In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This balance and protection from stressors is maintained through interactions both within the bacterial ecosystem as well as with its host. As a consequence, the gut microbiome plays a critical role in various physiological processes including maintaining the structure and function of the gut barrier, educating the gut immune system, and modulating the gut motor, digestive/absorptive, as well as neuroendocrine system all of which are crucial for human health and disease pathogenesis. Pre- and probiotics, widely available and clinically established, offer various health benefits primarily by beneficially modulating the gut microbiome. However, their clinical outcomes can vary significantly due to differences in host physiology, diets, individual microbiome compositions, and other environmental factors. This perspective paper highlights emerging scientific insights into the importance of microbial micronutrient sharing, gut redox balance, keystone species, and the gut barrier in maintaining a diverse and functional microbial ecosystem, and their relevance to human health. We propose a novel approach that targets microbial ecosystems and keystone taxa performance by supplying microbial micronutrients in the form of colon-delivered vitamins, and precision prebiotics [e.g. human milk oligosaccharides (HMOs) or synthetic glycans] as components of precisely tailored ingredient combinations to optimize human health. Such a strategy may effectively support and stabilize microbial ecosystems, providing a more robust and consistent approach across various individuals and environmental conditions, thus, overcoming the limitations of current single biotic solutions.

Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress, but its structure and functions in heavy metal-hyperaccumulating plants remain elusive. Here, the phyllosphere microbiome, inhabiting hyperaccumulating (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii grown in soils with varying heavy metal concentration, was characterized. Compared with NHE, the microbial community α-diversity was greater in HE. Core phyllosphere taxa with high relative abundance (>10 %), including Streptomyces and Nocardia (bacteria), Cladosporium and Acremonium (fungi), were significantly related to cadmium (Cd) and zinc (Zn) concentration and biomass of host plants. Moreover, microbial co-occurrence networks in HE exhibited greater complexity than those in NHE. Additionally, proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration, indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress. Furthermore, in contrast to NHE, microbial community functions, primarily involved in heavy metal stress resistance, were more abundant in HE, in which microbiome assisted hosts to resist heavy metal stress better. Collectively, this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress, and provided new insights into phyllosphere microbial application potential in phytoremediation.

Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.

Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.

Freshwater bacterioplankton communities play a pivotal role in global carbon fixation and energy exchange. However, establishing direct linkages between environmental stressors like organophosphorus pesticides (OPPs) and the ecological functions, such as carbon-fixing related microorganisms (CFMs), remains challenging. This study investigated the effects of four OPPs - two phosphates (dichlorvos, monocrotophos) and two phosphorothioates (omethoate, parathion) - on bacterioplankton communities using stable isotope probing, high-throughput sequencing and oligotyping analysis. Seven CFMs were identified. All OPPs significantly reduced total biomass (from 7.87 ×104 to 2.30-4.11 ×104 cells/mL) but stimulated CFMs proliferation. Notably, phosphorothioates induced a greater increase in CFMs abundance (36.84 %-57.18 %, up from 21.1 %) compared to phosphates (23.85 %-37.10 %; p < 0.05). Principal coordinate analysis (PCoA) revealed that phosphorothioates exerted stronger effects on microbial community and CFMs oligotypes structure compared to phosphates (p < 0.05). Variance partitioning analysis (VPA) identified pesticide type as the dominant driver of community structure. PICRUSt2 prediction demonstrated that OPPs suppressed oxidoreductase pathways linked to energy metabolism while activating transferase pathways associated with microbial stress resistance. Phosphorothioates depleted 64 pathways and enhanced 208 pathways, far exceeding phosphate impacts (2 depleted, 22 enhanced), indicating the phosphorothioates played a more important role on bacterioplankton communities than phosphate. Additionally, OPPs exposure reduced functional redundancy and destabilized community stability in bacterioplankton, potentially granting CFMs a long-term competitive advantage and elevating algal bloom risks. These findings provide insights into active CFMs in aquatic systems and their responses to diverse OPPs, offering new perspectives for managing organophosphorus pesticide contamination.

Organophosphate esters (OPEs) are widely used as flame retardants and plasticizers, and they have raised global concern due to their persistence, bioaccumulation, and potential toxicity. However, OPE contamination characteristics and microbial degradation mechanisms in agricultural soils remain poorly understood. This study investigated agricultural soils from the riparian zone of the Anning River Basin in southwest China. The concentrations of 12 OPEs were determined using gas chromatography-tandem mass spectrometry. The results revealed that the total OPE concentration was moderate, with triethyl phosphate being the most abundant compound. Metagenomic techniques and Bayesian linear regression analysis were employed in combination with the Kyoto Encyclopedia of Genes and Genomes database to identify potential degradation pathways for triethyl phosphate and tris (2-chloroethyl) phosphate. The phoA, phoB, phoD, and glpQ genes, which encode phosphatases, catalyze ester bond cleavage, thereby facilitating the degradation of OPEs. Further microbial interaction network analysis identified core OPE-degrading microorganisms, including Pimelobacter simplex, Nocardioides sp. JS614, Nocardioides daphniae, and Methylocystis heyeri. Additionally, neutral community models indicated that environmental selection drives microbial community structure. In conclusion, this study provides an in-depth understanding of OPE contamination and its microbial degradation mechanisms in agricultural soils, offering theoretical insights for pollution management and remediation strategies.

