Function and functional redundancy in microbial systems

Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems

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.

Microbial taxonomic diversity and functional genes mirror soil ecosystem multifunctionality in nonferrous metal mining areas

The pollution of metal ions triggers great risks of damaging biodiversity and biodiversity-driven ecosystem multifunctioning, whether microbial functional gene can mirror ecosystem multifunctionality in nonferrous metal mining areas remains largely unknown. Macrogenome sequencing and statistical tools are used to decipher linkage between functional genes and ecosystem multifunctioning. Soil samples were collected from subdams in a copper tailings area at various stages of restoration. The results indicated that the diversity and composition of soil bacterial communities were more sensitive than those of the fungal and archaeal communities during the restoration process. The mean method revealed that nutrient, heavy metal, and soil carbon, nitrogen, and phosphorus multifunctionality decreased with increasing bacterial community richness, whereas highly significant positive correlations were detected between the species richness of the bacterial, fungal, and archaeal communities and the multifunctionality of the carbon, nitrogen, and phosphorus functional genes and of functional genes for metal resistance in the microbial communities. SEM revealed that soil SWC and pH were ecological factors that directly influenced abiotic factor-related EMF; microbial diversity was a major biotic factor influencing the functional gene multifunctionality of the microbiota; and different abiotic and biotic factors associated with EMF had differential effects on whole ecosystem multifunctionality. These findings will help clarify the contributions of soil microbial diversity and functional genes to multifunctionality in degraded ecosystems.

Stochastic and deterministic mechanisms jointly drive the assembly of microbial communities in cold-rolling wastewater across China

Microorganisms play a pivotal role in industrial wastewater treatment, serving as a critical barrier to water purification and safeguarding human and environmental health. Despite their importance, the biogeographic distribution and assembly mechanisms of microbial communities in cold-rolling wastewater treatment systems remain poorly understood. This study analyzed 101 microbial samples from nine regions using high-throughput sequencing, revealing rich microbial diversity and distinct regional aggregation patterns. Random forest analysis identified key biomarkers, often low-abundance species, while a unique core microbial community was strongly correlated with pollutant removal efficiencies, including chemical oxygen demand (COD), total organic carbon (TOC), and total nitrogen (TN). Neutral community model analysis demonstrated that microbial community assembly is driven by both stochastic and deterministic processes. Co-occurrence network analysis further highlighted o__1-20 and g__Ellin6067 as pivotal taxa influencing community structure. Among environmental factors, nitrite nitrogen (NO₂-N) and COD were identified as critical drivers of community assembly. This study provides the first comprehensive characterization of microbial biogeographic patterns in cold-rolling wastewater treatment plants across China. The findings deepen our understanding of microbial diversity, distribution, and community dynamics in industrial wastewater systems, offering valuable insights for optimizing treatment processes.

Water regime alters microbial mechanisms of N2O emission in metal-contaminated paddy soils

Microorganisms are essential for soil nitrous oxide (N2O) emissions through participating in key nitrogen (N)-related processes. However, the effect of water regimes on the interactions between N2O emissions and microbial processes in metal-contaminated soils is unclear. Here, we conducted a soil microcosm experiment with two water management strategies (non-flooding and flooding) and six metal addition treatments including low (2 and 200 mg kg-1) and high (10 and 1000 mg kg-1) levels of individual and combined Cd and Cu. The effects of high levels of individual Cd and Cu contamination on soil N2O emissions varied depending on water regimes, showing antagonistic effects under non-flooding conditions and synergistic effects under flooding conditions. High levels of co-contamination significantly inhibited nitrification under both water regimes, primarily due to reduced abundance of Nitrosospira. In contrast, this co-contamination decreased the abundance of Ramlibacter, thereby inhibiting denitrification and dissimilatory nitrate reduction to ammonium (DNRA) under flooding conditions. The inhibition of these key microorganisms and their mediated N-cycle processes reduced soil N2O emissions under both water regimes. This reduction was greater under flooding conditions because more N-related processes were inhibited. Metagenomic binning further indicated that Nitrosospira carried nitrifying genes, while Ramlibacter contained genes involved in denitrification, assimilatory nitrate reduction to ammonium (ANRA), and DNRA. These findings implied that both microorganisms had potential to produce N2O. Overall, water management strategies and metal contamination altered the microbial processes of N2O emissions, highlighting the importance of appropriate water management in mitigating greenhouse gas emissions from metal-contaminated paddy soils in southern China.

Active restoration facilitates sedge colonization in degraded alpine meadows on the Qinghai-Tibetan Plateau

Extremely degraded alpine meadow is among the most challenging types of grasslands to restore due to its severely deteriorated habitat and limited self-recovery capability. Since the 2000s, cultivating artificial grasslands has been widely applied as the primary method for restoring theses meadows on the Qinghai-Tibetan Plateau (QTP). However, the performance of climax species (sedges of alpine meadows on the QTP), which is crucial to determine the restoration efforts of alpine meadow, has not received sufficient attention yet. With this context, field data of cultivated grasslands with different restoration stages (S1: 1-6 years, S2: 7-12 years, S3: over 13 years), was collected to examine the change and influencing factors of sedges over restoration time. The results demonstrated that restoration actions facilitated increases in the sedge biomass and the percentage of sedge biomass in S3, though these values remained lower than those in healthy alpine meadow. A clear difference in plant community structure was observed among different grasslands, characterized by an increase in forb abundance and species richness alongside a decrease in grass abundance over restoration time. Soil moisture and organic carbon of S2 and S3, and soil total nitrogen of S3 were significantly improved, while soil available nutrients remained stable compared to the degraded meadow. The relative abundance of most nitrogen- and phosphorus-related functional genes either declined or stabilized during the restoration process. The sedge biomass (77.36 %) and the percentage of sedge biomass (88.35 %) were largely explained by the coupling effects of plant indicators (grass abundance and species richness) and soil indicators (soil bulk density, moisture, organic carbon, and total nitrogen). This study highlights the positive influence of active restoration actions on sedge colonization and the asynchronous dynamics between aboveground (plant community) and belowground components (soil available nutrients and microbial community). These findings imply that accelerating soil nutrients accumulation and cycling should be prioritized in post-restoration management of cultivated grasslands on the QTP and other alpine regions.

Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors

Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m2·d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m2·d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.

Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.)

