园林或植物园与微生物相结合

Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.

Intensive ornamental planting is increasingly prevalent in urban green spaces, yet its effects on soil microbial community assembly and interaction networks remain poorly understood. Here, we examined shifts in soil properties, microbial diversity, community composition, and interaction networks across successive planting cycles. Bacterial alpha-diversity remained relatively stable, whereas fungal communities showed pronounced sensitivity to early planting stages. Beta-diversity analyses revealed that bacterial community composition was jointly influenced by planting stage and site type, while fungal communities were primarily structured by site characteristics. Co-occurrence network analysis revealed contrasting reassembly trajectories between microbial groups. Bacterial networks exhibited increasing complexity and modularity, indicating enhanced interaction intensity and competitive structuring under intensive management. In contrast, fungal networks displayed reduced connectivity but maintained or recovered modular organization, suggesting structural buffering. Notably, keystone taxa remained taxonomically conserved, indicating that network reorganization was driven by interaction rewiring rather than species turnover. We propose a dual-speed reassembly framework in which bacteria function as fast-responding components with dynamic interaction networks, whereas fungi act as slow-buffering, structurally persistent elements. This decoupling of short-term functional responsiveness and long-term stability provides new insights into how intensive management reshapes soil microbiomes in botanical garden ecosystems.

Mangroves play a globally significant role in carbon capture and storage, known as blue carbon ecosystems. Yet, there are fundamental biogeochemical processes of mangrove blue carbon formation that are inadequately understood, such as the mechanisms by which mangrove afforestation regulates the microbial‐driven transfer of carbon from leaf to below‐ground blue carbon pool. In this study, we addressed this knowledge gap by investigating: (1) the mangrove leaf characteristics using state‐of‐the‐art FT‐ICR‐MS; (2) the microbial biomass and their transformation patterns of assimilated plant‐carbon; and (3) the degradation potentials of plant‐derived carbon in soils of an introduced (Sonneratia apetala) and a native mangrove (Kandelia obovata). We found that biogeochemical cycling took entirely different pathways for S. apetala and K. obovata. Blue carbon accumulation and the proportion of plant‐carbon for native mangroves were high, with microbes (dominated by K‐strategists) allocating the assimilated‐carbon to starch and sucrose metabolism. Conversely, microbes with S. apetala adopted an r‐strategy and increased protein‐ and nucleotide‐biosynthetic potentials. These divergent biogeochemical pathways were related to leaf characteristics, with S. apetala leaves characterized by lower molecular‐weight, C:N ratio, and lignin content than K. obovata. Moreover, anaerobic‐degradation potentials for lignin were high in old‐aged soils, but the overall degradation potentials of plant carbon were age‐independent, explaining that S. apetala age had no significant influences on the contribution of plant‐carbon to blue carbon. We propose that for introduced mangroves, newly fallen leaves release nutrient‐rich organic matter that favors growth of r‐strategists, which rapidly consume carbon to fuel growth, increasing the proportion of microbial‐carbon to blue carbon. In contrast, lignin‐rich native mangrove leaves shape K‐strategist‐dominated microbial communities, which grow slowly and store assimilated‐carbon in cells, ultimately promoting the contribution of plant‐carbon to the remarkable accumulation of blue carbon. Our study provides new insights into the molecular mechanisms of microbial community responses during reforestation in mangrove ecosystems.

Upon mutation of the core autophagy protein ATG5, disrupted autophagy pathways result in alterations in several biological processes important for plant‐root microbe interaction mechanisms, including the expression of cell wall‐ and defense‐related proteins and the secretion of root metabolites, all of which affect the root microbial community diversity.

Context Seeds harbour a diversity of microbes, which in some plants aid with germination and establishment. Seeds form a critical part in the lifecycle of plants and a role in many conservation and restoration activities. Aims Because this is an emerging field in seed biology, we aim to highlight the key research gaps of interest to seed on the basis of restoration and ex situ conservation. Methods We identify knowledge gaps associated with the seed endophytic microbiome of native Australian plants through undertaking a literature review. Additionally, culturing methods were used to identify the fungal seed endophytes of five native Australian species. Key results We identified a diversity of taxa within the native seed and show three taxa that are common to all study hosts. Sampling seed from additional hosts at a site and additional sites of a host species showed new fungal diversity. Our literature review showed that little information is available on native seed microbiomes and we identified four key areas where research gaps exist, linking with seed-based restoration practices. Conclusions We provide evidence that there is a complex and diverse seed microbiome within some Australian native plants and suggest ways that it could be integrated into restoration and conservation practices. Implications We propose that by taking into consideration the presence of a seed microbiome and its potential impacts on plant health, seed microbiomes could be used as one method to restore microbial diversity into an ecosystem and to contribute to the seedling microbiome and plant health at restored sites.

Microbiome-Inspired Green Infrastructure (MIGI) was recently proposed as an integrative system to promote healthy urban ecosystems through multidisciplinary design. Specifically, MIGI is defined as nature-centric infrastructure restored, designed, and managed to enhance health-promoting interactions between humans and environmental microbiomes while sustaining microbially mediated ecosystem functionality and resilience. MIGI also aims to stimulate a research agenda that focuses on considerations for the importance of urban environmental microbiomes. In this article, we provide details of what MIGI entails from a bioscience and biodesign perspective, highlighting the potential dual benefits for human and ecosystem health. We present ‘what is known’ about the relationship between urban microbiomes, green infrastructure, and environmental factors that may affect urban ecosystem health - taken here to mean ecosystem functionality and resilience, as well as human health. We discuss how to start operationalising the MIGI concept based on current available knowledge and present a horizon-scan of emerging and future considerations in research and practice. We conclude by highlighting challenges to implementing MIGI and propose a series of workshops to discuss multi-stakeholder needs and opportunities. This research will enable urban landscape managers to incorporate initial considerations for the microbiome in their development projects to promote human and ecosystem health. However, overcoming the challenges to operationalising MIGI will be essential to furthering its practical development. Although the research is in its infancy, there is considerable potential for MIGI to help deliver sustainable urban development driven by considerations for reciprocal relations between humans and the foundations of our ecosystems – the microorganisms.

Many grape endophytic microorganisms exhibit high potential for suppressing the development of grape diseases and stimulating grapevine growth and fitness, as well as beneficial properties of the crop. The microbiome of wild grapevines is a promising source of biocontrol agents, which can be beneficial for domesticated grapevines. Using next-generation sequencing (NGS) and classical microbiology techniques, we performed an analysis of bacterial and fungal endophytic communities of wild grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat growing in the Russian Far East. According to the NGS analysis, 24 and 18 bacterial taxa from the class level were present in V. amurensis and V. coignetiae grapevines, respectively. Gammaproteobacteria (35%) was the predominant class of endophytic bacteria in V. amurensis and Alphaproteobacteria (46%) in V. coignetiae. Three taxa, namely Sphingomonas, Methylobacterium, and Hymenobacter, were the most common bacterial genera for V. amurensis and V. coignetiae. Metagenomic analysis showed the presence of 23 and 22 fungi and fungus-like taxa of class level in V. amurensis and V. coignetiae, respectively. The predominant fungal classes were Dothideomycetes (61–65%) and Tremellomycetes (10–11%), while Cladosporium and Aureobasidium were the most common fungal genera in V. amurensis and V. coignetiae, respectively. A comparative analysis of the endophytic communities of V. amurensis and V. coignetiae with the previously reported endophytic communities of V. vinifera revealed that the bacterial biodiversity of V. amurensis and V. coignetiae was similar in alpha diversity to V. vinifera’s bacterial biodiversity. The fungal alpha diversity of V. amurensis and V. coignetiae was statistically different from that of V. vinifera. The beta diversity analysis of bacterial and fungal endophytes showed that samples of V. vinifera formed separate clusters, while V. amurensis samples formed a separate cluster including V. coignetiae samples. The data revealed that the endophytic community of bacteria and fungi from wild V. amurensis was richer than that from V. coignetiae grapes and cultivated V. vinifera grapes. Therefore, the data obtained in this work could be of high value in the search for potentially useful microorganisms for viticulture.