Micro(nano)plastics (M/NPs) are pervasive in marine environments. Benzo[a]pyrene (B[a]P), a typical polycyclic aromatic hydrocarbon (PAH), possesses teratogenic, mutagenic, and carcinogenic properties. B[a]P can accumulate on M/NPs, altering their toxicity. This study investigated individual and combined effects of M/NPs and B[a]P on the intestinal regeneration of the benthic invertebrate Apostichopus japonicus. Eviscerated sea cucumbers were exposed to 0.1 mg L-1 M/NPs (80 nm [NP80] or 20 μm [MP20]) and/or 0.03 μg L-1 B[a]P for 28 days. Cell proliferation, antioxidant and immunoenzyme activity, gene expression, and microbial community in the regenerated intestine were assessed. It demonstrated that combined exposure prolonged regeneration process, leading to increased oxidative stress and intestinal damage. Differential gene expression analysis revealed that co-exposure and single NP80 exposure both significantly changed translation-related processes, while single MP20 exposure primarily affected lipid metabolism. All treatments significantly altered the intestinal microbiota. Under the MP20+B[a]P treatment, Ralstonia abundance significantly increased, while Cobetia and Paracoccus abundances decreased. In general, co-exposure exerted more detrimental effects on intestinal regeneration than any single exposure, with MP20+B[a]P demonstrating more severe impacts. This study provides novel insights into the biotoxicity of M/NPs and B[a]P, contributing to better understanding of the detriments of microplastics and PAHs on marine benthic invertebrates.

Reflective agricultural films are widely used in vegetable production and orchards to repel pests, accelerate fruit ripening, and boost yields. These films, composed of a plastic base metallized with aluminum (Al), degrade over time in soil, releasing Al and microplastics. This study investigated the aging and weathering of Al-coated reflective films (polyethylene terephthalate, PET-based) under UV radiation, simulated rainfall, and soil burial for up to 120 days, assessing the effects of released Al and microplastics on soil chemistry and microbial communities. Weathering was confirmed by the formation of C-O/CO functional groups, an increasing carbonyl index, and the oxidation of Al to Al₂O₃, as shown by Fourier-transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS). Faster Al-coated shedding and PET oxidation were observed in the soil environment. Microplastics (0.5 % w/w) from the films reduced soil micronutrient availability (Fe, Mn, Cu), suppressed functional genes involved in carbon, nitrogen, and phosphorus cycling, and shifted microbial communities towards oligotrophic bacteria enrichment (e.g., RB41, Candidatus_Udaeobacter, Gemmatimonadetes, and Chloroflexi) while reducing copiotrophic bacteria (e.g., Sphingomonas, Ellin6067, Dongia, Puia, and Flavisolibacter). Therefore, these findings highlight that reflective film weathering strongly alters soil nutrient content and microbial community composition, with potential implications for soil health and agricultural sustainability.

Plant-metabolite-microbe interactions play essential roles in disease suppression. Most studies focus on the root exudates and rhizosphere microbiota to fight soil-borne pathogens, but it is poorly understood whether the changes in phyllosphere metabolites can actively recruit beneficial microbes to enhance disease resistance. In this study, the differences of phyllosphere microbial communities and key leaf metabolites were systematically explored in resistant and susceptible black currant cultivars related to powdery mildew (PM) by integrating microbiome and metabolomic analyses. The results showed that the diversity and composition of microbiome changed, as highlighted by a reduction in microbial alpha-diversity and beta-diversity of susceptible cultivars. An increasing fungal network complexity and a decreasing bacterial network complexity occurred in resistant cultivar. Bacillus, Burkholderia (bacteria), and Penicillium (fungi) were identified as keystone microorganisms and resistance effectors in resistant cultivar. Metabolites such as salicylic acid, trans-zeatin, and griseofulvin were more abundant in resistant cultivar, which had a positive regulatory effect on the abundance of bacterial and fungal keystones. These findings unravel that resistant cultivar can enrich beneficial microorganisms by adjusting leaf metabolites, thus showing the external disease-resistant response. Moreover, the reduced stomatal number and increased tissue thickness were observed in resistant cultivar, suggesting inherent physical structure also provides a basic defense against PM pathogens. Therefore, resistant black currant cultivar displayed multilevel defense responses of physical structures, metabolites, and microorganisms to PM pathogens. Collectively, our study highlights the potential for utilizing phyllosphere microbiome dynamics and metabolomic adjustments in agricultural practices, plant breeding, and microbiome engineering to develop disease-resistant crops.

Estuaries, a vital coastal system, exhibit extensive anthropogenic impacts on their ecological integrity. However, little is known about microbial responses and associated risks in marine sediments around Yellow River estuary (YRE) at an outbreak of oil pollution. Herein, via molecular sequencing and physicochemical experiments, the characteristics of microbiota, potential pathogens and antibiotic resistance were comprehensively investigated in sediments collected from three areas with varying distances to YRE at diesel-polluted microcosms. Specifically, higher stability, stronger stochasticity-dominated assembly processes and more abundant petroleum metabolic pathways were observed in bacterial community nearest to the estuary (YE). Furthermore, an enrichment of potential pathogens and antibiotics resistance genes (ARGs), those mainly related to multidrug-resistance efflux pumps, as well as the accelerated dissemination of ARGs, all were found across all regions along the pollution time, especially those in YE. Several core pathogens (e.g., Pseudomonas) were simultaneously related with multidrug resistances and their transmissions, and a more robust relationship among them was found in YE. Culturable experiments demonstrated numerous potential pathogens were capable of efficiently degrading oil contaminants. A global investigation revealed the sediment pathogens with oil degradation potential were widely distributed in shallow- and deep-sea water bodies, with higher abundance in coastal zones, suggesting extensive pathogenic risks from these bacteria also in oil-polluted aquatic environments. Altogether, the findings unmask the sound resistibility but with serious hazard of potential pathogens and antibiotic resistance in oil-contaminated sediment ecosystem nearest to YRE, and offer novel insights and potential targets for estuarine risk assessment and control.