Grasslands are important centers of biodiversity; however, these ecosystems have been in decline. Although many methods for grassland restoration have been developed, the abundant microbial communities in these regions are understudied and could be used to assist in these efforts. In this study, we aimed to understand how microbial communities varied by soil type, grassland site, and environmental conditions. Samples were taken from rhizosphere soil (attached to plant roots), proximal soil (close to the plant roots), and from bulk cores at Ricketts Glen State Park and Nescopeck State Park in northeastern Pennsylvania, USA, during June and August of 2021 and 2022. Rhizosphere soil samples were taken from the native common grassland plant, Solidago rugosa. 16S rRNA gene sequencing revealed that pH as well as soil type (bulk, proximal, or rhizosphere) significantly influenced the microbial community composition of each soil. Each soil type had its own distinct microbial communities, and proximal soil was identified as a transition zone between rhizosphere and bulk microbial communities. We also observed that the rhizosphere communities were dependent upon geography, as these communities were significantly different between grasslands even though the plant species remained the same. Our results highlight the complex nature of soil microbial communities and how many factors, including pH, soil type, and geography, can be overlayed to impact soil microbes. Results suggest future avenues of conservation research through modification and regulation of specific soil microbial communities in order to aid in the rehabilitation of these diminished regions.

Effects of ecological water replenishment on microbial denitrification in aquatic environment of infiltration area

Ecological water replenishment (EWR) is a crucial strategy for solving regional water shortages, yet its ecological impacts warrant further exploration. This study investigated the microbial community succession mechanism in surface water (SW) and groundwater (GW), the denitrification potential of functional bacteria, and their responses to water replenishment events of the South-to-North Water Diversion (SNWD), the largest water transfer project in China. Nitrogen and antibiotic contamination, resulting from prolonged infiltration of reclaimed water, decreased following water replenishment event. During water replenishment, both SW and GW showed an increase of microbial denitrification capacities. Post-replenishment, SW microbial denitrification capacity continued to rise, while GW returned to the baseline levels. Total organic carbon (TOC) and antibiotic resistance genes (ARGs) were the primary factors influenced denitrification before and after water replenishment. Among the denitrification steps, NO2--N reduction was most affected, linked to microbial community reassembly and resource utilization alteration after water replenishment. Furthermore, random forest analysis identified potential bacterial indicators and combinations sensitive to water replenishments highlighting key denitrification functional bacteria. These findings offer critical insights for optimizing water resource management and improving EWR effectiveness.

Algae biofilm produces less microbe-derived dissolved organic nitrogen under higher C/N ratio conditions

The increased release of microbe-derived dissolved organic nitrogen (mDON) during biological nutrient removal (BNR) processes, particularly under carbon dosing conditions, has emerged as a primary cause to eutrophication. Although algae biofilm (AB) has potential in mitigating mDON discharge, the influence of wastewater carbon-to-nitrogen (C/N) ratios on mDON formation remains poorly understood. Here, we investigated AB's mDON formation and utilization performance, molecular characteristics, and metabolic traits under C/N ratios ranging from 1 to 8. All AB reactors reached mDON concentrations <1.3 mg/L, presenting a trend of first rising and then falling as C/N ratios rose. At the highest C/N ratio, AB effectively reduced mDON concentrations to 0.88 ± 0.08 mg/L, representing a reduction greater than 50 % compared to conventional BNR processes, and achieved a total nitrogen removal efficiency of 97.19 %. Redundancy and network analysis revealed that dominant algae (Chlorophyta and Cyanobacteria) and bacteria (Bacteroidota and Proteobacteria) exhibited distinct mDON production and utilization patterns across different C/N ratios. Algae proliferated under higher C/N ratios promoted the synergistic algal-bacteria interactions, enabling labile DON recycling and reducing its chemodiversity. This was also supported by the increased genetic investments in DON metabolism under higher C/N ratios. Conversely, bacterial activity, responsible for diversifying mDON pools via cross-module transformation reactions, was inhibited under elevated C/N ratios. Overall, AB is demonstrated robust for DON-related eutrophication control, even under high C/N ratios. This study first investigates the effects of C/N ratios on the mDON fates within algae biofilm systems and reveals the taxon-specific formation and utilization patterns.

Soil Microbial Adaptation and Biogeochemical Feedback in Degraded Alpine Meadows of the Qinghai-Tibetan Plateau

Alpine meadows on the Qinghai-Tibetan Plateau are experiencing rapid degradation due to climate change and anthropogenic disturbances, leading to severe ecological consequences. In this study, we investigated the response of soil microbial communities and their metabolic functions across a degradation gradient using metagenomic sequencing and comprehensive soil physicochemical analysis in the city of Lhasa, China. Results showed that soil pH increased with degradation, while most nutrients, including different forms of nitrogen, phosphorus, and potassium, declined. pH, ammonium nitrogen, and organic matter were identified as key factors driving degradation dynamics. Microbial community composition shifted markedly, with distinct biomarker taxa emerging at different degradation levels. Network analysis revealed a progressive loss of microbial connectivity, with Actinobacteria dominance increasing in heavily degraded soils, while cross-phylum interactions weakened. Functional analysis of biogeochemical cycling genes showed that carbon, nitrogen, and phosphorus cycling were all disrupted by degradation, but each exhibited unique response patterns. These findings will extend our understanding of microbial-mediated soil processes under degradation and provide a scientific foundation for ecosystem management, conservation, and targeted restoration strategies in alpine meadows.

Operational Taxon-Function Framework in MetaX: Unveiling Taxonomic and Functional Associations in Metaproteomics

Metaproteomics analyzes the functional dynamics of microbial communities by identifying peptides and mapping them to the most likely proteins and taxa. One challenge in this field lies in seamlessly integrating taxonomic and functional annotations to accurately represent the contributions of individual microbial taxa to functional diversity. We introduce MetaX, a comprehensive tool for analyzing taxon-function relationships in metaproteomics by mapping peptides to their lowest common ancestors and assigning functions based on proportional thresholds, ensuring accurate peptide-level mappings. Importantly, MetaX introduces the Operational Taxon-Function (OTF), a new conceptual unit for exploring microbial roles and interactions within ecosystems. Additionally, MetaX includes extensive statistical and visualization tools, establishing it as a robust platform for metaproteomics analysis. We validated MetaX by reanalyzing ex vivo gut microbiome metaproteomic data exposed to various sweeteners, yielding more detailed results than traditional protein analysis. Furthermore, using the peptide-centric approach and OTF, we observed that Parabacteroides distasonis significantly responds to certain sweeteners, highlighting its role in modifying specific metabolic functions. With its intuitive, user-friendly interface, MetaX facilitates a detailed study of the complex interactions between microbial taxa and their functions in metaproteomics. It enhances our understanding of microbial roles in ecosystems and health.