… Studies have shown that root exudates shape the microbiome … , modulate the rhizosphere microbiome to improve plant growth … microbiome assembly, shape the “functional microbiome” (…

Plant–microbe interactions in the phyllosphere provide invaluable information on plant ecology, with implications for ecosystem functioning and plant–atmosphere feedbacks. The composition of phyllosphere microbes varies significantly depending on host lineages, geographic regions, and climatic conditions. However, the factors driving these variations in interactions with plants remain poorly understood. Biogenic volatile organic compounds (BVOCs) emitted by plants may be important in these interactions. Here, we quantified the composition of phyllosphere microbial communities and terpene emissions from leaves of Japanese cedar (Cryptomeria japonica) trees grown in two common gardens from cuttings collected from natural populations across Japan. Amplicon sequencing revealed that microbial communities differed significantly between gardens and among host populations. Analysis of BVOC profiles showed that the camphene and total terpene emission rates were associated with bacterial composition, whereas that of ent-kaurene was marginally linked to fungal composition. The relative abundances of certain fungal genera that include the species reported to cause disease in Japanese cedar, the emission rates of most monoterpenes and a sesquiterpene β-farnesene were correlated with the climatic conditions at the origin sites of the cedar trees. These findings highlight the intricate relationships between phyllosphere microbes and terpene emission from host trees and suggest the role of climatic factors in shaping these associations.

… The Botanical Garden has a cistern that catches rain- our lifetimes in built environments in many parts of the world, water and serves as a reservoir for watering of the plants. Two this is …

A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys. We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria–Bertani (LB), LB01, yeast extract–mannitol (YMA), yeast extract–flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies. This study gives first insights into the total bacterial community of the H. helix phylloplane, including an evaluation of its culturability using five different growth media. We further provide a collection of 200 bacterial isolates underrepresented in current databases, including the characterization of PGP profiles. Here we highlight the potential of simple strategies to obtain higher microbial diversity from environmental samples and the use of high-throughput sequencing to guide isolate selection from a variety of growth media.

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seed, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a thus-far-neglected reservoir of phyllosphere microbiota. Therefore, rain microbiota were compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S ribosomal RNA amplicon sequencing, 104 operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomato plants exposed to rain outdoors than on tomato plants grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

ABSTRACT Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves. Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.

Significance The role of flowers as environmental filters for bacterial communities and the provenance of bacteria in the phyllosphere are currently poorly understood. We experimentally tested the effect of induced variation in soil communities on the microbiota of plant organs. We identified soil-derived bacteria in the phyllosphere and show a strong convergence of floral communities with an enrichment of members of the Burkholderiaceae family. This finding highlights a potential role of the flower in shaping the interaction between plants and a bacterial family known to harbor both plant pathogens and growth-promoting strains. Because the flower involves host–symbiont feedback, the selection of specific bacteria by the reproductive organs of angiosperms could be relevant for the modulation of fruit and seed production. Leaves and flowers are colonized by diverse bacteria that impact plant fitness and evolution. Although the structure of these microbial communities is becoming well-characterized, various aspects of their environmental origin and selection by plants remain uncertain, such as the relative proportion of soilborne bacteria in phyllosphere communities. Here, to address this issue and to provide experimental support for bacteria being filtered by flowers, we conducted common-garden experiments outside and under gnotobiotic conditions. We grew Arabidopsis thaliana in a soil substitute and added two microbial communities from natural soils. We estimated that at least 25% of the phyllosphere bacteria collected from the plants grown in the open environment were also detected in the controlled conditions, in which bacteria could reach leaves and flowers only from the soil. These taxa represented more than 40% of the communities based on amplicon sequencing. Unsupervised hierarchical clustering approaches supported the convergence of all floral microbiota, and 24 of the 28 bacteria responsible for this pattern belonged to the Burkholderiaceae family, which includes known plant pathogens and plant growth-promoting members. We anticipate that our study will foster future investigations regarding the routes used by soil microbes to reach leaves and flowers, the ubiquity of the environmental filtering of Burkholderiaceae across plant species and environments, and the potential functional effects of the accumulation of these bacteria in the reproductive organs of flowering plants.

ABSTRACT The oomycete pathogen Phytophthora palmivora, which causes black pod rot (BPR) on cacao (Theobroma cacao L.), is responsible for devastating yield losses worldwide. Genetic variation in resistance to Phytophthora spp. is well documented among cacao cultivars, but variation has also been observed in the incidence of BPR even among trees of the same cultivar. In light of evidence that the naturally occurring phyllosphere microbiome can influence foliar disease resistance in other host-pathogen systems, it was hypothesized that differences in the phyllosphere microbiome between two field accessions of the cultivar Gainesville II 164 could be responsible for their contrasting resistance to P. palmivora. Bacterial alpha diversity was higher but fungal alpha diversity was lower in the more resistant accession MITC-331, and the accessions harbored phyllosphere microbiomes with distinct community compositions. Six bacterial and 82 fungal amplicon sequence variants (ASVs) differed in relative abundance between MITC-333 and MITC-331, including bacterial putative biocontrol agents and a high proportion of fungal pathogens, and nine fungal ASVs were correlated with increased lesion development. The roles of contrasting light availability and host mineral nutrition, particularly potassium, are also discussed. Results of this preliminary study can be used to guide research into microbiome-informed integrated pest management strategies effective against Phytophthora spp. in cacao. IMPORTANCE Up to 40% of the world’s cacao is lost each year to diseases, the most devastating of which is black pod rot, caused by Phytophthora palmivora. Though disease resistance is often attributed to cacao genotypes (i.e., disease-resistant rootstocks), this study highlights the role of the microbiome in contributing to differences in resistance even among accessions of the same cacao cultivar. Future studies of plant-pathogen interactions may need to account for variation in the host microbiome, and optimizing the cacao phyllosphere microbiome could be a promising new direction for P. palmivora resistance research. Up to 40% of the world’s cacao is lost each year to diseases, the most devastating of which is black pod rot, caused by Phytophthora palmivora. Though disease resistance is often attributed to cacao genotypes (i.e., disease-resistant rootstocks), this study highlights the role of the microbiome in contributing to differences in resistance even among accessions of the same cacao cultivar. Future studies of plant-pathogen interactions may need to account for variation in the host microbiome, and optimizing the cacao phyllosphere microbiome could be a promising new direction for P. palmivora resistance research.

… Phyllosphere microbiota of tea plants play a key role in the … investigating the soil-phyllosphere continuum and revealing … tea phyllosphere microbial diversity in tea gardens ecosystem…

Phyllosphere bacteria are an important component of environmental microbial communities and are closely related to plant health and ecosystem stability. However, the relationships between the inhabitation and assembly of phyllosphere bacteria and leaf microtopography are still obscure. In this study, the phyllosphere bacterial communities and leaf microtopographic features (vein density, stomatal length, and density) of eleven tree species were fully examined. Both the absolute abundance and diversity of phyllosphere bacterial communities were significantly different among the tree species, and leaf vein density dominated the variation. TITAN analysis showed that leaf vein density also played more important roles in regulating the relative abundance of bacteria than stomatal features, and 6 phyla and 62 genera of phyllosphere bacteria showed significant positive responses to leaf vein density. Moreover, LEfSe analysis showed that the leaves with higher vein density had more bacterial biomarkers. Leaf vein density also changed the co-occurrence pattern of phyllosphere bacteria, and the co-occurrence network demonstrated more negative correlations and more nodes on the leaves with larger leaf vein density, indicating that higher densities of leaf veins improved the stability of the phyllosphere bacterial community. Phylogenetic analysis showed that deterministic processes (especially homogeneous selection) dominated the assembly process of phyllosphere bacterial communities. The leaf vein density increased the degree of bacterial clustering at the phylogenetic level. Therefore, the inhabitation and assembly of the phyllosphere bacterial community are related to leaf microtopography, which provides deeper insight into the interaction between plants and bacteria.