As important methane hydrate storage sites, cold seep areas are threatened by microplastics (MPs) contamination. To assess the environmental impact of MPs on microbial communities in cold seep sediments, an incubation experiment was conducted using cold seep sediment amended with different concentration of polyamide (PA), polyethylene (PE), polyethylene terephthalate (PET), and polypropylene (PP) microplastics. The results showed that the different type and concentration of MPs significantly altered the prokaryotic community structures. The PE and PET addition highly changed the relative abundance of bacterial taxa in the bacterial community, while the proportion of archaeal species in the archaeal community was significantly altered in 0.5 % MPs treatments. All of the MPs reduced the network complexity of the bacterial and archaeal communities, such as the lower average degree and greater average path length. Furthermore, the MPs treatments also significantly decreased the network stability of prokaryotic communities. The lower network complexity led to lower network stability was observed in the archaeal community. The formation of oxidative functional groups on PE and PET MP surface based on FTIR analysis suggested that biodegradation could occur in cold seep sediment. Together, these results provide new evidence that MPs could change the structures and species coexistence of prokaryotic communities in cold seep sediments.

Use of synthetic microbial communities (SynComs) is a promising approach that harnesses nature-based solutions to support soil fertility and food security, mitigate climate change impacts, and restore terrestrial ecosystems. Several microbial products are in the market, and many others are at different stages of development and commercialization. Yet, we are still far from being able to fully harness the potential and successful applications of such biotechnological tools. The limited field efficiency and efficacy of SynComs have significantly constrained commercial opportunities, resulting in market growth falling below expectations. To overcome these challenges and manage expectations, it is critical to address current limitations, failures, and potential environmental consequences of SynComs. In this Viewpoint, we explore how using multiple eco-evolutionary theories can inform SynCom design and success. We further discuss the current status of SynComs and identify the next steps needed to develop and deploy the next generation of tools to boost their ability to support multiple ecosystem services, including food security and environmental sustainability.

The salt lake ecosystem, characterized by extreme environmental gradients, harbors microbes that uniquely adapt to high salt stress through natural selection. However, how abiotic and biotic factors shape the microbial community assembly in Yuncheng Salt Lakes remains unclear. Here, we investigated the assembly processes and meta co-occurrence patterns of microbiota in both water and sediment sampled from 14 distinct wide range of salinity lakes in the Shanxi Yuncheng area, Midwest of China, using 16S rRNA and 18S rRNA gene sequencing technology combined with multivariate ecological and statistical methods. Habitat differentiation led to the differences in microbial diversity, co-occurrence patterns, and community assembly between sedimentary and planktonic communities. Sedimentary prokaryotes were more shaped by deterministic processes than planktonic bacterial communities. Salinity was a major abiotic factor influencing the balance between stochastic and deterministic processes in both sediment and water. Enhanced microbial interactions within sediments exhibited a more prominent impact in shaping community assembly, as indicated by the stronger association between network-inferred species and prokaryotic βNTI. Moreover, we revealed significant differences in how core species concerning βNTI responded to biotic and abiotic factors. Our findings elucidated the ecological process underlying microbial communities in Yuncheng Salt Lakes and shed light on the mechanism of microorganisms to maintain community complexity and diversity in the extreme environment. KEY POINTS: • Sedimentary prokaryotes were more shaped by deterministic processes than planktonic prokaryotic communities. • Salinity was a major factor influencing the balance between stochastic and deterministic process. • Inter-domain and intra-domain symbiotic interactions within sedimentary communities represent key biotic factors influencing their community assembly.

One Health seeks to integrate and balance the health of humans, animals, and environmental systems, which are intricately linked through microbiomes. These microbial communities exchange microbes and genes, influencing not only human and animal health but also key environmental, agricultural, and biotechnological processes. Preventing the emergence of pathogens as well as monitoring and controlling the composition of microbiomes through microbial effectors including virulence factors, toxins, antibiotics, non-ribosomal peptides, and viruses holds transformative potential. However, the mechanisms by which these microbial effectors shape microbiomes and their broader functional consequences for host and ecosystem health remain poorly understood. Metaproteomics offers a novel methodological framework as it provides insights into microbial dynamics by quantifying microbial biomass composition, metabolic functions, and detecting effectors like viruses, antimicrobial resistance proteins, and non-ribosomal peptides. Here, we highlight the potential of metaproteomics in elucidating microbial effectors and their impact on microbiomes and discuss their potential for modulating microbiomes to foster desired functions.

Drought is one of the most devastating environmental challenges, severely affecting agriculture, ecosystems, and global food security. Effective strategies to predict and mitigate drought are limited. The root-soil-microbiome interface is pivotal in mediating plant resilience to drought. Recent studies highlight dynamics between plant root exudates and microbial communities, influencing stress tolerance through chemical signaling under drought. By integrating plant molecular biology, root chemistry, and microbiome research, we discuss insights into how these mechanisms can be harnessed to enhance crop resilience. Here, we focus on the interplay between plants and their microbiomes with metabolites as a central point of interactions. We synthesize recent developments, identify critical knowledge gaps, and propose future directions to leverage plant-microbe interactions to improve plant drought tolerance.