Ecological mechanisms of microbial assembly in clonal plant Glechoma longituba: from soil to endosphere

Climate change presents significant challenges to plant growth and reproduction. Clonal plants, with low genetic diversity, are particularly vulnerable due to their limited adaptive capacity. Plant-associated microbiomes can play a crucial role in enhancing clonal plant survival and adaptability, yet the mechanisms governing microbial community assembly along the soil-episphere-endosphere continuum remain unclear. In this study, we investigated microbial community assembly patterns in the clonal plant Glechoma longituba. Our findings demonstrate that the assembly of microbial communities is primarily driven by host-related factors rather than external environmental filtering. First, host selection reduced α-diversity and network complexity while increasing β-diversity and community stability. Second, the mechanisms of microbial assembly transitioned from stochastic dominance in bulk soil and epiphytic compartments to deterministic processes within endophytic niches. Third, the taxonomic structure exhibited significant turnover along the soil-episphere-endosphere continuum, accompanied by functional redundancy to maintain ecosystem functions. The results support the hypothesis that host selection optimizes the functional composition of microbial communities by reducing diversity and network complexity while ensuring the stability of key functional microorganisms. The study emphasizes the critical role of host-microbe interactions in sustaining the adaptive and functional advantages of clonal plants, offering insights into managing sustainable plant communities under climate change.IMPORTANCEThis study highlights the vital role of plant-associated microbiomes in helping clonal plants, which have low genetic diversity, adapt to climate change. By examining the clonal plant Glechoma longituba, the research reveals that the plant itself plays a key role in shaping its microbial communities, rather than external environmental factors. Host selection simplifies microbial diversity and network complexity but enhances community stability and functional efficiency. These findings suggest that clonal plants can optimize their microbiomes to maintain critical functions. This work provides valuable insights into how plants and microbes interact to improve resilience, offering potential strategies for managing plant communities in a changing climate. By understanding these mechanisms, we can better support sustainable ecosystems and agricultural practices in the face of global environmental challenges.

Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry

Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.

Bacterial community assembly processes mediate soil functioning under cadmium stress in the agroecosystem

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.

Optimization hardness constrains ecological transients

Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of interactions within versus among subcommunities. Here, we use tools from computational complexity theory to frame equilibration in complex ecosystems as the process of solving an analogue optimization problem. We show that functional redundancies among species in an ecosystem produce difficult, ill-conditioned problems, which physically manifest as transient chaos. We find that the recent success of dimensionality reduction methods in describing ecological dynamics arises due to preconditioning, in which fast relaxation decouples from slow solving timescales. In evolutionary simulations, we show that selection for steady-state species diversity produces ill-conditioning, an effect quantifiable using scaling relations originally derived for numerical analysis of complex optimization problems. Our results demonstrate the physical toll of computational constraints on biological dynamics.

Decoupling of bacterial production and respiration in the surface water of the North Pacific Subtropical Gyre

Heterotrophic bacterial production and respiration, two important contributors to carbon cycling, play an important role in global biogeochemical cycles. However, recent research suggests that these two processes may be decoupled, and the underlying changes in community structure and their interactions remain unclear. In this study, two research expeditions to the North Pacific Subtropical Gyre (NPSG) during the summer and winter of 2020-2021 revealed seasonal shifts in bacterial metabolism and community structure in response to environmental factors. The findings indicated notable seasonal fluctuations in bacterial abundance and production in the surface waters. Both peaked in winter compared to summer. Alterations in bacterial abundance that were further evident at the community level demonstrated significant seasonal differences in bacterial community structure and diversity and revealed, in particular, the intricacy of the networks and interactions among bacterial communities in winter. Bacterial respiration displayed no significant seasonal variations and was decoupled from bacterial abundance and production. The implication was that bacterial production did not directly dictate bacterial respiration. Specific taxa exerted a more substantial influence on bacterial respiration, potentially including groups with high respiration rates but relatively low abundance, thus challenging the notion that highly abundant taxa are invariably the most metabolically active. Moreover, the interplay between different bacterial taxa and their interactions may also impact the overall strength of bacterial community respiration. These findings significantly enhance our understanding of the decoupling between bacterial production and respiration, which is crucial for unraveling the complex mechanisms underlying carbon cycling and energy flow in marine ecosystems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-025-00279-9.

Influence of high-load shocks on achieving mainstream partial nitrification: Microbial community succession

Driving microbial community succession through the regulation of operational strategies is crucial for achieving partial nitrification (PN) in municipal wastewater. However, at present, there is a decoupling between the strategic regulation of PN systems and the succession characteristics of the microbial community. This study examined the correlation between microbial community succession and PN performance under two high-load shocks (HLS1 and HLS2) treating actual sewage. During HLS1, the influent organic loading rate (OLR) and nitrogen loading rate (NLR) increased from 116.7 ± 37.7 to 219.7 ± 24.7 mg COD/(g VSS·d) and 0.21±0.02 to 0.33±0.02 kg N/m3/d respectively, with the nitrite concentration and nitrite accumulation ratio only reaching 11.7 ± 2.7 mg/L and 49.3 ± 13.9 %, respectively. During HLS2, the influent OLR and NLR increased from 123.5 ± 17.2 to 300.3 ± 49.2 mg COD/(g VSS·d) and 0.19±0.03 to 0.32±0.03 kg N/m3/d respectively, resulting in a nitrite accumulation ratio of 89.4 ± 10.7 %. The system achieved efficient PN performance and sustained for 124 days. High-throughput sequencing results showed that community diversity remained consistently high, and the community composition returned to its initial state following a minor succession during HLS1. During HLS2, the high-load shock reduced the richness and evenness of the microbial community. The community underwent succession in a new direction, leading to community composition and function changes. The results indicate that the realization, stabilization, and disruption of PN are influenced not only by operational parameters but also by microbial community structure.

Keystone microbial taxa identified by deep learning reveal mechanisms of phosphorus stoichiometric homeostasis in submerged macrophytes under different hydrodynamic states

Phosphorus (P) pollution in aquatic ecosystems triggers eutrophication, disrupting ecological processes. Although phytoremediation using submerged macrophytes is promising, its efficacy depends on plant-microbe interactions and stoichiometric homeostasis. A significant knowledge gap exists regarding the assembly and impact of key microbial communities on stoichiometric homeostasis under fluctuating environmental conditions, hindering the optimization of phytoremediation strategies. Given that hydrodynamic fluctuations are a primary source of environmental variability in aquatic systems, this study explored the intricate relationships among stoichiometric homeostasis, microbial community structure, and ecosystem stability, with a specific focus on their impact on rhizosphere P metabolism in Vallisneria natans and Myriophyllum spicatum under different hydrodynamic states. A Deep Learning-based Keystoneness Taxa Identification (DLKTI) framework was developed to identify key microbial taxa. Microbial community stability analysis preceded key taxa determination to enhance result reliability and ecological relevance based on the premise that distinct states provide a more dependable baseline for attributing observed changes to specific perturbations rather than to inherent fluctuations. These findings indicate that the key taxa identified by the DLKTI framework adequately characterized the overall ecological features of the microbial community (average ρ = 0.39, p<0.05). Moreover, including microbial pools and diversity indices of the screened key microbial taxa improved the explanatory power for submerged macrophyte traits (5% and 6%, respectively) and rhizosphere oxidative stress responses (25% and 4%, respectively). Partial least squares path modeling demonstrated the crucial role of stoichiometric homeostasis for P in ecosystem functioning (path coefficient of inhibition of phytoplankton growth = 0.58, p<0.001). The findings elucidating plant-microbe interaction patterns under different hydrodynamic states allow for the development of targeted interventions to enhance rhizosphere P metabolism, thereby increasing the efficiency of phytoremediation for eutrophication management and aquatic ecosystem restoration.