Plant microbiomes and immune responses have coevolved through history, and this applies just as much to the phyllosphere microbiome and defense phytohormone signaling. When in homeostasis, the phyllosphere microbiome confers benefits to its host. However, the phyllosphere is also dynamic and subject to stochastic events that can modulate community assembly. Investigations into the impact of defense phytohormone signaling on the microbiome have so far been limited to culture-dependent studies; or focused on the rhizosphere. In this study, the impact of the foliar phytohormone salicylic acid (SA) on the structure and composition of the phyllosphere microbiome was investigated. 16S rRNA amplicons were sequenced from aerial tissues of two Arabidopsis mutants that exhibit elevated SA signaling through different mechanisms. SA signaling was shown to increase community diversity and to result in the colonization of rare, satellite taxa in the phyllosphere. However, a stable core community remained in high abundance. Therefore, we propose that SA signaling acts as a source of intermediate disturbance in the phyllosphere. Predictive metagenomics revealed that the SA-mediated microbiome was enriched for antibiotic biosynthesis and the degradation of a diverse range of xenobiotics. Core taxa were predicted to be more motile, biofilm-forming and were enriched for traits associated with microbe-microbe communication; offering potential mechanistic explanation of their success despite SA-mediated phyllospheric disturbance.

Abstract Foliar fungal communities are essential components of the plant microbiome, playing a vital role in maintaining plant health and influencing ecosystem dynamics. Despite increasing interest in plant–microbe associations, the drivers shaping foliar fungal community composition remain poorly understood, including the roles of host phylogeny, functional traits, and belowground mycorrhizal symbiosis. We used the MycoPhylo experimental field, in which plant species are planted in a replicated, phylogenetically diverse design, to investigate the influence of host plant identity, mycorrhizal type, and leaf functional traits on foliar fungal assemblages. We examined foliar fungal communities across 158 plots representing 110 distinct plant species using a metabarcoding approach. The resulting operational taxonomic units (OTUs) were dominated by Dothideomycetes (44.5%), Tremellomycetes (12.7%), and Taphrinomycetes (9.0%). Functional guild analysis revealed that plant pathogens and saprotrophs were the most abundant ecological groups. Foliar fungal alpha diversity and community composition were significantly influenced by plant growth form and mycorrhizal association. Although plant deciduousness did not affect fungal richness, it significantly affected fungal community composition. The measured leaf traits (hairiness and thickness) showed the least influence on fungal richness. Mantel tests revealed weak, guild-dependent relationships between host phylogenetic distance and foliar fungal community dissimilarity. Moreover, plant phylogenetic eigenvectors accounted for up to 25.8% of the variation in fungal richness. These findings indicate that host phylogeny and plant traits contribute to—but do not solely determine—the structure of foliar fungal assemblages under field conditions.

The phyllosphere encompasses all above‐ground plant parts, covering ~109 km2 and hosting as many as 1026 microbial cells, yet its chemical ecology remains understudied compared to the rhizosphere. This review synthesizes recent advances in metabolite‐mediated communication orchestrating phyllosphere microbiome assembly, function and host feedback. Leaf structural traits, host immune genes, developmental stage, and fluctuating environmental drivers create spatiotemporal chemical niches that filter incoming microbes. We then examine four major classes of plant‐derived signals, including primary metabolites, secondary metabolites and phytohormones, with an emphasis on their dual functionality. Microbial feedback occurs through phytohormone synthesis/catabolism, volatile and soluble effectors and antimicrobial metabolites that collectively modulate plant immunity, growth and stress tolerance while structuring inter‐microbial competition. These bidirectional exchanges form a dynamic network where plants and microbes continuously negotiate cooperation and conflict under diurnal and seasonal oscillations. We outline translational prospects, including probiotic foliar applications, metabolite priming and breeding for beneficial consortia, while identifying key challenges in signal attribution, microbiota stabilization and deciphering community‐level crosstalk dynamics for sustainable crop protection.

Phyllosphere microbiota represents a substantial but hardly explored reservoir for disease resistance mechanisms. The goal of our study was to understand the link between grapevine cultivars susceptibility to Plasmopara viticola, one of the most devastating leaf pathogens in viticulture, and the phyllosphere microbiota. Therefore, we analyzed a 16S rRNA gene library for the dominant phyllosphere bacterial phyla Alphaproteobacteria of seven Vitis genotypes at different developmental stages, i.e., flowering and harvesting, via amplicon sequencing. Young leaves had significantly higher Alphaproteobacterial richness and diversity without significant host-specificity. In contrast, the microbial communities of mature leaves were structurally distinct in accordance with P. viticola resistance levels. This statistically significant link between mature bacterial phyllosphere communities and resistant phenotypes was corroborated by beta diversity metrics and network analysis. Beyond direct host-driven effects via the provision of microhabitats, we found evidence that plants recruit for specific bacterial taxa that were likely playing a fundamental role in mediating microbe-microbe interactions and structuring clusters within mature communities. Our results on grape-microbiota interaction provide insights for targeted biocontrol and breeding strategies.

… Here, we examined bacterial communities in the leaf surface (phyllosphere) and root-associated (root and rhizospheric soil) habitats of 13 tree species. Bacterial richness substantially …

… the potential of rhizosphere engineering presents numerous … Despite being in its infancy, rhizosphere engineering has … other rhizosphere microorganisms, rhizosphere engineering may …

… rhizospheric soil samples were collected from different surveyed areas such as Gulmarg, Sonamarg, Daksum, and Kashmir University Botanical Garden (… associated with rhizosphere of …

Global ecosystems are increasingly threatened by the synergistic pressures of invasive plant species and soil microplastic contamination, yet the mechanisms by which microplastics enhance invasive species establishment remain unclear. In this study, we employ a mesocosm experiment using two types of microplastics, biodegradable polylactide (PLA), and nonbiodegradable polyvinyl chloride (PVC), to compare the responses of invasive and native plant species. We measured plant biomass, nutrient fluxes, soil enzyme activities, and microbial communities in the rhizosphere using soil zymography and 16S rRNA gene sequencing. Invasive plants experienced less growth inhibition than native plants under microplastic exposure, accompanied by the selective enrichment of bacterial genera in the rhizosphere such as Arthrobacter, Sphingomonas, Microvirga, and Azospirillum. These microbes were associated with more interconnected and stable microbial networks, which may have enhanced invasive plant tolerance to microplastic-induced stress. Our results suggest that microplastics can reshape rhizosphere microbial communities in ways that have profound implications for ecological restoration and invasive species management. Future research should experimentally validate the functional roles of these enriched microbial taxa in promoting plant resilience under environmental stress.

… denseserrulata seedlings were collected from the Wuhan Botanical Garden of the Chinese … in the rhizosphere, thus altering the structure of the rhizosphere microbial community. …

This study aimed to reveal the effects of crude oil addition on the characteristics of soil microbial communities and ecosystem multifunctionality in Achnatherum splendens and Pennisetum alopecuroides. Specifically, it explored how crude oil addition influences the relationship between soil nutrient regulation, microbial community characteristics, and ecosystem multifunctionality. The results indicated that as crude oil addition increased, the Shannon index and Chao1 index for soil bacteria and fungi in both Achnatherum splendens and Pennisetum alopecuroides increased. Conversely, while the Shannon index for soil archaea in both species increased, the Chao1 index decreased. The ecological network analysis indicated that a strong collaborative relationship existed between species in the soil bacterial communities of Achnatherum splendens and Pennisetum alopecuroides exposed to 10 g/kg crude oil, as well as between species in the soil fungal and archaeal communities of Achnatherum splendens exposed to 40 g/kg crude oil. A strong collaborative relationship was also observed between species in the soil fungal and archaeal communities of Pennisetum alopecuroides exposed to 10 g/kg crude oil. The bacterial and fungal communities exerted a significant direct negative regulatory effect on the soil ecosystem multifunctionality of Achnatherum splendens and Pennisetum alopecuroides, while the archaeal communities had a significant direct positive regulatory effect. Additionally, the multifunctionality index of the soil ecosystem in Achnatherum splendens and Pennisetum showed a significant decline with increasing crude oil addition. This is likely due to the higher toxicity of high-concentration crude oil, which negatively impacts the soil biological community, leading to reduced biodiversity and disruptions in nutrient cycles. This study explores the characteristics of bacterial, fungal, and archaeal communities and ecosystem multifunctionality under different levels of crude oil, which can provide theoretical support for evaluating the restoration of Achnatherum splendens and Pennisetum alopecuroides from crude oil pollution.

