by Bray-Curtis dissimilarity and LCBD. Collectively, our findings reveal the importance of generalist species in contributing to the change of beta diversity of microbial communities along trophic gradients, which have profound implications for a comprehensive understanding of the effects of eutrophication on microbial community.

Bacterial antimicrobial resistance (AMR) has emerged as a significant concern worldwide. The microbial community profile and potential AMR level in aquaculture ponds are often undervalued and attract less attention than other aquatic environments. We used amplicon and metagenomic shotgun sequencing to study microbial communities and AMR in six freshwater polyculture ponds in rural and urban areas of Bangladesh. Amplicon sequencing revealed different community structures between rural and urban ponds, with urban ponds having a higher bacterial diversity and opportunistic pathogens including Streptococcus, Staphylococcus, and Corynebacterium. Despite proteobacterial dominance, Firmicutes was the most interactive in the community network, especially in the urban ponds. Metagenomes showed that drug resistance was the most common type of AMR found, while metal resistance was only observed in urban ponds. AMR and metal resistance genes were found mainly in beta and gamma-proteobacteria in urban ponds, while AMR was found primarily in alpha-proteobacteria in rural ponds. We identified potential pathogens with a high profile of AMR and metal resistance in urban aquaculture ponds. As these ponds provide a significant source of protein for humans, our results raise significant concerns for the environmental sustainability of this food source and the dissemination of AMR into the food chain.

We herein designed novel PCR primers for universal detection of the pepA gene, which encodes the representative leucine aminopeptidase gene, and investigated the genetic characteristics and diversity of pepA genes in sediments of hypereutrophic Lake Kasumigaura, Japan. Most of the amino acid sequences deduced from the obtained clones (369 out of 370) were related to PepA-like protein sequences in the M17 family of proteins. The developed primers broadly detected pepA-like clones associated with diverse bacterial phyla—Alpha-, Beta-, Gamma-, and Deltaproteobacteria, Acidobacteria, Actinobacteria, Aquificae, Chlamydiae, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, Planctomycetes, and Spirochetes as well as the archaeal phylum Thaumarchaeota, indicating that prokaryotes in aquatic environments possessing leucine aminopeptidase are more diverse than previously reported. Moreover, prokaryotes related to the obtained pepA-like clones appeared to be r- and K-strategists, which was in contrast to our previous findings showing that the neutral metalloprotease gene clones obtained were related to the r-strategist genus Bacillus. Our results suggest that an unprecedented diversity of prokaryotes with a combination of different proteases participate in sedimentary proteolysis.

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With the rapid development of microorganism biodiversity estimation and community profiling via DNA metabarcoding, there is a growing need to identify key stages affecting the results of experiment. In order to ensure high-quality reproducible results, all potential sources of bias should be explored. While bioinformatic pipelines can be often corrected and optimized to recalculate results, the initial steps of sample collection procedure, potentially influencing the downstream results of bacterial community profiling, are much harder to correct easily, without repeating the whole experiment. We examined the differences of the amplicon bacterial community profiles generated from aquatic microbial communities captured by polycarbonate (PC) and cellulose acetate (CA) filters. The microbial community profiles were shown to be significantly different by biodiversity. When using a PC-filters, alpha- and beta-diversity of communities were significantly higher. Differential abundance analysis showed enrichment of major cyanobacterial OTUs in CA-treated communities. Based on these results, the use of PC-filters is the most optimal for bacterial community profiling by metabarcoding of the 16S rRNA gene fragments.