Climate-driven succession in marine microbiome biodiversity and biogeochemical function

Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. Here we quantify changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observe seasonal oscillations between large-genome lineages during cold, nutrient rich conditions in winter and spring versus small-genome lineages, including Prochlorococcus and Pelagibacter, in summer and fall. Parallel interannual changes separate communities depending on ENSO condition. Biodiversity shifts translate into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.

Bio-Organic Fertilizer Application Enhances Silage Maize Yield by Regulating Soil Physicochemical and Microbial Properties

Silage maize is vital to livestock development in northern China, but intensive chemical fertilization has led to soil degradation and reduced productivity. Bio-organic fertilizers offer a sustainable alternative, though their effects on soil multifunctionality remain underexplored. This study evaluated the impact of combining decomposed cow manure, Bacillus amyloliquefaciens, and mineral potassium fulvic acid with chemical fertilizers (NPK) on silage maize yield, soil microbial diversity, and ecosystem multifunctionality (EMF). Field experiments showed that bio-organic fertilization increased silage maize yield by 10.23% compared to chemical fertilizers alone, primarily by boosting labile organic carbon and soil enzyme activity. It also enhanced bacterial richness and diversity, with little effect on fungal communities. Microbial network analysis revealed more complex and stable bacterial networks under bio-organic treatments, indicating strengthened microbial interactions. Random forest and structural equation modeling (SEM) identified soil carbon storage and bacterial diversity as key drivers of EMF, which integrates soil functions such as nutrient cycling, decomposition, enzyme activity, and microbial diversity. These findings suggest that soil bacterial diversity and its interactions with soil properties are critical to both crop productivity and soil health. The optimal fertilization strategy for silage maize in this region involves the combined use of cattle manure, Bacillus amyloliquefaciens, mineral potassium fulvic acid, and NPK fertilizers. This approach improves yield, microbial diversity, and soil multifunctionality. Future studies should consider environmental variables and crop varieties across diverse regions to support broader application.

Unveiling the prevalence of metal resistance genes and their associations with antibiotic resistance genes in heavy metal-contaminated rivers

Heavy metals can drive antibiotic resistance through co-selection mechanisms. Current knowledge predominantly focuses on relationships between metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) at the river reach scale. It remains unclear the links between MRGs and ARGs at the large river basin scale, as does the role of MRG-ARG colocalization in resistance dissemination. This study employed metagenomics to investigate the prevalence of MRGs in the Xiangjiang River, a historically heavy metal-contaminated river, and their connections with ARGs by combining resistome profiling with colocalization analyses. Results revealed the significant prevalence of MRGs in the river compared to nationwide rivers, but it showed weak correlations with metal concentrations in either water or sediment. The prevalence of MRGs in water was weakly driven by abiotic parameters, but was strongly influenced by microbial composition. The proportion of water MRGs attributable to sewage sources was tightly positively correlated with MRG abundances, suggesting the significant contribution of external waste input. Plasmid-originated MRGs were more abundant in water, while chromosomal MRGs dominated in sediment, indicating medium-specific transfer dynamics. The profile of MRGs were strongly correlated with that of ARGs in both media, encompassing several clinically high-risk ARGs. However, MRG-ARG colocalization events were rarely detected (eight instances in total), consistent with low frequencies in nationwide rivers (3.5 % in sediment; 2.0 % in water), implying their limited roles in resistance dissemination. Overall, the findings enhance our understanding of riverine metal resistome and its associations with antibiotic resistome, while emphasize the rare presence of MRG-ARG colocalization in riverine environments.

Effect of graded inclusion of black soldier fly (Hermetia illucens, Linnaeus, 1758) pre-pupae meal in diets for gilthead seabream (Sparus aurata, Linnaeus, 1758) on gut microbiome and liver morphology

Over the last decades, an insect meal has received great attention for finfish diets, due to its nutritional composition and low ecological footprint. In the present study, we assessed the response of gut microbiota composition and liver histology of gilthead seabream (Sparus aurata) fed four experimental diets including the black soldier fly (Hermetia illucens) meal (HI) used to replace 0 (HI0), 25 (HI25), 35 (HI35) and 50 (HI50) percent of fish meal in a 131-day feeding trial. At the end of the experiment, a remarkable change in gut microbiota composition related to HI inclusion was observed, with a preponderance of Cyanobacteriain the control and low HI groups (HI0, HI25) while Chloroflexi became prevalent in the higher HI inclusion groups (HI35, HI50). Predictive analysis on bacterial metabolic pathways showed a clear separation between HI0-HI25 and HI35-HI50 groups. The microbiota shifts observed suggest a pivotal role of HI in inducing a bacterial-mediated physiological response in this fish species, probably due to chitin content and the fatty acid profile of this ingredient. Liver histology showed a higher hepatocyte size in fish from the HI50 group, suggesting lipid dysmetabolism due to the HI meal fatty acid profile, while a marginal adaptive response was observed in the HI25 group. In conclusion, while up to 25% inclusion of black soldier fly meal showed limited adverse effects, 50% HI dietary inclusion is not recommended in gilthead seabream diet, since possible alteration in lipid deposition, particularly at hepatic level, were highlighted in this fish species.

Relative importance of microbial abundance and taxonomic types in driving the processes and functions of coral reef seawater in the Wuzhizhou Island

Abundant and rare taxa of diverse microbial groups may play different roles in coral reefs, yet comprehensive and fine - scale analyses are still lacking. Using high-throughput sequencing methods, we investigated the microbial community and function of impacted reef seawater. Here, we focused on the effects of distinct microbial abundance (abundant versus rare biospheres) and taxonomic types (prokaryotic versus eukaryotic communities). Our study revealed that community assembly processes were more closely related to microbial abundance than to taxonomic types. Rare taxa increased partial functional redundancy compared to the abundant taxa, and bacterial composition had stronger associations with the overall functional attributes than the microeukaryotic taxa. We further demonstrated that taxonomic signatures were more sensitive to temperature and nutrient dynamics in the impacted coral reef than other functional features. These results suggest that community assembly and functional response are highly correlated with microbial abundance and taxonomic types, and that they have different sensitivities as potential indicators of environmental changes. Our findings can promote understanding about community assembly and promising indicators related to microbial abundance and taxonomic types in coral reefs.