RIPENING-INHIBITOR (RIN) transcriptional factor is a central gene governing fruit ripening. While RIN also affects other physiological signals, its potential role in triggering interactions with rhizosphere microbiome and plant health is unknown. Here we show that RIN affects microbiome-mediated disease resistance via root exudation, leading to recruitment of microbiota that suppresses soil-borne, phytopathogenic Ralstonia solanacearum bacterium. Compared to the wildtype (WT) plant, RIN mutants (rin and rin-KO) had different root exudate profiles, which were associated with distinct changes in the microbiome composition and diversity. Specifically, the relative abundances of antibiosis-associated genes and pathogen-suppressing Actinobacteria (Streptomyces) were clearly lower in the rhizosphere of rin mutants. The composition, diversity and suppressiveness of rin plant microbiomes could be restored using 3-hydroxyflavone and riboflavin exudates, which were exudated much less by the rin mutant. Interestingly, RIN-mediated effects on root exudates, Actinobacteria and disease suppression were evident from the seedling stage, indicating that RIN plays a dual role in the early assembly of disease-suppressive microbiota and late fruit development. Our work suggests that while plant disease resistance is a complex trait driven by interactions between the plant, rhizosphere microbiome and the pathogen, it can be indirectly manipulated using 'prebiotic' compounds that promote the recruitment of disease-suppressive microbiota.

Trees are essential to ecosystems in both natural and urban environments, yet they are increasingly threatened by abiotic and biotic stresses linked to climate change and human activities. The use of microbial-based approaches and microbiome engineering to safeguard plants and crop production is promising, but their application in trees raises specific challenges. Here, we review knowledge on the tree microbiome and outline opportunities to leverage tree-associated microbial communities. We describe the specific challenges inherent to working with tree species and highlight how Synthetic Microbial Communities (SynComs) can be used to study and engineer tree microbiomes. Finally, we propose that future research priorities include (1) developing model tree systems for experimental work, (2) obtaining tree-specific culture collections and SynComs, and (3) optimising methods for tree SynCom inoculation. Unlocking these methodological challenges will enable us to realise the potential of the tree microbiome and address global challenges in tree health and the provision of ecosystem services.

Rhizosphere microbial colonization of the tea plant provides many beneficial functions for the host, But the factors that influence the composition of these rhizosphere microbes and their functions are still unknown. In order to explore the interaction between tea plants and rhizosphere microorganisms, we summarized the current studies. First, the review integrated the known rhizosphere microbial communities of tea tree, including bacteria, fungi, and arbuscular mycorrhizal fungi. Then, various factors affecting tea rhizosphere microorganisms were studied, including: endogenous factors, environmental factors, and agronomic practices. Finally, the functions of rhizosphere microorganisms were analyzed, including (a) promoting the growth and quality of tea trees, (b) alleviating biotic and abiotic stresses, and (c) improving soil fertility. Finally, we highlight the gaps in knowledge of tea rhizosphere microorganisms and the future direction of development. In summary, understanding rhizosphere microbial interactions with tea plants is key to promoting the growth, development, and sustainable productivity of tea plants.

Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. The plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume-rhizobia symbiosis, in their roots. Nevertheless, the relationship between the AM and rhizobial symbioses in native soil is poorly understood. Here, we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula, by quantitative microbiota profiling (QMP) of 16S rRNA genes. We found that M. truncatula mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load (quantitative abundance) in rhizosphere and roots, and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native soil. Moreover, quantitative microbial co-abundance network analyses revealed that the AM symbiosis impacts Rhizobiales-hubs among the plant microbiota and benefit the plant holobiont. Through QMP of rhizobial rpoB and AM fungal SSU rRNA genes, we revealed a new layer of interaction, whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of M. truncatula. We further showed that AM symbiosis-conditioned microbial communities within the M. truncatula rhizosphere could promote nodulation in different legume plants in native soil. Given that the AM and rhizobial symbioses are critical for crop growth, our findings might inform strategies to improve agricultural management. Moreover, our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.

… stomatal adjustments enhance FZB42 rhizosphere colonization through root exudate-… by ABA signaling components, shows temporal overlap with the initial stages of rhizosphere …

Phytoremediation that depends on excellent plant resources and effective enhancing measures is important for remediating heavy metal-contaminated soils. This study investigated the cadmium (Cd) tolerance and accumulation characteristics of Dahlia pinnata Cav. to evaluate its Cd phytoremediation potential. Testing in soils spiked with 5–45 mg kg–1 Cd showed that D. pinnata has a strong Cd tolerance capacity and appreciable shoot Cd bioconcentration factors (0.80–1.32) and translocation factors (0.81–1.59), indicating that D. pinnata can be defined as a Cd accumulator. In the rhizosphere, Cd stress (45 mg kg–1 Cd) did not change the soil physicochemical properties but influenced the bacterial community composition compared to control conditions. Notably, the increased abundance of the bacterial phylum Patescibacteria and the dominance of several Cd-tolerant plant growth–promoting rhizobacteria (e.g., Sphingomonas, Gemmatimonas, Bryobacter, Flavisolibacter, Nocardioides, and Bradyrhizobium) likely facilitated Cd tolerance and accumulation in D. pinnata. Comparative transcriptomic analysis showed that Cd significantly induced (P < 0.001) the expression of genes involved in lignin synthesis in D. pinnata roots and leaves, which are likely to fix Cd2+ to the cell wall and inhibit Cd entry into the cytoplasm. Moreover, Cd induced a sophisticated signal transduction network that initiated detoxification processes in roots as well as ethylene synthesis from methionine metabolism to regulate Cd responses in leaves. This study suggests that D. pinnata can be potentially used for phytoextraction and improves our understanding of Cd-response mechanisms in plants from rhizospheric and molecular perspectives.

Garden waste compost (GWC) has been applied as an amendment to improve the desalination efficiency, nutrient availability and diversity of the microbial community in coastal saline soil. Understanding the response of the microbial community to garden waste compost application is of great significance in coastal ecological restoration. Four treatments were established: CK, nonamended control; T1, application of 68 kg·m−3 garden waste compost; T2, application of 15 kg·m−3 bentonite; and T3, a mixture of garden waste compost and bentonite. In addition, soil physicochemical properties, soil enzymes, microbial biomass carbon and the soil microbial community were measured. The results show that T3 had a more significant effect on increasing soil enzymes, as well as microbial biomass carbon and nitrogen, urease, sucrase and dehydrogenase activities. Based on the relative abundance, microbial diversity and linear discriminant effect size (LEfSe) analyses, the amendments can be seen to have increased the microbial abundance and alpha diversity of the bacterial structure and also altered the microbial community structure. RDA and Pearson correlation analysis at the phylum level indicated that available nitrogen, total porosity, hydraulic conductivity, bulk density and EC were the primary determinants of microbial communities associated with this amendment. In conclusion, the application of garden waste compost enables more microorganisms to participate in the soil material cycle, indicating that garden waste composting is beneficial to the restoration of coastal soils.

Biological soil health is recognized as an important component of sustainable agriculture due to microbial biomineralization of nutrients. However, soil health can be difficult to assess consistently across urban agricultural systems due to diverse land use histories, soil heterogeneity, and lack of mechanistic links to agricultural management practices (e.g., recycled compost addition) and crop outcomes. In this study, we characterized soil microbial activity profiles in an urban agriculture system in Minnesota, USA, including microbial abundance, soil respiration, extracellular enzyme activity, and crop yield. Garden plots were fertilized with recycled organic compost (either manure or municipal) at high or low rates (ranging from 2.6 to 39 tons ha−1) targeted to crop N and P demands. Control plots received inorganic fertilizer or no fertilizer. We found that a high application rate of manure compost supported 6–10x higher basal respiration than municipal compost or inorganic fertilizer. Enzyme activity data demonstrated that soil microbial communities exhibited unique profiles of biochemical function that varied among fertilizers of different compositions. Microbial biochemical function predicted 50% of the variability in bell pepper (Capsicum annuum) yield, while soil microbial community size alone was a poor predictor of yield. Yield was highest in plots fertilized with municipal compost, outperforming inorganic fertilizer by threefold. High‐yield plots exhibited higher ratios of N to P enzyme activity compared to those with lower yield. Our findings demonstrate that “more is better” may not necessarily be true regarding soil microorganisms in biological soil health, and that measures of soil microbial biochemical function may be more important.

