Organism body size structures the soil microbial and nematode community assembly at a continental and global scale

Salinity-driven differentiation of bacterial and fungal communities in coastal wetlands: Contrasting assembly processes and spatial dynamics

Coastal wetlands are critical for carbon sequestration and coastal protection, yet increasingly threatened by salinization. While soil microbiota mediate these ecosystems' functioning and stability, the mechanisms governing bacterial and fungal assembly across intermediate spatial scales remain poorly resolved. Here, we investigated microbial communities across a 30-km seaward-to-landward gradient in the Yellow River Delta during May 2020 using 16S rRNA and ITS sequencing coupled with ecological modeling. Our results revealed a striking dichotomy: bacterial communities were predominantly structured by deterministic environmental filtering (explained 49.2 % of variation), whereas fungal communities exhibited stronger spatial dependence (Mantel r = 0.28 vs 0.06 for bacteria, P < 0.01). Null model analyses confirmed salinity-driven variable selection for bacteria (60.0 % contribution) and stochastic homogenizing dispersal for fungi (44.9 %). Microbial interaction network analysis (based on taxon co-occurrence patterns) demonstrated the fungal network resisted salinity perturbations through high modularity (0.87 vs 0.68 for bacteria) and short path lengths (3.10 vs 4.90). Path analysis further showed geographic distance indirectly stabilized fungal networks (indirect effect = 0.33) but minimally affected bacteria. These findings highlight contrasting ecological strategies: bacteria prioritize deterministic variable selection for rapid resource acquisition, whereas fungi rely on homogenizing dispersal for spatial stability. These findings advance our understanding of microbial responses to salinization under climate change, informing adaptive management strategies to preserve microbial-mediated carbon storage and ecosystem functionality in salt-affected soils.

Targeted manipulation of food webs in the plant rhizosphere

Trophic interactions between micro- and macro-organisms structure food webs in the plant rhizosphere. These interactions affect the plant-associated microbiota and nutrient dynamics, and influence plant health and performance. In this forum article we discuss the need for, and challenges associated with, targeted manipulation of soil food webs toward the development of multitrophic synthetic communities.

Uncovering Microbial Diversity and Community Structure of Black Spots Residing in Tomb Mural Painting

Microbes colonizing cultural artifacts are a ubiquitous phenomenon which may occur during burial, post-excavation, and storage periods, thereby seriously affecting sustainable heritage conservation. In this study, high-throughput sequencing technology was applied to analyze the microbial community structure in ancient mural paintings and the surrounding air, as well as to identify the most characteristic taxa causing black spot contamination. The results showed that members of the genera Gliomastix and Ochroconis were highly abundant in black-spots-contaminated areas and rarely detected in the air and uncontaminated mural paintings. Air samples of the two tombs showed no significant difference in Chao1 and Shannon indices, whereas statistically significant differences were observed compared to those samples collected from black spots. The taxonomic diversity of the microbial community in the soil-covered mural paintings and air exhibited similar structures at the genus level. Moreover, when compared to other areas of the two tombs, the samples from black spots differed not only in microbial community composition but also in microbial assembly processes and the co-occurrence patterns, such as much less network complexity in the black spots area. Functional predictions uncover the presence of microbial functional profiles involved in nitrogen cycling, organic matter degradation, and animal and human pathogens, representing a potential threat to cultural relics and public health. These results advance our understanding of the impacts of archeological excavations on the microbial community variation in tomb mural paintings.

New insights into the assembly processes of biofilm microbiota communities: Taking the world's largest water diversion canal as a case study

Systematic studies on the assembly process and drivers of biofilm microbiota communities are still limited. In this study, we used the artificial concrete channel of the world's largest interbasin water diversion project, the middle route of the South-to-North Water Diversion Project in China, as a model system to investigate the assembly mechanisms of biofilm microbiota communities. Our study revealed that water temperature (p < 0.001) and hydrodynamic disturbance (p < 0.05) significantly influenced biofilm biomass. The bacterial communities exhibited substantial spatial heterogeneity, whereas the eukaryotic communities presented pronounced spatial and seasonal variations (PERMANOVA, p < 0.05). Neutral model and null model analyses indicated that dispersal limitation and homogeneous selection (54.8 %-69.7 % in bacteria and 55.9 %-76.1 % in eukaryotes) predominantly governed community assembly. Deterministic effects such as hydrodynamic conditions and temperature strongly influence eukaryotes (homogeneous selection accounts for 63.9 % of eukaryotes in spring). The metacommunity network could be divided into five primary modules with key nodes, including many species from Proteobacteria, Chlorophyta, Bacillariophyta, and Cyanobacteria. Bacteria, such as Proteobacteria, Chlorophyta, Cyanobacteria, and Bacteroidota, act as connectors and a vital role in maintaining the coexistence of modules. Finally, we confirmed that physicochemical (hydrodynamic conditions, temperature, dissolved oxygen conductivity permanganate index), spatial, and biological factors have significant effects on both bacterial and eukaryotic communities as well as metacommunity networks. Our findings provide new insights into the different assembly processes and drivers of bacterial and eukaryotic communities in biofilms, which is highly important for water quality monitoring and sustainable water diversion.