High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel

Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7 ± 15% but a wide range between 1.2% and 61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.

Synergic interactions between Trichoderma and the soil microbiomes improve plant iron availability and growth

Iron bioavailability is often limited especially in calcareous soils. Trichoderma harzianum strongly improves plant iron uptake and growth in calcareous soils. However, little is known about the mechanisms by which T. harzianum mobilizes iron in calcareous soils. Here, the model strain T. harzianum NJAU4742 and a synthetic microbial community (SynCom) was used to show that the efficacy of T. harzianum in enhancing plant iron nutrition in calcareous soils depends on the soil microbiome. Enhanced iron-mobilization functions of the SynCom were observed in the presence of T. harzianum NJAU4742. Concurrently, T. harzianum NJAU4742 improved the iron-mobilization capacity of the SynCom by enriching strains that are able to do so. Finally, Chryseobacterium populi was identified as a key driver of iron mobilization, while their synergistic colonization further enhances this process. This study unveils a pivotal mechanism by which T. harzianum NJAU4742-mediated re-structuring of the soil microbiome and ameliorates plant iron nutrition.

Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism

Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.

Reapplication of glyphosate mitigate fitness costs for soil bacterial communities

Glyphosate (GLP) is a globally ubiquitous herbicide that poses a threat to living organisms due to its widespread presence in soil ecosystems. However, the results of current research regarding the effects of glyphosate on soil microorganisms and its ecological risks are vague and inconsistent. In this study, we investigated the impact of single (low/high-dose) and reapplication (high-dose) of glyphosate applications on soil microbes through indoor incubation experiments using 16S rRNA gene high-throughput sequencing technology. Our findings indicate that in the short term, whether it's single or reapplication glyphosate applications, changes in diversities of soil bacterial community were less than those in community composition. Glyphosate exerts selective pressure on soil microbial communities, resulting in a predominant process of species replacement after glyphosate application, and quantitative analysis revealed a higher turnover rate of microbial communities under glyphosate reapplication. Factors related to nitrogen cycling, especially NH4+-N and NO3--N, were identified as the main drivers responsible for the changes in soil microbial community composition following glyphosate addition. Changes in the functionality of soil microbial communities are observed after glyphosate application, with the adaptability of microbial communities resulting in smaller changes with reapplication addition compared to a single application. Furthermore, We observed that glyphosate application leads to a phenomenon resembling the "fitness cost" found in resistant bacteria. When glyphosate as a single application, it has a significant impact on bacterial communities, leading to decreased community diversity, stability, and function, alongside alterations in community structure, however, the effect can be mitigated by reapplying glyphosate.

Cyanobacteria microbiomes for bioplastic production: Critical review of key factors and challenges in scaling from laboratory to industry set-ups

Cyanobacteria are photoautotrophic microorganisms capable of accumulating polyhydroxybutyrate (PHB). A novel approach for PHB production involves the exploration of cyanobacterial microbiomes, potentially reducing costs through non-sterile cultivation with non-pure substrates. Although still in its early stages, this approach shows promise for high yields and sustained synthesis. However, managing microbiome population dynamics in non-sterile environments requires effective monitoring and control. This review covers PHB production by cyanobacteria microbiomes, from sample procurement to laboratory-scale production. It highlights recent insights into optimizing cultivation parameters for enhanced biopolymer yield. Strategies to overcome challenges in PHB production are evaluated, emphasizing integrated molecular biology techniques with quantitative and qualitative PHB analysis. Finally, key challenges in scaling up production to industrial-scale scenarios are discussed, along with potential solutions to support the development of sustainable industrial processes. Cyanobacteria microbiomes show promise PHB production but challenges like managing non-sterile conditions and scaling up require optimized strategies and integrated approaches.

Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems

Soils play a critical role in supporting agricultural production. Subsoils, below 20 cm, underpin fundamental agroecosystem sustainability traits including soil carbon storage, climate regulation and water provision. However, little is known about the ecological stability of subsoils in response to global change. Here we conducted a microcosm experiment to determine whether subsoils were more sensitive to global changes across 40 agricultural ecosystems in China, in combination with a multiple global change factor experiment and an in situ field study. We found that subsoils exhibited greater fluctuation in species diversity, community composition, and complexity of microbial networks and ecosystem functions than topsoils, indicating lower resistance to global changes. Soil biodiversity was a major driver of ecosystem resistance, surpassing climate and soil parameters. A reciprocal microorganism transplant experiment showed that microorganisms isolated from the topsoil are more resistant to global changes than those from subsoil. Our study emphasizes that subsoil ecosystems are sensitive to global changes, underscoring the importance of including subsoils in predictions of agricultural sustainability and crop productivity under changing environmental conditions.

Microbiome and climate: skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate

The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Understanding these effects is particularly important because amphibians are poikilotherms and, thus, more susceptible to temperature fluctuations. Here, we investigated the skin microbiome of the rhacophorid tree frog Polypedates megacephalus across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of P. megacephalus adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus Pseudomonas. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to higher climate variability, particularly in temperature fluctuations. Additionally, the functional traits of microbial communities changed in parallel with shifts in community diversity and composition. The significant correlations of the functional redundancy index with climatic factors suggest that environmental filtering driven by climate change impacts microbial community functional stability. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.IMPORTANCEThis study is important in understanding the association between climate variability, microbial diversity, and host adaptation in amphibians, which are particularly vulnerable to environmental changes due to their poikilothermic nature. Amphibians rely on their skin microbiome for key functions like disease resistance, yet little is known about how climate fluctuations impact these microbial communities. By analyzing the microbiome of Polypedates megacephalus across different climatic regimes, our analysis reveals that warmer climates could reduce the microbial diversity and community functional redundancy, indicating the functional stability of skin microbiome could be susceptible to climate variability, particularly in hosts adapted to relatively cooler conditions. These findings highlight the potential ecological consequences of climate change and emphasize the need to integrate microbiome health into amphibian conservation strategies.

Replicating community dynamics reveals how initial composition shapes the functional outcomes of bacterial communities

Bacterial communities play key roles in global biogeochemical cycles, industry, agriculture, human health, and animal husbandry. There is therefore great interest in understanding bacterial community dynamics so that they can be controlled and engineered to optimise ecosystem services. We assess the reproducibility and predictability of bacterial community dynamics by creating a frozen archive of hundreds of naturally-occurring bacterial communities that we repeatedly revive and track in a standardised, complex resource environment. Replicate communities follow reproducible trajectories and the community dynamics closely map to ecosystem functioning. However, even under standardised conditions, the communities exhibit tipping-points, where small differences in initial community composition create divergent compositional and functional outcomes. The predictability of community trajectories therefore requires detailed knowledge of rugged compositional landscapes where ecosystem properties are not the inevitable result of prevailing environmental conditions but can be tilted toward different outcomes depending on the initial community composition. Our results shed light on the relationship between composition and function, opening new avenues to understand the feasibility and limitations of function prediction in complex microbial communities.