Sewage sludge (SS) and garden waste (GW) compost can be used as soil amendments to improve the soil environment. Studies done till date have been focused on the changes of harmful substances during sludge composting, but the safety and efficacy of SS and GW composting on woodland soil environment are still unclear. In the study, a field experiment was performed using to investigate the safety and efficacy of SS and GW compost as a soil amendment on woodland soil. Soil nutrients (such as nitrogen, phosphorus and potassium), organic matter and electrical conductivity were significantly increased after the addition of the SS and GW compost, while there were no significant changes in soil heavy metals content and soil enzyme activities. From these soil properties, it was found that SS and GW compost was safe and efficacious in improving the soil environment. The application of SS and GW compost had no significant effect on microbial diversity. Co-occurrence network analysis revealed that SS and GW compost efficaciously enhanced the interaction between bacterial communities, which proved that it was safe and efficacious. Furthermore, SS and GW compost enhanced ABC transporters and carbohydrate metabolism of bacterial community, while reduced the pathotroph action (such as the plant pathogen) and wood saprotrophs. Overall, these results proved the safety and efficacy of SS and GW compost as soil amendments after being added to the soil. This study contributes to the use of harmless treatments and reutilization processes of SS and GW.

With increasing urbanization and critical issues of food insecurity emerging globally, urban agriculture is expanding as an agroecosystem with a distinct soil type. Growing food in cities is challenged by legacy contaminants in soils, which necessitates the use of imported, safe soils and composts. To promote the long-term sustainability of urban agriculture, we examined the agronomic potential of constructing safe, locally sourced soils to support food production. We collected composts from four municipal composting facilities in New York City: Big Reuse, Long Island City, Queens (BRL), New York Department of Sanitation, Fresh Kills, Staten Island (DNY), Lower Eastside Ecology Center (LES) and Queens Botanic Garden (QBG). We then created two types of constructed soils using each compost: 100% pure compost and a 50:50 blend of compost and clean excavated sediments from the New York City Clean Soil Bank. We then assessed the growth of tomato, pepper and kale in the constructed soils within a plant growth chamber facility. We found Clean Soil Bank sediments enhanced tomato aboveground biomass production by 98%, kale aboveground biomass production by 50% and pepper plant height by 52% when mixed with compost from BRL. At the same time, Clean Soil Bank Sediments decreased tomato plant height by 16% and aboveground biomass production by 29% in LES compost and tomato plant height by 18% in QBG compost, likely due to compost properties. The addition of Clean Soil Bank sediments showed no decline in the symbiosis of arbuscular mycorrhizal fungi across all composts, which is an important beneficial plant–microbe interaction in agroecosystems. A positive ecosystem service was found when Clean Soil Bank sediments were added to municipal composts, with up to a 74% decrease in greenhouse gas emissions of soil CO2 in BRL compost. The results indicate that urban agricultural soils can be constructed using clean, locally sourced materials, such as composted organic waste and excavated sediments from city development sites to support sustainable urban agriculture while enhancing ecosystem services.

… Objective Resource utilization of garden waste is an effective way to improve soil fertility … of garden waste on soil chemical properties and microbial community in the plantation soil can …

There is a paucity of data on the state of urban agriculture soils. In order to develop efficient management practices, it is necessary to understand the seasonal dynamics of the soil health of these systems. This study sampled two community gardens, and one commercial urban agriculture site on a monthly basis over the span of one year. The dynamic analysis examined soil nutritional, chemical and microbial properties. Plant biodiversity was significantly higher in community gardens compared to commercial sites. Analysis of soil nutrients revealed fluctuations of mineral nitrogen with seasonal conditions and consistently high concentrations of plant-available phosphorus. We identified gradually decreasing soil total nitrogen and carbon concentrations throughout the year. Soils were abundant in arbuscular mycorrhizal fungi spores. Soil metabarcoding using 16S and ITS amplicons revealed a seasonal gradient of the microbial diversity and changes after the application of organic fertilizer. Soil-borne potential human pathogens were also detected in the soils. The results of this study provide relevant information about soil management principles in urban agriculture systems. These principles include mulching and the use of nutrient-balanced composts to counteract decreasing carbon pools and the excessive accumulation of phosphorus.

Community gardens, as common spaces where people gather to grow food, help foster public health, greener urban environments, life‐long learning and vibrant communities. However, despite being promoted as sustainable horticulture and conservation agriculture, their soil health and carbon (C) sequestration potential, with implication for climate change mitigation, remains underexplored. This study assessed soil samples collected from raised beds (gardening area) and adjacent bare ground (control) at six community gardens in the Perth metropolitan area, Australia. These sites covered three soil mapping units (SMUs): calcareous deep sands, coloured sand and pale sands The soil in raised beds exhibited superior characteristics than surrounding urban soil including lower bulk density, higher pH buffering capacity, available nutrients including nitrogen (N), phosphorus (P) and potassium (K), cation exchange capacity (CEC), total C and microbial biomass. Notably, we estimated that raised bed soils accumulated significant levels of C in the top 10 cm layer (0.55 kg/m2 or 5.5 T/ha). Our findings also indicate no significant heavy metal contamination in any of the community garden soils. Although the global area of community gardens is marginally small, these results suggest they hold potential for carbon sequestration, especially in urban and peri‐urban environments. The improved soil health and C storage potential in community garden soil are largely attributed to the regular application of compost produced within the community gardens.

In this study, we evaluated the impact of washing of Pb, Zn and Cd contaminated soil using EDTA-based technology (ReSoil®) on soil biological properties by measuring some of the most commonly used/sensitive biological indicators of soil perturbation. We estimated the temporal dynamics of the soil respiration, the activities of soil enzymes (dehydrogenase, β-glucosidase, urease, acid and alkaline phosphatase), and the effect of the remediation process on arbuscular mycorrhizal (AM) fungi in original (Orig), remediated (Rem) and remediated vitalized (Rem+V) soils during a more than one-year garden experiment. ReSoil® technology initially affected the activity level of soil microbial respiration and all enzyme activities except urease and reduced AM fungal potential in the soil. However, after one year of vegetable cultivation and standard gardening practices, soil microbial respiration, acid and alkaline phosphatase in the Rem and Rem+V reached similar activities as in the Orig. Only the activities of dehydrogenase and β-glucosidase remained lower in the remediated soil compared to the Orig. The frequency of arbuscular mycorrhiza in the root system, arbuscular density in the colonized root fragment, and the intensity of mycorrhizal colonization in the colonized root fragments in the remediated treatments increased with time; at the end of the experiment, no consistent differences in these parameters of mycorrhizal colonization were found among the treatments. Our results suggest a restored biological functioning of the remediated soil after one year of vegetable cultivation. In general, no differences were found between the Rem and Rem+V treatments, indicating that simple common garden practices are sufficient to restore soil functioning after remediation.

Soils in urban settings are often degraded, which can prevent growers from optimizing the health and productivity of their crops. In this study, we investigated whether amending soil with a locally made leaf‐mold compost could (a) improve soil chemical and biological properties, (b) increase survival of a microbial inoculant with plant growth promoting and disease suppressive capabilities, and (c) enhance the yield and quality of a tomato crop. Results were promising, with dramatically greater concentrations of active soil organic matter (SOM) and marketable fruit in plots receiving the amendment in both years of the study. Foliar disease severity was also lower in compost‐amended plots in the second year of the trial. Inoculating tomato (Solanum lycopersicum L.) transplants with Trichoderma harzianum T‐22 reduced deaths that are due to transplant stress in one of the cultivars evaluated, and the compost supported greater populations of this microbe in soil demonstrating that it is possible to enhance the efficacy of beneficial microbial inoculants in field settings using targeted practices. These results indicate that urban farmers can improve the productivity of their farms by amending soils with leaf mold compost, which will help ensure the long‐term sustainability of urban farming initiatives. However, all composts should be tested to ensure they do not contain toxic levels of heavy metals or pathogens, and farmers should avoid overapplication since this can reduce crop health and lead to environmental challenges.