Rapid development of aquaculture industry and increasing demand of various inputs (especially antibiotics), are suspected to promote the occurrence and spread of ARGs in aquaculture related environments. However, the occurrences of ARGs under different freshwater aquaculture practices are rarely known. Here, we investigated the seasonal profiles of the main ARGs, intI1 and bacteria in waters from three kinds of predominant freshwater aquaculture practices around the Honghu Lake (China), as well as their co-occurrences and interrelationships with antibiotics, heavy metals and general water quality. The results indicate that quinolone resistance genes (qnrB), tetracycline resistance genes (tetB and tetX) and sulfonamide resistance genes (sul1 and sul2) were the top five predominant ARGs with seasonal variations of abundance. Fish ponds were of the highest absolute abundances of tested ARGs than the other two modes. Crayfish ponds and their adjacent ditches shared similar ARGs profile. Different subtypes of ARGs belonging to the same class of resistance were varied in abundances. Some bacteria were predicted to carry different ARGs, which indicating multi-antibiotic resistances. Moreover, the combined environmental factors (antibiotics, heavy metals and water quality) partially shaped the profiles of ARGs and bacteria composition. Overall, this study provides new comprehensive understanding on the characterization of ARGs contamination in different freshwater aquaculture practices from the perspectives of environmental chemistry, microbiology and ecology. The results would benefit the optimization of aquaculture practices toward environmental integrity and sustainability.

Marine plastic debris (MPD) harbors potentially pathogenic bacterial communities (PPBs); however, their substrate specificity and environmental influences remain unclear. We aimed to identify the key drivers for the formation of PPB and to elucidate the ecological mechanisms regulating these assemblages. We analyzed MPD samples in South Korea to evaluate PPBs across plastic types, seasons, sampling hot-spot sites, and environmental factors, in comparison to ambient seawater. The bacterial community on the surface of MPD was analyzed using 16S rDNA metabarcoding. The abundance of PPB among the attached bacteria was significantly higher than in the surrounding seawater (PERMANOVA, p < 0.001). PPB on MPD showed significant differences based on water temperature and eutrophication levels (p < 0.001). However, no significant differences were observed among different types of MPD and sampling sites. Vibrio and Pseudoalteromonas were abundant on MPD and included species that infect both marine organisms and humans. Vibrio splendidus and Pseudoalteromonas nigrifaciens thrived under eutrophic conditions below 17 °C. In contrast, Vibrio parahaemolyticus appeared more frequently at temperatures above 17 °C, with lower eutrophic conditions. Therefore, PPB are influenced by environmental factors but exhibit substrate specificity on MPD, indicating that MPD poses a potential risk in facilitating the spread of pathogenic diseases.

Bacterial diversity and its distribution characteristics in sediments are critical to understanding and revealing biogeochemical cycles in sediments. However, little is known about the relationship between biogeochemistry processes and vertical spatial distribution of bacterial communities in sandy sediments. In this study, we used fluorescence quantitative PCR, high-throughput sequencing technology and statistical analysis to explore the vertical distribution pattern of bacterial community diversity and its influencing factors in sandy sediments of the Yangtze River Basin. The aim is to enrich the understanding of the ecological characteristics and functions of bacteria in river ecosystems. The results showed that both sediment bacterial abundance and diversity showed a gradual decrease from surface to bottom in the vertical distribution. The main environmental factors that influenced the bacterial distribution pattern were pore water dissolved oxygen (DO), total nitrogen (TN) concentration and sediment nitrogen (N) content. The dominant bacterial species, Massilia and Flavobacterium, are suitable for growth and reproduction in high oxygen and nutrient-richer environments, while Limnobacter prefers low oxygen or anaerobic conditions. The vertical distribution pattern of bacteria and its influencing factors in river sandy sediment found in this study differ from the results in mud sediment, which may be related to the larger granular gap between sandy sediment and the lower content of organic matter. The findings of this study further our understanding of the distribution patterns and ecological preferences of microbial communities in river sediments, providing insights into how these communities may adapt to varying environmental conditions.

The proliferation of marine invasive species is a mounting concern. While the role of microbial communities in invasive ascidian species is recognized, the role of seasonal shifts in microbiome composition remains largely unexplored. We sampled five individuals of the invasive ascidian Styela plicata quarterly from January 2020 to October 2021 in two harbours, examining gills, tunics, and surrounding water. By analysing Amplicon Sequence Variants (ASVs) and seawater trace elements, we found that compartment (seawater, tunic, or gills) was the primary differentiating factor, followed by harbour. Clear seasonal patterns were evident in seawater bacteria, less so in gills, and absent in tunics. We identified compartment-specific bacteria, as well as seasonal indicator ASVs and ASVs correlated with trace element concentrations. Among these bacteria, we found that Endozoicomonas, Hepatoplasma and Rhodobacteraceae species had reported functions which might be necessary for overcoming seasonality and trace element shifts. This study contributes to understanding microbiome dynamics in invasive holobiont systems, and the patterns found indicate a potential role in adaptation and invasiveness.