Seasonal freeze-thaw significantly alters the distinct aquifers solute transport, microbial community assembly patterns, and molecular ecological networks in the hyporheic zone

Elucidating the diversity patterns and assembly mechanisms of microbial communities is crucial for comprehending ecological processes and assessing biogeochemical cycles in the hyporheic zones of cold regions. The spatial and temporal diversity patterns and mechanisms governing these microbial communities are not yet well understood. Our study revealed that microbial richness decreased rapidly during the initial freezing period. However, it began to increase during the deep freezing period due to the role of cold-resistant microorganisms. Meanwhile, the diversity of microorganisms showed a trend that was in line with the lake water- groundwater changes in temperature. Achromobacter and Crenothrix have been designated as biomarkers for the initial freezing period and deep freezing period, respectively. In these phases, factors such as dispersal limitation (26.8 %-47.6 %) and drift (15.1 %-45.2 %), along with other random factors, are the primary drivers of bacterial community assembly. Physical properties (pH, T, DO, EC, Eh) have been identified as the predominant factors (r = 0.75, p < 0.01) affecting the progression of community succession in hyporheic systems throughout the freeze-thaw cycles. Conversely, nutrient properties (r = 0.36, p < 0.01) and the presence of heavy metals (r = 0.18, p < 0.01) play lesser roles, influencing community composition according to partial least squares path modeling. Our insights significantly enhance the understanding of microbial communities in the HZ of frigid areas and carry important consequences for the stewardship and safeguarding of lacustrine ecosystems.

Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent

Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by a core gut microbiota composed of a few bacterial taxa. However, the taxonomic composition and community structure of bumble bee gut microbiotas can vary with bee species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial Bombus impatiens suppliers, wild B. impatiens, and three other wild bumble bee species sampled from sites within the native range of all four species. We found that the community structure of gut microbiotas varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that Apibacter is consistently present in some wild bumble bee species-suggesting it may be a previously unrecognized core phylotype of bumble bees-and that commercial B. impatiens colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, the high-level metabolic potential of gut microbiotas was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated.IMPORTANCEOur study is the first to compare genome-level taxonomic structure and metabolic potential of whole bumble bee gut microbiotas between commercial suppliers and between commercial and wild populations. In addition, we profiled the full gut microbiotas of three wild bumble bee species for the first time. Overall, our results provide new insight into bumble bee gut microbiota community structure and function and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species. Research on taxonomic and metabolic variation in bumble bee gut microbiotas across species and origins is of increasing relevance as we continue to discover new ways that social bee gut microbiotas influence host health, and as some bumble bee species decline in range and abundance.

Quantifying compositional variability in microbial communities with FAVA

Microbial communities vary across space, time, and individual hosts, generating a need for statistical methods capable of quantifying variability across multiple microbiome samples at once. To understand heterogeneity across microbiome samples from different host individuals, sampling times, spatial locations, or experimental replicates, we present FAVA (FST-based Assessment of Variability across vectors of relative Abundances), a framework for characterizing compositional variability across two or more microbiome samples. FAVA quantifies variability across many samples of taxonomic or functional relative abundances in a single index ranging between 0 and 1, equaling 0 when all samples are identical and 1 when each sample is entirely composed of a single taxon (and at least two distinct taxa are present across samples). Its definition relies on the population-genetic statistic FST, with samples playing the role of "populations" and taxa playing the role of "alleles." Its mathematical properties allow users to compare datasets with different numbers of samples and taxonomic categories. We introduce extensions that incorporate phylogenetic similarity among taxa and spatial or temporal distances between samples. We demonstrate FAVA in two examples. First, we use FAVA to measure how the taxonomic and functional variability of gastrointestinal microbiomes across individuals from seven ruminant species changes along the gastrointestinal tract. Second, we use FAVA to quantify the increase in temporal variability of gut microbiomes in healthy humans following an antibiotic course and to measure the duration of the antibiotic's influence on temporal microbiome variability. We have implemented this tool in an R package, FAVA, for use in pipelines for the analysis of microbial relative abundances.

Positive Linkage in Bacterial Microbiota at the Plant-Insect Interface Benefits an Invasive Bark Beetle

Symbiotic microbes facilitate rapid adaptation of invasive insects on novel plants via multifaceted function provisions, but little was known on the importance of cross linkages in symbiotic microbiota to insect invasiveness. Novel host pine Pinus tabuliformis is inherently unsuitable for invasive red turpentine beetle (RTB) in China; however, Novosphingobium and Erwinia/Serratia in gallery microbiota (at the interface between RTB larvae and pine phloem) have been discovered to help beetles via biodegrading pine detrimental compounds naringenin and pinitol, respectively. Here, we further revealed significant positive linkage of the two functions, with higher activity level conferring more growth benefit to RTB larvae. Abundance of Erwinia/Serratia was remarkably increased in response to pinitol, while naringenin-biodegrading Novosphingobium was unable to utilize this main phloem carbohydrate directly. High-activity bacterial microbiota produced nutritive metabolites (sucrose and hexadecanoic acid) from pinitol consumption that facilitated growth of both Novosphingobium and beetle larvae. Functional proteins of several bacterial taxa were enriched in high-activity microbiota that appeared to form a metabolic network collectively to regulate the nutrient production. Our results indicate that positive interaction between Erwinia/Serratia and Novosphingobium is critical for RTB invasion success, while Bacilli bacteria might restrict this linkage, providing new insights into symbiotic microbial interactions for insect herbivores.

Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats

The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.