… urban agricultural soil from the San Francisco Bay Area (USA). We hypothesized that organic soil amendments could enhance microbial abundance, activity, and diversity in urban soils, …

(1) Aims: This study was aimed to investigate the effects of organic and inorganic fertilizer application on the soil nutrients and microbiota in tea garden soil. (2) Method: Illumina Hiseq sequencing technique was conducted to analyze the microbial diversity and density in different fertilizer-applied tea garden soil. (3) Results: The results showed that Acidobacteria, Proteobacteria and Actinobacteria were the predominant bacterial species observed in the tea garden soil. Besides, the relative abundance of Basidiomycota, Ascomycota and Zygomycota fungal species were higher in the tea garden soil. Correlation analysis revealed that Acidibacter and Acidothermus were significantly correlated with chemical properties (such as total organic carbon (TOC), total phosphorus (TP) and available phosphorus (AP) contents) of the tea garden soil. Furthermore, all these microbes were abundant in medium rapeseed cake (MRSC) + green manure (GM) treated tea garden soil. (4) Conclusion: Based on the obtained results, we conclude that the application of MRSC + GM could be a preferred fertilizer to increase the soil nutrients (TOC, TP and AP content) and microbial population in the tea garden soil.

Abstract This study evaluated the phytoremediation potential of pot marigolds on green wall systems for removing soil cadmium. The experiment was a factorial arrangement in a randomized complete block design. The first factor was cadmium (0, 1, 2, and 3 mg/kg soil), and the second was seven single or mixed plant growth-promoting rhizobacteria (PGPR) and the control treatments. All root and flower-related traits significantly increased after bacterial treatments (p ≤ 0.05). Substrates inoculated with Thiobacillus thioparus strain 300, Mix2 (Aztobactor chorococcum strain D0941 + Azosporillum liposferum strain So131), and Mix3 (Thiobacillus thioparus strain 300+ Pseudomonas putida strain G0951+ Aztobactor chorococcum strain D0941+ Azosporillum liposferum strain So131) increased phytoremediation of pot marigold in roots and shoots up to 3 mg/kg soil cadmium. The transfer factor (TF) was under one in flowers, showing the low potential of the flowers for phytoremediation. TF was above one in aerial vegetative plant sections, indicating the species as a cadmium accumulator and extractor for managing cadmium contaminant sites. Based on purification ratios and transfer factors, Thiobacillus thiolates (alone or combined) is recommended for enhancing pot marigold esthetics in landscapes, while Pseudomonas strains (single or mixed) improve its phytoremediation potential in urban green infrastructure. NOVELTY STATAMENT This study introduces an innovative approach to sustainable green infrastructure by developing multifunctional green walls capable of remediating cadmium, a common urban heavy metal pollutant. Utilizing Calendula officinalis (pot marigold) and plant growth-promoting bacteria, the system leverages nature-based solutions for urban sustainability. Unlike conventional wastewater treatment, which faces high costs and technical challenges, this approach integrates phytoremediation with esthetic and functional benefits. Using low-quality irrigation water, the study demonstrates a practical strategy for enhancing urban landscaping while mitigating pollution, offering a cost-effective and scalable solution for sustainable city environments. The findings provide practical insights for urban, industrial, and agricultural sectors, demonstrating how natural systems can be leveraged for heavy metal remediation and sustainable urban development.

A Gram-positive, rod-shaped, spore-forming, aerobic bacterium, with biocontrol potential designated as RMG6T, was isolated from the rhizosphere of the mulberry plant located in the mulberry garden of Raiganj University, West Bengal, India. The strain demonstrated significant antimicrobial activity against Enterococcus faecalis MTCC 439 (1.92 cm inhibition zone) and Escherichia coli MTCC 43 (1.62 cm inhibition zone) in agar-well diffusion assays. Scanning electron microscopy (SEM) confirmed bacterial cell lysis and cytoplasmic leakage. Phylogenetic analysis of the 16S rDNA sequence (1545 bp) revealed that RMG6T is closely associated to Bacillus siamensis KCTC 13,613 (99.93% similarity). Additionally, multilocus sequence analysis (MLSA) suggested that RMG6T represents a novel Bacillus species. The morphological characteristics of RMG6T colonies further distinguished it from closely related Bacillus species. RMG6T remained unidentified through Vitek-2 analysis. Fatty acid methyl ester (FAME) profiling revealed the predominant cellular fatty acids in RMG6T were anteiso-C15:0 (28.13%), iso-C15:0 (20.72%), C18:0 (10.72%), iso-C17:0 (7.00%), iso-C16:0 (5.88%), and anteiso-C17:0 (5.87%). MALDI-TOF MS analysis validated that RMG6T belongs to Bacillus genus. RMG6T exhibited optimal growth at 35 °C, pH 6, and up to 14% NaCl tolerance. The strain produced indole-3-acetic acid (IAA) through the indole-3-pyruvic acid pathway, with a maximum yield of 73.4 µg/mL at 0.2% L-tryptophan supplementation. The Vigna radiata seed germination assay validated its plant growth-promoting potential, with significantly enhanced radicle growth compared to control treatments, highlighting the potential of RMG6T for cross-species bioaugmentation. Antibiotic susceptibility profiling revealed that RMG6T was resistance to beta-lactam antibiotics, aligning with the genomic identification of resistance genes. Whole-genome sequencing (3,818,111 bp; G + C content 46.62%) identified 3723 coding sequences, including biosynthetic gene clusters (BGCs) associated with antimicrobial compound biosynthesis. Moreover, the highest recorded values for average nucleotide identity (ANI) and Genome-to-Genome Distance Calculator 3.0 analysis were 94.44 and 56.80%, respectively, with Bacillus siamensis KCTC 13,613. Comparative genomic and phylogenomic analyses confirmed the novelty of RMG6T, leading to its proposed designation as Bacillus ayatagriensis sp. nov., with RMG6T (= MCM-B-1537). We propose Bacillus ayatagriensis RMG6T as a novel species with significant biocontrol potential and plant growth-promoting capabilities, advocating its expanded use in agriculture and industry.

Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.

Centella asiatica is a traditional herbaceous plant with numerous beneficial effects, widely known for its medicinal and cosmetic applications. Maximizing its growth can lead to beneficial effects, by focusing on the use of its active compounds. The use of plant growth-promoting rhizobacteria (PGPR) is known to be an alternative to chemical fertilizers. In this study, we used the PGPR Priestia megaterium HY-01 to increase the yield of C. asiatica. In vitro assays showed that HY-01 exhibited plant growth-promoting activities (IAA production, denitrification, phosphate solubilization, and urease activity). Genomic analyses also showed that the strain has plant growth-promoting-related genes that corroborate with the different PGP activities found in the assays. This strain was subsequently used in field experiments to test its effectiveness on the growth of C. asiatica. After four months of application, leaf and root samples were collected to measure the plant growth rate. Moreover, we checked the rhizosphere microbiome between the treated and non-treated plots. Our results suggest that treatment with Hyang-yak-01 not only improved the growth of C. asiatica (leaf length, leaf weight, leaf width, root length, root width, and chlorophyll content) but also influenced the rhizosphere microbiome. Biodiversity was higher in the treated group, and the bacterial composition was also different from the control group.

Plant-growth-promoting rhizobacteria (PGPR) play an important role in plant growth and rhizosphere soil. In order to evaluate the effects of PGPR strains on tea plant growth and the rhizosphere soil microenvironment, 38 PGPR strains belonging to the phyla Proteobacteria with different growth-promoting properties were isolated from the rhizosphere soil of tea plants. Among them, two PGPR strains with the best growth-promoting properties were then selected for the root irrigation. The PGPR treatment groups had a higher Chlorophyll (Chl) concentration in the eighth leaf of tea plants and significantly promoted the plant height and major soil elements. There were significant differences in microbial diversity and metabolite profiles in the rhizosphere between different experimental groups. PGPR improved the diversity of beneficial rhizosphere microorganisms and enhanced the root metabolites through the interaction between PGPR and tea plants. The results of this research are helpful for understanding the relationship between PGPR strains, tea plant growing, and rhizosphere soil microenvironment improvement. Moreover, they could be used as guidance to develop environmentally friendly biofertilizers with the selected PGPR instead of chemical fertilizers for tea plants.