In this study, we determined the presence of class 1 integron-integrase gene in culturable heterotrophic bacteria isolated from river water and sediment sampled upstream and downstream of a wastewater treatment plant effluent discharge. Moreover, we quantified intI1 and sulfonamide resistance genes (sul1 and sul2) in the water and sediment using qPCR. There was no correlation between the results from water and sediment samples, which suggests integron-containing bacteria are differentially retained in these two environmental compartments. The discharge of treated wastewater significantly increased the frequency of intI1 among culturable bacteria and the gene copy number in river water, and increased the number of sul1 genes in the sediment. We also observed seasonal differences in the frequency of the class 1 integron-integrase gene among culturable heterotrophs as well as intI1 copy number in water, but not in sediment. The results suggest that the abundance of class 1 integrons in aquatic habitat depends on anthropogenic pressure and environmental factors.

In large-scale seaweed farming, an understanding of the decomposition process plays a pivotal role in optimizing cultivation practices by considering the influence of the bacterial community. Therefore, we assessed the bacterial community structure and its influence on environmental factors during Gracilaria lemaneiformis decomposition, utilizing both microcosms and in-situ simulations. The decomposition rates in the microcosms and in situ simulations reached 79 % within 180 days and 81 % within 50 days, respectively In the microcosms, the dissolved oxygen content decreased from 5.3 to 0.4 mg/L, while the concentrations of total organic carbon, nitrogen, and phosphorus in the water increased by 165 %, 1636 %, and 2360 %, respectively. The common dominant bacteria included Proteobacteria, Planctomycetes, Firmicutes, Bacteroidetes, and Spirochaetae. Planctomycetes and Firmicutes were positively correlated with the total organic carbon, nitrogen, and phosphorus concentrations. Planctomycetes species played significant roles during the decomposition process. The overall findings of this study could inform more sustainable seaweed cultivation practices.

No abstract available

Salmonellosis is an important but neglected disease in sub-Saharan Africa. Food or fecal-oral associated transmissions are the primary cause of infections, while the role of waterborne transmission is unclear. Samples were collected from different dug wells in a rural area of Ghana and analyzed for contamination with bacteria, and with Salmonella in particular. In addition, temporal dynamics and riks factors for contamination were investigated in 16 wells. For all Salmonella isolates antibiotic susceptibility testing was performed, serovars were determined and strains from the same well with the same serovar were genotyped. The frequency of well water contamination with Gram-negative rod-shaped bacteria was 99.2% (n = 395). Out of 398 samples, 26 (6.5%) tested positive for Salmonella spp. The serovar distribution was diverse including strains not commonly isolated from clinical samples. Resistance to locally applied antibiotics or resistance to fluoroquinolones was not seen in the Salmonella isolates. The risk of Salmonella contamination was lower in wells surrounded by a frame and higher during the rainy season. The study confirms the overall poor microbiological quality of well water in a resource-poor area of Ghana. Well contamination with Salmonella poses a potential threat of infection, thus highlighting the important role of drinking water safety in infectious disease control.

Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. ABSTRACT Fish bacterial communities provide functions critical for their host’s survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host’s genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities’ structure, while pairwise fixation indexes (FST) from the hosts’ genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host’s genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.