Streptomyces spp. are known for producing bioactive compounds that suppress phytopathogens. However, previous studies have largely focused on their direct interactions with pathogens and plants, often neglecting their interactions with the broader soil microbiome. In this study, we hypothesized that these interactions are critical for effective pathogen control. We investigated a diverse collection of Streptomyces strains to select those with strong protective capabilities against tomato wilt disease caused by Ralstonia solanacearum. Leveraging a synthetic community (SynCom) established in our lab, alongside multiple in planta and in vitro co-cultivation experiments, as well as transcriptomic and metabolomic analyses, we explored the synergistic inhibitory mechanisms underlying bacterial wilt resistance facilitated by both Streptomyces and the soil microbiome.

Our findings indicate that direct antagonism by Streptomyces is not sufficient for their biocontrol efficacy. Instead, the efficacy was associated with shifts in the rhizosphere microbiome, particularly the promotion of two native keystone taxa, CSC98 (Stenotrophomonas maltophilia) and CSC13 (Paenibacillus cellulositrophicus). In vitro co-cultivation experiments revealed that CSC98 and CSC13 did not directly inhibit the pathogen. Instead, the metabolite of CSC13 significantly enhanced the inhibition efficiency of Streptomyces R02, a highly effective biocontrol strain in natural soil. Transcriptomic and metabolomic analyses revealed that CSC13's metabolites induced the production of Erythromycin E in Streptomyces R02, a key compound that directly suppressed R. solanacearum, as demonstrated by our antagonism tests.

Collectively, our study reveals how beneficial microbes engage with the native soil microbiome to combat pathogens, suggesting the potential of leveraging microbial interactions to enhance biocontrol efficiency. These findings highlight the significance of intricate microbial interactions within the microbiome in regulating plant diseases and provide a theoretical foundation for devising efficacious biocontrol strategies in sustainable agriculture. Video Abstract.

Synthetic microbial communities (SynComs) are powerful tools for investigating microbial interactions and community assembly by focusing on minimal yet functionally representative members. Here, we will highlight key principles for designing SynComs, specifically emphasizing the anaerobic digestion (AD) microbiome for waste treatment and upcycling. The AD process has traditionally been used to reduce organic waste volume while producing biogas as a renewable energy source. Its microbiome features well-defined trophic layers and metabolic groups. There has been growing interest in repurposing the AD process to produce value-added products and chemical precursors, contributing to sustainable waste management and the goals of a circular economy. Optimizing the AD process requires a better understanding of microbial interactions and the influence of both biotic and abiotic parameters, where SynComs offer great promise. Focusing on AD microbiomes, we review the principles of SynComs' design, including keystone taxa and function, cross-feeding interactions, and metabolic redundancy, as well as how modeling approaches could guide SynComs design. Furthermore, we address practical considerations for working with AD SynComs and examine constructed SynComs designed for anaerobic waste digestion. Finally, we discuss the challenges associated with designing and applying SynComs to enhance our understanding of the AD process. This review aims to explore the use of synthetic communities in studying anaerobic digestion and highlights their potential for developing innovative biotechnological processes.

Differentiating significant microbial community changes from normal fluctuations is vital for understanding microbial dynamics in human and environmental ecosystems. This knowledge could enable early warning systems to monitor critical changes affecting human or environmental health. We applied 16S rRNA gene sequencing and time-series analysis to model bacterial abundance trajectories in human gut and wastewater microbiomes. We evaluated various model architectures using datasets from two human studies and five wastewater settings. Long short-term memory (LSTM) models consistently outperformed other models in predicting bacterial abundances and detecting outliers, as measured by multiple metrics. Prediction intervals for each genus allowed us to identify significant changes and signaling shifts in community states. This study proposes a machine learning model capable of monitoring microbial communities and providing insights into their responses to internal and external factors in medical and environmental settings.

As the primary raw material for Baijiu brewing, sorghum variety exerts an intricate influence on the taste profile of strong-flavor Baijiu. However, how sorghum variety comprehensively affects Baijiu flavor formation through fermentation by microorganisms and metabolites remains largely unknown. Using 16S&ITS rRNA gene sequencing and non-targeted metabolomics, in this study we comprehensively analyzed the changes in microbial communities and metabolites during fermentation of a glutinous and non-glutinous sorghum variety. The results showed that these varieties significantly affected microbial diversity and community structure, and their interactions, among which, there were particularly complex interactions among bacterial communities, while the effects of "functional differentiation" and "community aggregation" of fungal communities were prominent. Furthermore, three bacterial and nine fungal genera were identified as core microorganisms related to changes in glycerophospholipids during fermentation, that led to a change in ester content, ultimately improving Baijiu quality. These findings provide reference for the selection of brewing materials.