Microbiomes are the most important members involved in the regulation of soil nitrogen metabolism. Beneficial interactions between plants and microbiomes contribute to improving the nitrogen utilization efficiency. In this study, we investigated the Apiaceae medicinal plant Angelica dahurica var. formosana. We found that under a low-nitrogen treatment, the abundance of carbon metabolites in the rhizosphere secretions of A. dahurica var. formosana significantly increased, thereby promoting the ratio of C to N in rhizosphere and nonrhizosphere soils, increasing carbon sequestration, and shaping the microbial community composition, thus promoting a higher yield and furanocoumarin synthesis. Confirmation through the construction of a synthetic microbial community and feedback experiments indicated that beneficial plant growth-promoting rhizobacteria play a crucial role in improving nitrogen utilization efficiency and selectively regulating the synthesis of target furanocoumarins under low nitrogen conditions. These findings may contribute additional theoretical evidence for understanding the mechanisms of interaction between medicinal plants and rhizosphere microorganisms.

… bacterial taxa and enriches metabolically versatile taxa within Proteobacteria, increasing community-level antagonistic … to pathogen inhibition, yielding suppression beyond individual or …

The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.

Microbial-root associations are important to help plants cope with abiotic and biotic stressors. Managing these interactions offers an opportunity for improving the efficiency and sustainability of agricultural production. By characterizing the bacterial and archaeal community (via 16S rRNA sequencing) associated with bulk and rhizosphere soil of sixteen strawberry cultivars in two controlled field studies, we explored the relationships between the soil microbiome and plant resistance to two soil-borne fungal pathogens (Verticillium dahliae and Macrophomina phaseolina). Overall, the plants had a distinctive and genotype-dependent rhizosphere microbiome with higher abundances of known beneficial bacteria such as Pseudomonads and Rhizobium. The rhizosphere microbiome played a significant role in the resistance to the two soil-borne pathogens as shown by the differences in microbiome between high and low resistance cultivars. Resistant cultivars were characterized by higher abundances of known biocontrol microorganisms including actinobacteria (Arthrobacter, Nocardioides and Gaiella) and unclassified acidobacteria (Gp6, Gp16 and Gp4), in both pathogen trials. Additionally, cultivars that were resistant to V. dahliae had higher rhizosphere abundances of Burkholderia and cultivars resistant to M. phaseolina had higher abundances of Pseudomonas. The mechanisms involved in these beneficial plant-microbial interactions and their plasticity in different environments should be studied further for the design of low-input disease management strategies.

Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for the future use in modern agriculture.

Abstract Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities’ niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities’ niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity.

Bacillus velezensis strain GB03 is a Gram-positive rhizosphere bacterium known for its ability to promote plant growth and immunity. This review provides a comprehensive overview of the research on GB03 from its initial discovery in Australian wheat fields in 1971 to its current applications. Recognized as a model plant growth-promoting rhizobacterium (PGPR), GB03 has exhibited outstanding performance in enhancing the growth and protection of many crop plants including cucumber, pepper, wheat, barley, soybean, and cotton. Notably, GB03 has been reported to elicit plant immune response, referred to as induced systemic resistance (ISR), against above-ground pathogens and insect pests. Moreover, a pivotal finding in GB03 was the first-ever identification of its bacterial volatile compounds, which are known to boost plant growth and activate ISR. Research conducted over the past five decades has clearly demonstrated the potential of GB03 as an eco-friendly substitute for conventional pesticides and fertilizers. Validating its safety, the U.S. Environmental Protection Agency endorsed GB03 for commercial use as Kodiak® in 1998. Subsequently, other compounds, such as BioYield™, were released as a biological control agent against soil-borne pathogens and as a biofertilizer, utilizing a durable spore formulation. More recently, GB03 has been utilized as a keystone modulator for engineering the rhizosphere microbiome and for eliciting microbe-induced plant volatiles. These extensive studies on GB03 underscore its significant role in sustainable agriculture, positioning it as a safe and environmentally-friendly solution for crop protection.

… pumilus JZ38 and Bacillus albus JZ264 demonstrated the greatest efficacy … rhizosphere inoculant. These findings deepen the mechanistic understanding of PGPR-mediated rhizosphere …

Plant growth‒promoting rhizobacteria (PGPRs) are pivotal in forest cultivation and saline‒alkaline soil improvement by altering the structure of rhizosphere bacterial communities and improving soil nutrient utilization efficiency. However, there are few reports on the exploration of PGPR bacterial resources and the mechanism by which PGPR enhance the salt tolerance of Reaumuria soongorica (R. soongorica) in desert shrubs. This study focused on Bacillus tequilensis (B. tequilensis) S40, which is a PGPR isolated from the rhizosphere of R. soongorica by our research group. We investigated the effects of the S40 strain on the rhizosphere microbial community and functional genes of R. soongorica through pot experiments. The results demonstrated that inoculation with the S40 strain could alleviate the negative effects of NaCl stress on the plant height, total root length, and rhizome leaf biomass. Proteobacteria, Bacteroidetes, and Planctomycetota were the dominant phyla. Notably, inoculation with S40 strain significantly increased the absolute abundances of functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling (p < 0.05). Furthermore, the genes related to C, N, and P cycling were significantly correlated with soil properties (available phosphorus, urease activity, sucrase activity), and the biomass of R. soongorica leaves, stems, and roots (p < 0.05). In conclusion, the PGPR strain S40 mediates the reorganization of bacterial community, drives the element cycle, and enhances soil nutrient availability, thus promoting plant growth and enhancing salt tolerance of plants and providing a method and scientific basis for cultivating shrub seedlings and alleviating the degree of soil salinization.

… beneficial taxa such as Bacillus and Streptomyces, which may contribute to reduced abundance of soil-borne pathogens—particularly Fusarium—in the rhizosphere. This study aims to …

… ) of inoculants were evaluated by selective plating, and effects of BMc treatments on the native rhizosphere … sequencing of basal root and root tip rhizosphere of plants grown in loam. …

ABSTRACT Modulation of plant–microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant–microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa’s rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.’s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant–microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth. IMPORTANCE Plant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant–microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture. Plant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant–microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.

ABSTRACT The influence of microbially and plant-synthesized compounds on colonization of plant growth-promoting rhizobacteria (PGPR) on various regions of the plant root is underexplored. Here, we examine the influence of surfactin and glutamate on the level and specificity of colonization of Bacillus subtilis along different regions of tomato root by adding exogenous compounds and testing mutated bacterial strains. First, B. subtilis PY79 was modified to express a full-length phosphopantetheinyl transferase (sfp) native to other surfactin-producing B. subtilis strains, and surfactin biosynthesis was observed under static incubation at 25°C in plant culturing media. Microscopy was performed using PY79 sfp− (surfactin null), PY79 sfp+ (surfactin overproducing), and the wild isolate B. subtilis UD1022 to map the colonization of each strain along the entire root of young tomato plants incubated at 25°C. In addition, experiments involving supplementation of surfactin or glutamate were also performed to evaluate the root colonization of sfp+ and sfp− strains. Root mapping of a tomato seedling shows that B. subtilis prefers to colonize near the mature region of the root and that colonization patterns vary based on exogenous metabolite concentration. Inclusion of glutamate in the media or through transient priming of the plant prior to bacterial inoculation strongly promoted root colonization by B. subtilis strains (both sfp+ and sfp−). In addition, the data shows that the lab strains were less efficient in colonization compared to the wild-type B. subtilis strain. Interestingly, in the presence of glutamate, microbes lost their preference for colonization at the mature region, instead colonizing along the entire root. Overall, our work reveals a preference for colonization of these B. subtilis strains to the mature region of tomato in the absence of glutamate supplementation and demonstrates a smaller than anticipated role of biosynthesized or supplemented surfactin on root colonization, at least in a hydroponic culturing format. IMPORTANCE Plants are associated with large communities of microbes across the rhizosphere. However, comparatively little is known about the drivers underpinning the diversity of microbes, especially regarding how they are recruited by plants. Growing evidence indicates that the rhizospheric microbiome supports plant growth in response to biotic and abiotic stresses. Of late, the usage of a synthetic community of plant growth-promoting rhizobacteria (PGPR), especially Bacillus subtilis, has been recognized for its role as a potential biofertilizer and bio-fungicide agent. The role of PGPR-derived metabolites has been debated as a driver for enhanced root colonization. However, the knowledge pertaining to where and how PGPR colonize on the root surface is currently unknown. Therefore, it is prudent to elucidate the role of bacterially derived compounds and other carbon sources in the rhizosphere that drive root colonization. Plants are associated with large communities of microbes across the rhizosphere. However, comparatively little is known about the drivers underpinning the diversity of microbes, especially regarding how they are recruited by plants. Growing evidence indicates that the rhizospheric microbiome supports plant growth in response to biotic and abiotic stresses. Of late, the usage of a synthetic community of plant growth-promoting rhizobacteria (PGPR), especially Bacillus subtilis, has been recognized for its role as a potential biofertilizer and bio-fungicide agent. The role of PGPR-derived metabolites has been debated as a driver for enhanced root colonization. However, the knowledge pertaining to where and how PGPR colonize on the root surface is currently unknown. Therefore, it is prudent to elucidate the role of bacterially derived compounds and other carbon sources in the rhizosphere that drive root colonization.