No abstract available

Denitrifying bacteria harboring the nitrate reductase S (nirS) gene convert active nitrogen into molecular nitrogen, and alleviate eutrophication in aquaculture water. Suspended particulate matter (SPM) is an important component of aquaculture water and a carrier for denitrification. SPM with different particle sizes were collected from a coastal high-altitude aquaculture pond in Maoming City, China. Diversity, community structure, abundance of nirS-type denitrifying bacteria on SPM and environmental influencing factors were studied using high-throughput sequencing, fluorescence quantitative PCR, and statistical analysis. Pseudomonas, Halomonas, and Wenzhouxiangella were the dominant genera of nirS-type denitrifying bacteria on SPM from the ponds. Network analysis revealed Pseudomonas and Halomonas as the key genera involved in the interaction of nirS-type denitrifying bacteria on SPM in the ponds. qPCR indicated a trend toward greater nirS gene abundance in progressively larger SPM. Dissolved oxygen, pH, temperature, and SPM particle size were the main environmental factors influencing changes in the nirS-type denitrifying bacterial community on SPM in coastal high-altitude aquaculture pond water. These findings increase our understanding of the microbiology of nitrogen cycle processes in aquaculture ecosystem, and will help optimize aquatic tailwater treatment strategies.

Abstract. Escherichia coli pathotypes (i.e., enteropathogenic and enterotoxigenic) have been identified among the pathogens most responsible for moderate-to-severe diarrhea in low- and middle-income countries (LMICs). Pathogenic E. coli are transmitted from infected human or animal feces to new susceptible hosts via environmental reservoirs such as hands, water, and soil. Commensal E. coli, which includes nonpathogenic E. coli strains, are widely used as fecal bacteria indicator, with their presence associated with increased likelihood of enteric pathogens and/or diarrheal disease. In this study, we investigated E. coli contamination in environmental reservoirs within households (N = 142) in high-population density communities of Harare, Zimbabwe. We further assessed the interconnectedness of the environmental compartments by investigating associations between, and household-level risk factors for, E. coli contamination. From the data we collected, the source and risk factors for E. coli contamination are not readily apparent. One notable exception is the presence of running tap water on the household plot, which is associated with significantly less E. coli contamination of drinking water, handwashing water, and hands after handwashing. In addition, E. coli levels on hands after washing are significantly associated with handwashing water contamination, hand contamination before washing, and diarrhea incidence. Finally, we observed that animal ownership increases E. coli contamination in soil, and E. coli in soil are correlated with contamination on hands before washing. This study highlights the complexity of E. coli contamination in household environments within LMICs. More, larger, studies are needed to better identify sources and exposure pathways of E. coli—and enteric pathogens generally—to identify effective interventions.

Historically, pelagic Sargassum were only found in the Sargasso Sea. Since 2011, blooms were regularly observed in warmer water, further south. Their developments in Central Atlantic are associated with mass strandings on the coasts, causing important damages and potentially dispersion of new bacteria. Microbiomes associated with pelagic Sargassum were analysed at large scale in Central Atlantic and near Caribbean Islands with a focus on pathogenic bacteria. Vibrio appeared widely distributed among pelagic Sargassum microbiome of our samples with higher occurrence than previously found in Mexico Gulf. Six out the 16 Vibrio-OTUs (Operational Taxonomic Unit), representing 81.2 ± 13.1% of the sequences, felt in cluster containing pathogens. Among the four different microbial profiles of pelagic Sargassum microbiome, Vibrio attained about 2% in two profiles whereas it peaked, in the two others, at 6.5 and 26.8% respectively, largely above the concentrations found in seawater surrounding raft (0.5%). In addition to sampling and measurements, we performed backward Lagrangian modelling of trajectories of rafts, and rebuilt the sampled rafts environmental history allowing us to estimate Sargassum growth rates along raft displacements. We found that Vibrio was favoured by high Sargassum growth rate and in situ ammonium and nitrite, modelled phosphate and nitrate concentrations, whereas zooplankters, benthic copepods, and calm wind (proxy of raft buoyancy near the sea surface) were less favourable for them. Relations between Vibrio and other main bacterial groups identified a competition with Alteromonas. According to forward Lagrangian tracking, part of rafts containing Vibrio could strand on the Caribbean coasts, however the strong decreases of modelled Sargassum growth rates along this displacement suggest unfavourable environment for Vibrio. For the conditions and areas observed, the sanitary risk seemed in consequence minor, but in other areas or conditions where high Sargassum growth rate occurred near coasts, it could be more important.