Stability characteristics of bacterial and protistan communities along an estuarine continuum: Diversity, composition and co-occurrence networks

Estuarine ecosystems have been threatened by increasing anthropogenic and natural pressures, yet the integral understanding of their stability characteristics of microbial communities at taxonomic, habitat, and spatial scales remains limited. In this study, the Mulan River estuary in southeastern China was selected to compare the stability characteristics of bacterial and protistan communities in water and sediments over three hydrological periods, and to explore their spatial variations along the estuarine continuum from river to ocean. The potential driving mechanisms of stability characteristics were also explored. Results revealed that the estuarine ecosystem displayed varied stability at taxonomic, habitat, and spatial scales, separately. On the whole, protistan communities had a lower stability than bacterial communities in both water and sediments, with the higher coefficients of variation in alpha diversity (av. 0.82), the higher Bray-Curtis distances of community compositions (av. 0.98), and the lower robustness of networks (av. 0.23). Compared to the sediments, the lower stabilities of two taxa in water were also indicated via the above three indices. Along the estuarine continuum, the stability of bacterial communities in the middle reach was lowest, but the stability of protistan communities was lowest in the up reach. The null model and network analysis suggested that the assembly processes with stronger variable selection and homogeneous selection, coupled with higher positive interaction (r > 0.7) of microbial communities jointly accounted for the lower stabilities in the up and middle estuarine reaches. The partial least squares path model suggested that total nitrogen, total phosphorus, and dissolved oxygen controlled the community stability by influencing microbial assembly and interaction in the up and middle reaches. This study provides new insights on the varied stability characteristics of different microbial communities along the estuarine continuum, which are helpful for maintaining estuarine ecological function and formulating management strategies.

Climate and biological factors jointly shape microbial community structure in the Yarlung Zangbo River during the dry season

Microorganisms are crucial components of aquatic ecosystems, playing key roles in biogeochemical cycles. Understanding microbial diversity and community assembly mechanisms is essential for river management and sustainable utilization of freshwater resources. However, the role of inter-microbial taxonomic group relationships in shaping community structures within high-altitude river ecosystems is unclear. This study utilizes high-throughput sequencing and bioinformatics analysis to describe the spatial dynamics of fungal and bacterial communities in the Yarlung Zangbo River at a broad environmental scale and to elucidate their community assembly mechanisms. The results indicate a significant distance-decay pattern in the fungal (p < 0.001) and bacterial (p < 0.001) communities of the Yarlung Zangbo River, with substantial differences in microbial taxonomic composition, diversity, and community structure across different regions (fungi ANOSIM R = 0.20, bacteria ANOSIM R = 0.63). Homogeneous selection predominated the community assembly of fungi (average: 67.4 %) and bacteria (average: 74.5 %) in aquatic environments. As altitude decreases, the influence of deterministic processes on fungal communities increases, while their influence on bacterial communities decreases. At the basin scale, the community structures of fungi and bacteria are mainly influenced by the degree of functional or ecological niche differentiation of another taxonomic group, as well as the hydrothermal conditions of the basin that vary with longitude. This study enhances the understanding of fungal and bacterial biogeographic patterns and community assembly mechanisms in plateau rivers, providing new perspectives for microbial ecological research in these ecosystems.

Characterising functional redundancy in microbiome communities via relative entropy

Functional redundancy has been hypothesised to be at the core of the well-evidenced relation between high ecological microbiome diversity and human health. Here, we conceptualise and operationalise functional redundancy on a single-trait level for functionally annotated microbial communities, utilising an information-theoretic approach based on relative entropy that also allows for the quantification of functional interdependency across species. Via constraint-based microbiome community modelling of a public faecal metagenomic dataset, we demonstrate that the strength of the relation between species diversity and functional redundancy is dependent on specific attributes of the function under consideration such as the rarity and the occurring functional interdependencies. Moreover, by integrating faecal metabolome data, we highlight that measures of functional redundancy have correlates in the host's metabolome. We further demonstrate that microbiomes sampled from colorectal cancer patients display higher levels of species-species functional interdependencies than those of healthy controls. By analysing microbiome community models from an inflammatory bowel disease (IBD) study, we show that although species diversity decreased in IBD subjects, functional redundancy increased for certain metabolites, notably hydrogen sulphide. This finding highlights their potential to provide valuable insights beyond species diversity. Here, we formalise the concept of functional redundancy in microbial communities and demonstrate its usefulness in real microbiome data, providing a foundation for a deeper understanding of how microbiome diversity shapes the functional capacities of a microbiome.

Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake

BACKGROUND

Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS

We observed that the water column microbiome significantly varied by season (R2 = 0.59, P = 0.003). Temperature (R2 = 0.27, P = 0.004), dissolved organic matter (R2 = 0.13, P = 0.004), and dissolved oxygen (R2 = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS

Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.

Soil microbial communities in dry and moist tropical forests exhibit distinct shifts in community composition but not diversity with succession

Soil microbial communities are integral to ecosystem function but our understanding of how they respond to secondary succession in fragmented landscapes is limited, particularly in tropical dry forests. We used DNA metabarcoding to evaluate successional changes in soil bacteria and fungi, comparing land managed for cattle, young, and older secondary forests at moist and dry sites in the Republic of Panama. We highlight key functional groups of microbes that interact with plants, including arbuscular mycorrhizal fungi (AMF), nitrogen-fixing bacteria, and plant pathogenic fungi. Plant diversity was higher at the moist site and increased with succession as the plant communities changed at both sites. By contrast, bacterial diversity was similar across sites and successional stages, and while overall fungal diversity was higher at the moist site, it also showed no changes with succession at either site. However, microbial community composition did change, with pastures and older forests having distinct bacterial and fungal communities and young secondary forests often displaying transitional ones. Functional groups of microbes showed contrasting patterns between sites, with the dry forest having a higher diversity of Nitrogen-fixing bacteria despite lower densities of legumes, higher diversity and different communities of AMF, and a much lower incidence of putative fungal plant pathogens than the moist site. Our findings highlight the importance of looking at aboveground and belowground effects together and demonstrate that predictions generated for soil microbes in moist tropical forests may not apply to dry forests. These results may also inform the restoration of climate-resilient forests.

IMPORTANCE

Secondary forests are important components of neotropical landscapes and soil microbes help to shape these forests and the ecosystem services that they provide. This study demonstrates that soil microbial communities in moist and dry tropical forests can recover and reassemble after only 20 years of natural succession following the removal of cattle. However, successional patterns that are seen in the plant community are not always seen belowground. These patterns were more predictable at the moist than the dry site where the patchiness of the landscape likely restricts dispersal of both plants and soil microbes. We highlight the importance of preserving remaining tropical dry forests as they host unique microbial biodiversity that may help forests respond to drought conditions. As community shifts in soil microbes influence plant establishment, forest productivity, and other aspects of ecosystem functioning during the succession of tropical forest communities, our results can inform the restoration of climate-resilient forests.

Role of horizontal gene transfer and cooperation in rhizosphere microbiome assembly

Microbes employ a variety of mechanisms, encompassing chemical signaling (e.g., quorum-sensing molecules) and genetic processes like horizontal gene transfer (HGT), to engage in interactions. HGT, in particular, holds a pivotal role as it facilitates the generation of metabolic diversity, thus directly or indirectly influencing microorganisms' interactions and functioning within their habitat. In this study, we investigate the correlations between enhanced metabolic diversity through HGT and cooperative behavior in the rhizosphere. Despite the potential drawbacks of cooperative behavior, which renders it susceptible to exploitation by cheaters based on evolutionary theory, HGT emerges as a mitigating factor. It serves as a valuable and adaptive tool for survival in competitive environments, notably the rhizosphere. By initiating a comprehensive discussion on these processes combined, we anticipate achieving a profound understanding of the rhizosphere microbiome, ultimately enhancing soil microbiology management and the exploitation of this ecological niche.