The rhizosphere is a dynamic environment in which multiple microbial activities elicit phenotypical, physiological, and molecular crop responses. For a better understanding of the rhizosphere microbiome, researchers are utilizing next-generation sequencing to focus on microbiome regulations with an emphasis on multi-functional microbes. There are two main concepts currently being focused on: identifying microbial antagonists (between beneficial microbes and plant pathogens) from predominant stocks of plant-growth-promoting microbes, preferably with an aim towards bioprospecting soil-plant health; and secondly, developing a more microbially active rhizosphere through a process called rhizosphere hybridization (RH). The present review is focused on some recent studies on the outcome of RH in citrus cultivars, showing renewed functional corridors of the rhizosphere characterized by secondary metabolites providing a load-supporting functional dichotomy through elevated nutrient-supply, activated soil enzyme profiles, and improvements in root- shoot systems and plant defense enzymes. These response trade-offs collectively contributed to higher quality yield coupled with possibly a better shelf life of fruits. The rhizobiome of heritage trees viz., Azadirachta, Ficus, Dendrocalamus, Populus, Sasa, Acer, Alnus, Quercus, and Phyllostachys, could be effectively used in exercising RH. These observations on RH mean the concept could be expanded in other fruit crops, with an emphasis on developing a robust holobiont (climate-smart suppressive soils and engineering rhizosphere microbiomes for microbially engineered plants) as a part of regenerative agriculture.

Urban greening produces a large amount of garden waste, and the pyrolysis of garden waste into biochar is an effective waste management technology. Biochar has a large specific surface area and soil remediation ability. However, the knowledge about the co-recycling of sewage sludge and garden waste biochar to improve the growth of Monstera deliciosa needs to be highlighted. Therefore, we conducted a pot experiment by applying Ficus altissima litter-derived biochar (FB) at rates of 0, 1.5, and 3.0% (w/w, CK, FB1.5, and FB3) in soil amended with sewage sludge at 50% (w/w), to improve the soil properties, and further analyzed the effects of FB on growth and heavy metals (HMs) uptake of landscape plant M. deliciosa. Results showed in comparison with control setups, the addition of 3% FB treatment in sewage sludge amended soil improved the soil properties and significantly increased M. deliciosa dry weight (86.75%), root: shoot ratio (73.23%), N (99.44%), P (116.13%), K (124.40%), Pb (78.81%), and Cu (159.01%) accumulation respectively. In summary, FB3 treatment achieved the best effects in promoting plant growth and soil remediation. These findings revealed that sewage sludge and garden waste biochar could be recycled as amendments for poor acid soils under restoration, a sustainable development path for urban waste disposal.

As per Article 9 of Convention on Biological Diversity (CBD), Botanic Garden of Indian Republic (BGIR), NOIDA was established to conserve endemic and threatened plants of different habitats of the country under ex-situ conservation. Hence, an attempt is made to develop a prototype water body in sandy soil without using civil construction materials for biogenesis of aquatic flora and fauna and to conserve aquatic plants. To prevent water percolation, a thick layer of leftover bentonite wastes and a semi-permeable membrane was laid. Further, to overcome the adverse effects and to boost biogenesis, water was reclaimed by addition of fresh raw dung and organic compost in requisite proportion. As a result, microbial growth/film on the bottom of the water body, planktons and other biota were generated by its own. Furthermore, 5 species of Nymphaea, and 1 each species of Nelumbo and Victoria were introduced. Under micro and macroscopic observations, different planktonic forms of flora and fauna were recorded and attracted avian fauna and other terrestrial creatures for feeding and drinking purposes. Besides, Ceratophyllum demersum, Hydrilla verticillata, Potamogeton crispus and Potamogeton nodosus also occurred naturally. Thus, the aim of developing a water body for conservation of aquatic biodiversity in BGIR is achieved.

Water resources have been seriously polluted in terms of quality in the last hundred years, especially due to anthropogenic effects. The quality of the water in the storage structures (dam, lake, pond, etc.) has started to deteriorate due to the deterioration in the drainage basin, especially the insufficient feeding. In recent years, researches on the protection and improvement of the quality of water in storage structures have begun to increase. In this study, it was aimed to improve the water quality of Beytepe Pond located in the campus of the Turkish National Botanic Garden Directorate (TNBG) by using Active Microorganism (EM) in laboratory conditions. In the study, Baykal EM1, active microorganism, was used. For improvement water quality was used aerobic (A) and anaerobic (AN) systems in containers with a volume of 10 liters. EM was administered in 3 doses as 5, 10 and 20 ml L-1. pH, conductivity (EC), Dissolved Oxygen (DO), Chemical Oxygen Demand (COD) and chlorophyll-a values were measured in the pond water. Beytepe Pond water is 3rd class according to the US salinity laboratory salinity classification (USSL). COD and chlorophyll-a values exceed eutrophication limit values. At the beginning of the study, the raw water COD value was measured as 263 mg L-1. It was determined that 5 ml L-1 EM application was reduced up to 2 mg L-1 in anaerobic system application. The same application provided the best improvement in chlorophyll-a values. As a result of the study, it was observed that the EM application provided an improvement in the quality of the Beytepe Pond water.

The phytoavailability of copper (Cu) in productive soils poses a significant threat to ecosystems, predominantly due to its extensive use in mineral fertilizers aimed at enhancing crop yield. To address this issue, a pot trial was conducted to evaluate the efficacy of compost (CP) and vermicompost (VC) induced from agro‐industrial waste byproducts, applied at rates of 1%, 3% and 5% to immobilize Cu in contaminated calcareous soil. This trial was arranged with seven treatments along with their three replicates following a completely randomized design. Results presented that CP and VC significantly reduced soil alkalinity by reducing soil pH by 0.45 and 0.38 units, respectively, over control. In addition, incorporation of CP and VC at 5% expressed efficient reductions in Cu mobility by 34.4% and 48.8%, respectively over control soil. Furthermore, significant reductions in Cu were noticed by 47% and 37.9% in chili shoot and root when CP at 5% was applied. Likewise, the addition of VC at 5% also showed the prominent reduction in Cu absorption in chili shoot and root by 62.2% and 49% respectively, relative to control polluted soil. Moreover, a prominent increase in soil nutrients was observed after the incorporation of CP and VC at 5% respectively, over nontreated soil. Furthermore, the greater increase in chili yield, plant biomass, chlorophyll contents, as well as nutrient absorption by chili tissues was observed primarily due to the greater soil nutrient availability provided by the CP and VC in alkaline Cu polluted soil. These findings demonstrate that CP and VC, as byproducts of agricultural waste serve as sustainable, eco‐friendly soil amendments for restoring soil health. They not only mitigate the phyto‐toxicity of Cu but also improve the alkaline soil nutrients status and reduce the dependence on synthetic fertilizers by naturally restoring soil fertility. Future studies will evaluate the long‐term effectiveness of CP and VC in field‐scale applications, their interactions with soil microbiota and their potential for broader crop systems.