Biological diversity in mountain ecosystems has been increasingly studied over the last decade. This is also the case for mountain soils, but no study to date has provided an overall synthesis of the current state of knowledge. Here we fill this gap with a first global analysis of published research on cryptogams, microorganisms, and fauna in mountain soils above the treeline, and a structured synthesis of current knowledge. Based on a corpus of almost 1400 publications and the expertise of 37 mountain soil scientists worldwide, we summarise what is known about the diversity and distribution patterns of each of these organismal groups, specifically along elevation, and provide an overview of available knowledge on the drivers explaining these patterns and their changes. In particular, we document an elevation-dependent decrease in faunal diversity above the treeline, while for cryptogams there is an initial increase above the treeline, followed by a decrease towards the nival belt. Thus, our data confirm the key role that elevation plays in shaping the biodiversity and distribution of these organisms in mountain soils. The response of prokaryote diversity to elevation, in turn, was more diverse, whereas fungal diversity appeared to be substantially influenced by plants. As far as available, we describe key characteristics, adaptations, and functions of mountain soil species, and despite a lack of ecological information about the uncultivated majority of prokaryotes, fungi, and protists, we illustrate the remarkable and unique diversity of life forms and life histories encountered in alpine mountain soils. By applying rule- as well as pattern-based literature-mining approaches and semi-quantitative analyses, we identified hotspots of mountain soil research in the European Alps and Central Asia and revealed significant gaps in taxonomic coverage, particularly among biocrusts, soil protists, and soil fauna. We further report thematic priorities for research on mountain soil biodiversity above the treeline and identify unanswered research questions. Building upon the outcomes of this synthesis, we conclude with a set of research opportunities for mountain soil biodiversity research worldwide. Soils in mountain ecosystems above the treeline fulfil critical functions and make essential contributions to life on land. Accordingly, seizing these opportunities and closing knowledge gaps appears crucial to enable science-based decision making in mountain regions and formulating laws and guidelines in support of mountain soil biodiversity conservation targets.

Host-protective or disease-suppressive microorganisms are emerging as sustainable solutions for controlling crop diseases, such as bacterial wilt. However, the efficacy of biocontrol strategies is often constrained by limited resilience under varying environmental conditions and interactions with native microbial communities in the field. One major challenge is that introduced biocontrol microbes often face suppression by indigenous microbes due to competitive interactions. Synthetic communities (SynComs) offer a promising alternative strategy. However, conventional approaches to assembling SynComs by combining different microbial isolates often result in antagonism and competition among strains, leading to ineffective and inconsistent outcomes. In this study, we assembled a bacterial wilt-suppressive SynCom for tomato, composed of bacterial isolates derived from co-cultured microbial complexes associated with healthy plants. This SynCom demonstrates significant disease-suppressive effects against Ralstonia pseudosolanacearum in tomato seedlings under both axenic and soil conditions. Additionally, our findings suggest the presence of an optimal SynCom colonization level in plants, which is crucial for effective disease suppression. The SynCom also exhibits direct antibiotic activity and modulates the plant-associated microbiome. Our results provide an effective approach to constructing SynComs with consistent and effective disease-suppressive properties within microbial community contexts. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Due to the importance of biological nitrogen fixation in terrestrial ecosystems, actinorhizal symbiosis has attracted more and more attention. Alders (Alnus) are important actinorhizal plants, but little is known about the diversity of symbiotic microbiota in the actinorhizal nodules. In addition, it remains unclear about the influence of the host species and habitats on the microbial community of alder root nodules and rhizospheric soils.

In this study we sequenced the hyper-variable regions of the 16S rRNA from the root nodules and their rhizosphere soils of three alder species (Alnus mandshurica, A. sibirica, A. japonica) in northeastern China to explore the diversity, composition, network association, and nitrogen cycling pathway of the microbial communities in the actinorhizal nodules and associated soils.

The results showed that the microbial community α-diversity decreased significantly from the associated soil to the root nodule, and the microbial diversity in the root nodule of A. sibirica was not affected by the habitats. The dominant microbe genus in alder nodules was Frankia, whose abundance was significantly higher than that in associated soil samples. Furthermore, the abundance of Frankia was affected by alder tree species, but not by the habitats. The most significant taxon in the nodules of all the three alders was Frankia genus, which was negatively correlated with other six genera of microbes. The main function of microorganisms in alder nodules is nitrogen fixation, which is not affected by tree species and their habitats.

These findings suggest that the host determines the microbial community composition in the root nodule of three alders. This study provides valuable insights into the effects of alder species and habitats on the microbial communities of alder nodules and associated soils.

Xinjiang is situated in an arid and semi-arid region, where abundant heat and sunlight create highly favorable conditions for cotton cultivation. Xinjiang's cotton output accounts for nearly one-quarter of global production. Moreover, the implementation of advanced planting techniques, such as 'dwarfing, high-density, early-maturing' strategies combined with mulched drip irrigation, ensures stable and high yields in this region. Despite these advancements, limited research has focused on the microbial mechanisms in cotton fields employing these advanced planting methods. In this study, high-throughput sequencing technology was utilized to investigate the diversity and composition of bacterial and phoD (Alkaline phosphatases encoding gene) communities in the rhizosphere of cotton grown under different yield levels in Xinjiang Province, China. The Mantel test, redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were employed to explore the interactions between soil bacterial and phoD communities, their network structures, and environmental factors. The bacterial and phoD communities in the cotton rhizosphere were predominantly composed of nine bacterial phyla (i.e., Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes, Rokubacteria, Firmicutes, and Nitrospirae) and five phoD phyla (i.e., Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, and Firmicutes), respectively. Alpha diversity analysis indicated that the medium yield cotton field (MYF) exhibited higher bacterial richness and diversity indices compared to low yield (LYF) and high yield (HYF) fields. The symbiotic network analysis of LYF revealed greater values of average degree, number of edges, and modularity, suggesting a more complex network structure in both bacterial and phoD communities. The Mantel test, RDA, and PLS-PM model identified soil pH, electrical conductivity (EC), organic phosphorus (OP), available phosphorus (AP), total nitrogen (TN), microbial biomass carbon (MBC), and clay content as the main driving factors influencing changes in the rhizosphere bacterial community diversity and network structure. These findings provide a theoretical basis for future research aimed at improving soil quality and cotton yield.