Bacterial communities are an important part of biological diversity and biogeochemical cycling in aquatic ecosystems. In this study, the relationship amongst the phytoplankton species composition and abiotic environmental factors on seasonal changes in the community composition of free-living and attached bacteria in Lake Erhai were studied. Using Illumina high-throughput sequencing, we found that the impact of environmental factors on both the free-living and attached bacterial community composition was greater than that of the phytoplankton community, amongst which total phosphorus, Secchi disk, water temperature, dissolved oxygen and conductivity strongly influenced bacterial community composition. Microcystis blooms associated with subdominant Psephonema occurred during the summer and autumn, and Fragilaria, Melosira and Mougeotia were found at high densities in the other seasons. Only small numbers of algal species-specific bacteria, including Xanthomonadaceae (Proteobacteria) and Alcaligenaceae (Betaproteobacteria), were tightly coupled to Microcystis and Psephonema during Microcystis blooms. Redundancy analysis showed that although the composition of the bacterial communities was controlled by species composition mediated by changes in phytoplankton communities and abiotic environmental factors, the impact of the abiotic environment on both free-living and attached bacterial community compositions were greater than the impact of the phytoplankton community. These results suggest that the species composition of both free-living and attached bacterial communities are affected by abiotic environmental factors, even when under strong control by biotic factors, particularly dominant genera of Microcystis and Psephonema during algal blooms.

The gut microbiota of aquatic animals plays a crucial role in host health through nutrient acquisition and outcompetition of pathogens. In this study, on the basis of the high-throughput sequencing of 16S rRNA gene amplicons, we examined the bacterial communities in the gut of freshwater shrimp (Macrobrachium nipponense) and in their living environments (sediment and pond water) and analyzed the effects of abiotic and biotic factors on the shrimp gut bacterial communities. High bacterial heterogeneity was observed in the freshwater shrimp gut samples, and the result indicated that both the surrounding bacterial community and water quality factors (particularly dissolved oxygen and temperature) could affect the shrimp gut bacterial community. Despite the observed heterogeneity, 57 genera, constituting 38%-99% of the total genera in each of the 40 shrimp gut samples, were identified as the main bacterial population in the gut of M. nipponense. In addition, a high diversity and abundance of lactic acid bacteria (26 genera), which could play significant roles in the digestion process in shrimp, were observed in the shrimp gut samples. Overall, this study provides insights into the gut bacterial communities of freshwater shrimp and basic information for shrimp farming regarding the application of probiotics and disease prevention.

No abstract available

No abstract available

16S rRNA gene sequencing and bacteria- and genus-specific quantitative PCR was used to profile microbial communities and their associated functions in water, live feed (microalgae, Artemia, and rotifer), and European sea bass and gilthead sea bream larvae from hatcheries in Greece and Italy. The transfer to larvae of genus containing potential pathogens of fish was more likely with Artemia and rotifer than with microalgae or water, irrespective of geographic location. The presence of potentially pathogenic bacteria (Vibrio and Pseudoalteromonas) in the core microbiota of water, live feed, and fish larvae, the enrichment of different bacterial resistance pathways and biofilm formation, and the overall low beneficial bacteria load during larval ontogeny emphasizes the risk for disease outbreaks. The present data characterizing microbiota in commercial aquaculture hatcheries provides a baseline for the design of strategies to manage disease and to model or remediate potential adverse environmental impacts.

To investigate the spatial distribution of microbial communities and their drivers in petroleum reservoir environments, we performed pyrosequencing of microbial partial 16S rRNA, derived from 20 geographically separated water-flooding reservoirs and two reservoirs that had not been flooded, in China. The results indicated that distinct underground microbial communities inhabited the different reservoirs. Compared with the bacteria, archaeal alpha-diversity was not strongly correlated with the environmental variables. The variation of the bacterial and archaeal community compositions was affected synthetically, by the mining patterns, spatial isolation, reservoir temperature, salinity and pH of the formation brine. The environmental factors explained 64.22% and 78.26% of the total variance for the bacterial and archaeal communities, respectively. Despite the diverse community compositions, shared populations (48 bacterial and 18 archaeal genera) were found and were dominant in most of the oilfields. Potential indigenous microorganisms, including Carboxydibrachium, Thermosinus and Neptunomonas, were only detected in a reservoir that had not been flooded with water. This study indicates that: 1) the environmental variation drives distinct microbial communities in different reservoirs; 2) compared with the archaea, the bacterial communities were highly heterogeneous within and among the reservoirs; and 3) despite the community variation, some microorganisms are dominant in multiple petroleum reservoirs.