Study on the difference of gut microbiota in DLY and Diqing Tibetan pigs induce by high fiber diet

In order to investigate the regularity of fecal microorganisms changes in Landrace × Large White × Duroc (DLY) and Diqing Tibetan pigs (TP) induced by dietary fiber, and further explore the buffering effect of different intestinal flora structures on dietary stress. DLY (n = 15) and TP (n = 15) were divided into two treatments. Then, diet with 20% neutral detergent fiber (NDF) was supplemented for 9 days. Our results showed that the feed conversion efficiency of TP was significantly higher (p < 0.05) than that of DLY. The fecal microorganisms shared by the two groups gradually increased with the feeding cycle. In addition, the dispersion of Shannon, Simpson, ACE and Chao of TP decreased. Also, we found that the fecal microorganisms of TP (R2 = 0.2089, p < 0.01) and DLY (R2 = 0.3982, p < 0.01) showed significant differences in different feeding cycles. With the prolongation of feeding cycle, the similarity of fecal microbial composition between DLY and TP increased. Our study strongly suggests that the complex environment and diet structure have shaped the unique gut microbiota of TP, which plays a vital role in the buffering effect of high-fiber diets.

Contribution of the microbial community to operational stability in an anammox reactor: Neutral theory and functional redundancy perspectives

A comprehensive understanding of microbial assembly is essential for achieving stable performance in biological wastewater treatment. Nevertheless, few studies have quantified these phenomena in detail, particularly in anammox-based processes. This study integrated mathematical and microbial approaches to analyze a 330-day anammox reactor with stable nitrogen removal efficiency (97 - 99%) despite changes in the high nitrogen loading rate, nitrogen concentration, and hydraulic retention time. A high value of functional redundancy (0.82) was obtained, with 84.6% of the microbial species following the neutral community model in stochastic processes, thus maintaining the stability of the dominant species and function in the microbial community. This study represents an initial attempt to quantify and evaluate the importance of functional redundancy in an anammox reactor. Based on these findings, engineering strategies have also been proposed to preserve high functional redundancy in stabilizing system performance under varying operating conditions.

Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy

Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.

IMPORTANCE

Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.

A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential

With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.

Metagenomic insights into the functional potential of non-sanitary landfill microbiomes in the Indian Himalayan region, highlighting key plastic degrading genes

Solid waste management in the Indian Himalayan Region (IHR) is a growing challenge, intensified by increasing population and tourism, which strain non-sanitary landfills. This study investigates microbial diversity and functional capabilities within these landfills using a high-throughput shotgun metagenomic approach. Physicochemical analysis revealed that the Manali and Mandi landfill sites were under heavy metal contamination and thermal stress. Taxonomic annotation identified a dominance of bacterial phyla, including Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with genera like Pseudomonas and Bacillus prevalent. Squeezemeta analysis generated 9,216,983 open reading frames (ORFs) across the sampling sites, highlighting diverse metabolic potentials for heavy metal resistance and degrading organic, xenobiotics and plastic wastes. Hierarchical clustering and principal component analysis (PCA) identified distinct gene clusters in Manali and Mandi landfill sites, reflecting differences in pollution profiles. Functional redundancy of landfill microbiome was observed with notable xenobiotic and plastic degradation pathways. This is the first comprehensive metagenomic assessment of non-sanitary landfills in the IHR, providing valuable insights into the microbial roles in degrading persistent pollutants, plastic waste, and other contaminants in these stressed environments.

Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats

Wild animals face numerous challenges in less ideal habitats, including the lack of food as well as changes in diet. Understanding how the gut microbiomes of wild animals adapt to changes in food resources within suboptimal habitats is critical for their survival. Therefore, we conducted a longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome assembly over one year. The three gibbon species exhibited significantly different gut microbial diversity and composition. N. hainanus showed the lowest alpha diversity and highest nestedness, suggesting a more specialized and potentially stable microbial community in terms of composition, while H. tianxing displayed high species turnover and low nestedness, reflecting a more dynamic microbial ecosystem, which may indicate greater sensitivity to environmental changes or a flexible response to habitat variability. The gut microbial community of N. concolor was influenced by homogeneous selection in the deterministic process, primarily driven by Prevotellaceae. In contrast, the gut microbial communities of H. tianxing and N. hainanus were influenced by dispersal limitation in the stochastic process, driven by Acholeplasmataceae and Fibrobacterota, respectively. Further, the microbial response patterns to leaf feeding in N. hainanus differed from those of the other two gibbon species. In conclusion, this first cross-species comparative study provides initial insights into the different ecological adaptive strategies of gut microbiomes from a point of community assembly, which could contribute to the long-term conservation of wild primates. In this study, we conducted longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome (composition, alpha diversity, beta diversity and assembly process) over one year.

Ammonifying and phosphorus-solubilizing function of Aliikangiella maris sp. nov. isolated from Phaeocystis globosa bloom and algal-bacterial interactions

Phaeocystis globosa blooms are of escalating global concern due to their substantial ecological impacts on marine ecosystems. Emerging evidence indicates that algae-bacterial interactions play pivotal roles in shaping the ecology and evolution of harmful algal blooms, although much of this interplay remains unexplored. We successfully isolated and propagated two novel bacterial strains from Phaeocystis globosa bloom. Two novel Gram-negative, non-spore-forming, motile, rod-shaped, and yellow-pigmented bacteria were designated strains GXAS 306T and GXAS 311. According to phenotypic, chemotaxonomic, phylogenomic, and comparative genomic analyses data, strains GXAS 306T and GXAS 311 were considered to represent a novel species of the genus Aliikangiella. Genomic analysis revealed that strain GXAS 306T had many potential functions favorable for interacting with algae, and further experimental evidence confirmed the ammonifying and phosphorus-solubilizing function. Co-culture experiments showed that strain GXAS 306T significantly improved algal growth parameters of two typical P. globosa strains (Pg293 and PgV01), particularly under nitrogen or phosphorus deficiency. Specifically, cell densities were observed to increase by 19.6-86.0%, accompanied by substantial enhancements in photosynthetic performance with increases of 8.0-30.6% in F v /F m and 10.9-27.9% in r ETRmax. Overall, these results shed light on intricate relationships between P. globosa and its associated bacterial partners, which may influence the growth characteristics of algae.