In New Caledonia, nearly 2000 plant species grow on ultramafic substrates, which contain prominent levels of heavy metals and are deficient in essential plant nutrients. To colonize these habitats, such plants, known as metallophytes, have developed various adaptive behaviors towards metals (exclusion, tolerance, or hyperaccumulation). Ultramafic substrates also host many unique microorganisms, which are adapted to metallic environments and capable of boosting plant growth while assisting plants in acquiring essential micronutrients. Hence, plant-microbiota interactions play a key role in adapting to environmental stress. Here, we hypothesised that microbial associations in the different aboveground and underground compartments of metallophytes could be associated to their metal hyperaccumulation or exclusion phenotypes. This hypothesis was tested using a systematic comparative metabarcoding approach on the different compartments of two New Caledonian metallophytes belonging to the same genus and living in sympatry on ultramafic substrates: Psychotria gabriellae, a nickel-hyperaccumulator (Ni-HA), and Psychotria semperflorens, the related non-accumulator (nA) species.

The study of the diversity and specificity of fungal amplicon sequence variants (ASVs) reveals a structuring of fungal communities at both the plant phenotype and compartment levels. In contrast, the structure of bacterial communities was primarily shaped by the belowground compartments. Additionally, we observed a lower diversity in the bacterial communities of the aboveground compartments of each species. For each plant species, we highlighted a distinct global microbial signature (biomarkers), as well as compartment-specific microbial associations.

To our knowledge, this study is the first to systematically compare the microbiomes associated with different compartments of New Caledonian metallophyte species growing on the same substrate and under identical environmental conditions but exhibiting different adaptive phenotypes. Our results reveal distinct microbial biomarkers between the Ni-hyperaccumulator and non-accumulator Psychotria species. Most of the highlighted biomarkers are abundant in various plants under metal stress and may contribute to improving the phytoextraction or phytostabilization processes. They are also known to tolerate heavy metals and enhance metal stress tolerance in plants. The present findings highlight that the microbial perspective is essential for better understanding the mechanisms of hyperaccumulation and exclusion at the whole-plant level. Video Abstract.

Elucidating the effects of community assembly processes on soil functioning represents a crucial challenge in theoretical ecology, particularly under cadmium (Cd) stress, where our understanding remains limited. In this study, we therefore used amplicon sequencing and a quantitative-PCR-based chip to analyze the changes in bacterial community characteristics, soil functioning and their interrelationships in agroecosystems under different levels of Cd stress. The results indicated that Cd stress led to a decline in community diversity (Z-score), network complexity and stability, an increase in species turnover, and a regulation of community structure. Cd stress significantly increased the relative importance of dispersal limitation and homogeneous selection, reducing community drift and rendering the community more deterministic. Finally, Cd stress significantly reduced soil functional potential (Z-score) and soil functional stability (Z-score), impairing soil carbon, nitrogen, phosphorus, and sulfur cycling. It is noteworthy that correlation and random forest analyses revealed significant effects of specific community assembly processes, including dispersal limitation, homogeneous selection, drift (and others), on changes in soil functional potential (Z-score). The results emphasize the pivotal role of community assembly processes in dictating soil functioning under Cd stress, thereby offering novel insights into the comprehension of microbial-driven mechanisms governing soil functioning.

Acidic pit lakes (APLs) are a special type of ecosystem and represent a significant environmental issue worldwide. While previous studies have explored the structure and function of microbial communities in APLs stratification, natural attenuation, and remediation processes, little is known about the succession patterns of microbial association networks and the underlying assembly mechanisms during seasonal succession. In this study, the distribution characteristics and succession patterns of prokaryotic and eukaryotic microorganisms in APLs across different seasons were investigated using 16S rRNA and 18S rRNA high-throughput sequencing technologies, combined with ecological and multivariate statistical methods. The diversity, composition and structure of prokaryotic and eukaryotic microbial communities showed obvious seasonal differences, and the surface waters were more susceptible to seasonal disturbances. Temperature is the most critical factor influencing the seasonal succession of microbial communities. During the year-round succession, variable selection (40.86 %) dominated in the prokaryotic community and homogeneous selection (69.64 %) dominated in the eukaryotic community. Moreover, the proportion of deterministic processes increased with increasing water temperature differences. Co-occurrence networks were more complex and inter-kingdom exchanges were more frequent during the warm seasons (summer and autumn), and microbial communities were more stable during the cool seasons (spring and winter). Meanwhile, the inter-kingdom interactions between eukaryotes and prokaryotes are predominantly positive in all seasons except autumn, which may serve as a strategy to resist environmental stress. These findings indicate that there is a significant seasonal heterogeneity between eukaryotes and prokaryotes in APLs, providing valuable insights into the ecological processes of microbial community succession in extreme environments.

Composting is a microbial-driven process that plays a vital role in recycling waste and promoting sustainable production. To develop more effective bioaugmentation strategies, this study examined three successive stages in an aerobic composting system, focusing on microbial community adaptation to high-temperature stress (mode_2) and nutrient-poor conditions (mode_3). The results revealed a shift from an r-strategy (rapid growth) to a K-strategy (thriving under resource-limited conditions). Community succession was predominantly driven by deterministic processes (>90 %) and exhibited strong cooperative interactions. Using multiple statistical approaches, key species were identified for each condition. These species enhanced microbial network connectivity under environmental stresses, increasing network edges by 29 %-35 %. Under high-temperature stress, Bacillus and Ureibacillus maintained core functions, while Chelativorans and Aeribacillus contributed to key metabolic pathways, including amino acid metabolism. In nutrient-poor conditions, Saccharomonospora and Pseudoxanthomonas enhanced overall system functionality, and Novibacillus played a key role in carbon and nitrogen cycling, particularly nitrogen fixation. Predictive models for microbial community stability (R2 = 0.68-0.97) were developed based on these key species to enable rapid assessment of system stability. Overall, this study identifies essential microbes involved in composting across different environmental conditions and clarifies their functional roles, providing valuable insights for optimizing aerobic composting efficiency and advancing waste resource management.