No abstract available

Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.

No abstract available

BackgroundNothing is currently known about microbial composition of saline lakes of the Novosibirsk region and its dependence on physical-chemical parameters of waters. We studied the structure of microbial communities of saline lakes of the Novosibirsk region and the effect of physical-chemical parameters of waters on microbial communities of these lakes.ResultsAccording to the ion content, the lakes were classified either as chloride or chloride-sulfate types. Water salinity ranges from 4.3 to 290 g L−1. Many diverse microbial communities were found. Filamentous and colonial Cyanobacteria of the genera Scytonema, Aphanocapsa, and/or filamentous Algae dominated in littoral communities. Spatial and temporal organization of planktonic microbial communities and the quantities of Archaea and Bacteria were investigated using fluorescent in situ hybridization. We have found that the dominant planktonic component is represented by Archaea, or, less frequently, by Bacteria. Various phylogenetic groups (Bacteria, Archaea, Algae, and Cyanobacteria) are nonuniformly distributed. The principal component analysis was used to detect environmental factors that affect microorganism abundance. We found the principal components responsible for 71.1 % of the observed variation. It was demonstrated that two-block partial least squares was a better method than principal component analysis for analysis of the data. We observed general relationships between microbial abundance and water salinity.ConclusionsWe have performed the first-ever study of the structure of the microbial communities of eleven saline lakes in the Novosibirsk region along with their physical-chemical parameters of waters. Our study demonstrates that saline lakes in the Novosibirsk region contain a unique microbial communities that may become a prolific source of microorganisms for fundamental and applied studies in various fields of ecology, microbiology, geochemistry, and biotechnology, and deserve further metagenomic investigation.

Aerobic anoxygenic phototrophs (AAPs) are photoheterotrophic prokaryotes that are widespread in many limnic and marine environments. So far, little is known about their distribution in peat-bog lakes. Seventeen peat-bog lakes were sampled during three summer seasons 2009, 2011, and 2012, and the vertical distribution of AAPs was determined by infrared epifluorescence microscopy. The analysis demonstrated that in the surface layers of the studied lakes, AAP abundance ranged from 0.3 to 12.04 × 105 cells mL−1, which represents <1 to 18.3 % of the total bacteria. The vertical distribution of AAPs confirmed their presence in the upper parts of the water column with minimum numbers in the anoxic bottom waters. We have shown that the AAP abundance was significantly positively correlated with the water pH, and the highest proportion of photoheterotrophs was found in peat-bog lakes with a pH between 6.7 and 7.6. Our results demonstrated an influence of water acidity on the abundance of AAPs, which may reflect a fundamental difference in the microbial composition between acidic and pH neutral peat-bog lakes.

No abstract available

Drinking water samples were collected from 71 cities, including 28 provincial capital cities or municipalities, 20 prefecture cities and 23 counties, of 31 provincial-level administrative regions in China from July to August in 2017. Futhermore, 24 Antibiotic Resistance Genes (ARGs), 16S rRNA and 2 integrase genes were quantified by qPCR to investigate the pollution degree of ARGs. The results revealed that the 16S ranged from 105 - 108 copies/100 mL in the drinking water, and its treatment process could effectively remove bacteria. Moreover, sulfonamides-ARGs were the most prevalent ARGs in the drinking water of China, and the abundance of blaTEM ranked top five in all cities among the selected ARGs, indicating that the pollution condition of the genes should be aroused more attention. The data of qPCR and correlation analyses indicated that intI1 played a more crucial role than intI2 in the propagation of ARGs in the drinking water. Additionally, the pollution degree of ARGs among different city types showed no significant difference.