The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.

Terrestrial microbial communities drive many soil processes and can be pushed into a state of dysbiosis upon disturbance. This dysregulation negatively impacts soil biogeochemical cycles, which threatens plant and soil health. Effective treatment of soil dysbiosis requires simultaneous restoration of multiple system components, addressing both the physical structure of soil and its microbial communities. Hydrogels with microbial consortia simultaneously remedy soil hydrodynamics while promoting microbial reestablishment. The purpose of this review is to shed light on soil management practices through the lens of soil dysbiosis. This is important to address not only for soil health and crop productivity, but also to mitigate climate change through improved soil carbon sequestration and reduced greenhouse gas emissions. This review positions hydrogels and microbes as tools for the treatment of soil dysbiosis, contributing to agricultural and climate resilience.

To evaluate and characterise the microbial compositional changes of removable dentures after interventions by comparing the efficacy of the test arm (a portable self-operated ultrasonic cleaner combined with an enzymatic peroxide-based denture cleanser solution) to the control arm (immersion of the denture in the same cleanser solution followed by conventional brushing).

A prospective, single-blind, block-randomised, two-period crossover, controlled clinical trial was conducted, involving 56 community-dwelling older adults wearing removable acrylic dentures. They were block-randomized into the test/control or control/test denture cleaning sequence. Type IIB Restriction-site Associated DNA for Microbiome metagenomic sequencing was adopted to characterize the species-resolved microbial composition for denture biofilm.

For the intervention effect, the overall microbial richness in both arms was not significantly different based on the Chao 1 index (P = 0.343). However, Beta diversity analysis (Jaccard qualitative distance matrix) demonstrated significant differences in the microbial community structures between the Test and Control arms after interventions, confirmed by the Permanova test (R2 = 0.01118, P = 0.034). Among the opportunistic pathogenic bacteria, Pseudomonas aeruginosa was detected as one of the top 30 species by relative abundance at the end of the clinical trial, and Enterobacter kobei was significantly enriched in the control arm, as determined by LEfSe analysis.

The microbial community of denture biofilm samples after both interventions were significantly 'shifted' and had limited numbers of opportunistic pathogens, suggesting the interventions equally effective in mitigating the overall number of pathogenic bacteria.

Denture cleaning intervention using ultrasonic cleaner combined with immersion in denture cleanser solution appears to be effective in shifting the denture microbiome with reduced pathogenic bacteria among community-dwelling denture wearers.

Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.

Soil bacteria play a pivotal role in regulating multifaceted functions of terrestrial ecosystems. Unraveling the succession of bacterial communities and the feedback mechanism on soil organic carbon (SOC) dynamics help embed the ecology of microbiome into C cycling model. However, how wetland restoration drives soil bacterial community assembly and species association to regulate microbial C metabolism remains unclear. Here, we investigated soil bacterial diversity, community structure and co-occurrence network, enzyme activities and SOC decomposition in restored wetlands for one, three, and four years from paddy fields in Northeast China. Wetland restoration for three and four years increased taxonomic (richness) and phylogenetic diversities by 2.39-3.96% and 2.13-3.02%, respectively, and increased the relative contribution of nestedness to community dissimilarity, indicating increased richness changed soil bacterial community structure. However, wetland restoration for three and four years decreased the richness index of aerobic Firmicutes by 5.04-5.74% due to stronger anaerobic condition characterized by increased soil Fe2+/Fe3+ from 0.20 to 0.64. Besides, wetland restoration for four years decreased network complexity (characterized by decreased node number by 2.51%, edge number by 9.62%, positive/negative edge number by 6.37%, average degree by 5.74% and degree centralization by 6.34%). Robustness index decreased with the increase of restoration duration, while vulnerability index increased with the increase of restoration duration, indicating that wetland restoration decreased network stability of soil bacterial communities. These results might be because stronger anaerobic condition induced the decrease of aerobic Bacilli richness index in keystone module, thereby reducing positive association within keystone module. Decreased positive species association within keystone module in turn weakened microbial C metabolism by decreasing hydrolase activities from 7.49 to 5.37 mmol kg SOC-1 h-1 and oxidase activities from 627 to 411 mmol kg SOC-1 h-1, leading to the decrease of SOC decomposition rate from 1.39 to 1.08 g C kg SOC-1 during wetland restoration. Overall, our results suggested that although wetland restoration after agricultural abandonment increased soil bacterial diversity, it decreased positive association within Bacilli-dominated keystone module under stronger anaerobic condition, which weakened microbial C metabolism and SOC decomposition.

Benthic microbial communities are a vital component of coastal subtidal zones, playing an essential role in nutrient cycling and energy flow, and are fundamental to maintaining the stability and functioning of marine ecosystems. However, the response of benthic prokaryotic and eukaryotic microbial communities to environmental changes remains poorly understood. Herein, we conducted a nearly semimonthly annual sampling survey to investigate the temporal patterns and underlying mechanisms of benthic prokaryotic and eukaryotic microbial communities in the subtidal sediments of Sanshan Island, situated in the eastern Laizhou Bay of the Bohai Sea, China. The results showed that the temporal variations in benthic microbial communities followed a distinct seasonal pattern, with turnover playing a more dominant role in community succession. Nonetheless, contrasting temporal variations were observed in the alpha diversity of benthic prokaryotic and eukaryotic microbial communities, as well as in the dominant taxa across different microbial communities. Water temperature, dissolved oxygen, electrical conductivity, salinity, total nitrogen (TN), NH4+, and PO43- were identified as the predominant environmental drivers. The assembly of benthic microbial communities was driven by different ecological processes, in which stochastic processes mainly shaped the benthic prokaryotic communities, while deterministic processes dominated the assembly of benthic eukaryotic microbial communities. Interactions within benthic microbial communities were primarily characterized by mutualistic or cooperative relationships, but the ability of prokaryotic and eukaryotic microbial communities to maintain stability under environmental disturbances showed notable differences. These results shed light on the temporal dynamics and potential driving mechanisms of benthic prokaryotic and eukaryotic microbial communities under environmental disturbances, highlighting the distinct roles of prokaryotic and eukaryotic communities in coastal subtidal zones and providing valuable insights for the management and conservation of coastal subtidal marine ecosystems.

Skin bacteria on amphibian hosts play an important role in host health, but those communities are also constantly shifting based on environmental and host-related feedback. On some hosts, stability of skin communities depends on relatively abundant taxa, with less abundant taxa more readily entering and exiting the system. Cane toads (Rhinella marina) have invaded widespread, diverse tropical ecosystems, with varying ecology, physiology, and behaviour in different environments. In this study, we described temporal patterns of skin bacterial communities on cane toads at a site in northern Australia through the wet and dry seasons over two years. Toads in the wild population were paired with a captive-held population, housed in a semi-natural environment, to detect effects of time and season on wild toads, explore bacterial transience and volatility in skin taxa, and determine the extent to which skin communities on captive toads represent those on the wild population. We found community differences by captivity status, sampling timepoint, and season, with increased richness in the wet season on wild toads. Bacterial communities also became more similar among individuals (lower dispersion) in the wet season. Captive toads harboured more stable communities over time, likely owing to the reduced bacterial reservoirs experienced while in captivity. We propose that cane toads, with varied movement patterns among their diverse invaded habitats, provide an interesting direction for future work understanding the influences of habitat and movement on skin microbes, and the flexibility of microbial symbiotic interactions in invasive hosts.

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

Epiphytic biofilms play a crucial role in aquatic biogeochemical cycles but are simultaneously influenced by host selection and eutrophication. However, the compositional structure and interaction mechanisms of these factors on algal and bacterial communities remain poorly understood. In this study, we employed Confocal Laser Scanning Microscopy (CLSM), Scanning Electron Microscopy (SEM), and high-throughput sequencing to investigate the physicochemical properties, algal and bacterial diversity, and community structure of epiphytic biofilms on two submerged macrophytes - Vallisneria natans (VN) and Hydrilla verticillata (HV) - across three urban shallow lakes with varying trophic levels in the Yangtze River Basin. Our results revealed distinct algal and bacterial communities influenced by both host plants and lake nutrient conditions, with unique core species identified in VN, HV, and the surrounding water. Host-environment effects index (HEEI = 1.79) indicated that bacterial communities were predominantly shaped by host selection, exhibiting lower diversity in HV (1.66 ± 0.92) and VN (2.31 ± 1.12) biofilms compared to surrounding waters (3.80 ± 0.47). In contrast, algal communities were primarily regulated by environmental factors (HEEI = 0.43), with higher diversity in less eutrophic lakes. Algal-bacterial co-occurrence network analysis revealed greater network complexity in VN biofilms than that in HV, with predominantly synergistic interactions facilitating carbon and nitrogen cycling. Eutrophication increased biofilm thickness, nutrient content, and extracellular polymeric substance (EPS) production but reduced microbial diversity and altered community interaction patterns. This study advances our understanding of epiphytic biofilms and offers insights into optimizing host-microbe interactions for improving lake restoration strategies.

Along a food chain, microbiomes occur in each component and often contribute to the functioning or the health of their host or environment. 'One Health' emphasizes the connectivity of each component's health. Chemical stress typically causes dysbiotic microbiomes, but it remains unclear whether chemical stressors consistently affect the microbiomes of food chain components. Here, we challenged food chain components, including water, sediments, soil, plants, and animals, with three chemical stresses consisting of arsenic (toxic trace element), benzoxazinoids (bioactive plant metabolites), and terbuthylazine (herbicide). We analysed 1064 microbiomes to assess their commonalities and differences in their stress responses. We found that chemical stressors overall decreased microbiome diversity in soil, but not in the other microbiomes. In response to stress, all food chain communities strongly shifted in their composition, generally becoming compositionally more similar to each other. In addition, we observed stochastic effects in host-associated communities (plant, animal). Dysbiotic microbiomes were characterized by different sets of bacteria, which responded specifically to the three chemical stressors. Microbial co-occurrence patterns significantly shifted with either decreased (water, sediment, plant, animal) or increased (soil) network sparsity and numbers of keystone taxa following stress treatments. These results suggest major re-distribution of specific taxa in the overall stress- and component-specific responses of microbiomes with the community stability of plant and animal microbiomes being the most affected by chemical stresses.

Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.

This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.

This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.