Impacts of trophic interactions on carbon accrual in soils

The transformation and stabilization of soil organic carbon (SOC) are important processes of global carbon (C) cycling, with implications for climate change. Much attention has been given to microbial anabolic processes driving SOC accrual. These are referred to as the soil microbial carbon pump (MCP), which emphasizes the contribution of microbial metabolism and necromass to the stable soil C pool. However, we still lack a fundamental understanding of how trophic interactions between soil fauna and microbiota modulate microbial necromass production and, consequently, SOC formation. Here, we provide an ecological perspective on the impacts of trophic interactions on modulating necromass formation and C accrual in soils. We discuss the mechanisms of trophic interactions in the context of food web ecology, with a focus on trophic control of microbial population densities and their influences on soil microbiota assembly. We foresee that integrating trophic interactions into the soil MCP framework can provide a more comprehensive basis for guiding future research efforts to elucidate the mechanisms modulating microbial necromass and SOC formation in terrestrial ecosystems. This perspective offers an ecological foundation for leveraging the use of biological interventions to enhance SOC accrual, providing valuable insights for sustainable C management strategies.

Comparing field and lab quantitative stable isotope probing for nitrogen assimilation in soil microbes

Soil microbial communities play crucial roles in nutrient cycling and can help retain nitrogen in agricultural soils. Quantitative stable isotope probing (qSIP) is a useful method for investigating taxon-specific microbial growth and utilization of specific nutrients, such as nitrogen (N). Typically, qSIP is performed in a highly controlled lab setting, so the field relevance of lab qSIP studies remains unknown. We conducted and compared tandem lab and field qSIP to quantify the assimilation of 15N by maize-associated soil prokaryotic communities at two agricultural sites. Here, we show that field qSIP with 15N can be used to measure taxon-specific microbial N assimilation. Relative 15N assimilation rates were generally lower in the field, and the magnitude of this difference varied by site. Rates differed by method (lab vs field) for 19% of the top N assimilating genera. The field and lab measures were more comparable when relative assimilation rates were weighted by relative abundance to estimate the proportion of N assimilated by each genus with only ~10% of taxa differing by method. Of those that differed, the taxa consistently higher in the lab were inclined to have opportunistic lifestyle strategies, whereas those higher in the field had niches reliant on plant roots or in-tact soil structure (biofilms, mycelia). This study demonstrates that 15N-qSIP can be successfully performed using field-incubated soils to identify microbial allies in N retention and highlights the strengths and limitations of field and lab qSIP approaches.

IMPORTANCE

Soil microbes are responsible for critical biogeochemical processes in natural and agricultural ecosystems. Despite their importance, the functional traits of most soil organisms remain woefully under-characterized, limiting our ability to understand how microbial populations influence the transformation of elements such as nitrogen (N) in soil. Quantitative stable isotope probing (qSIP) is a powerful tool to measure the traits of individual taxa. This method has rarely been applied in the field or with 15N to measure nitrogen assimilation. In this study, we measured genus-specific microbial nitrogen assimilation in two agricultural soils and compared field and lab 15N qSIP methods. Our results identify taxa important for nitrogen assimilation in agricultural soils, shed light on the field relevance of lab qSIP studies, and provide guidance for the future application of qSIP to measure microbial traits in the field.

Vertical Stratification Reduces Microbial Network Complexity and Disrupts Nitrogen Balance in Seasonally Frozen Ground at Qinghai Lake in Tibet

Global climate change has accelerated the reduction of permafrost regions across different altitude gradients, shortening the duration of the freezing period to varying extents. However, the response of the soil microorganisms of frozen soils along altitude gradients remains unclear. In this study, we employed 16S rRNA sequencing and LC-MS metabolomics to investigate the response of soil microbial communities and soil metabolites to vertical stratification in the permafrost soils of the Qinghai Lake region. The results indicated that Proteobacteria, Firmicutes, and Actinobacteria were key soil bacterial phyla in the permafrost soils of Qinghai Lake during the freezing period, with Proteobacteria and Firmicutes showing significant sensitivity to vertical stratification (p < 0.05). The majority of the physicochemical factors exhibited a trend of initially increasing and then decreasing with increasing altitude, whereas pH showed the opposite trend. pH and moisture content were identified as the most important environmental factors influencing soil bacterial community structure. Deterministic processes dominated the assembly of bacterial communities of frozen soils in the Qinghai Lake basin. Co-occurrence network analysis showed that increasing altitude gradients led to a higher average degree of the bacterial network, while reducing network complexity and inter-species connectivity. Soil metabolomics analysis revealed that vertical stratification altered the metabolic profiles of 27 metabolites, with the significantly changed metabolites primarily associated with carbohydrate and amino acid metabolism. In conclusion, the characteristics of the Qinghai Lake permafrost were regulated by regional vertical stratification, which further influenced microbial community structure and soil metabolic characteristics, thereby altering carbon and nitrogen stocks. Specifically, higher altitudes were more favorable for the retention of the carbon and nitrogen stocks of frozen soils in the Qinghai Lake basin.

Habitat-specific regulation of microbiota in long-distance water diversion systems

Long-distance water diversion projects typically utilize various hydro-engineering facilities, creating complex and dynamic habitats. However, the microbial dynamics of multi-trophic microorganisms during water diversion and their responses to different hydro-engineering habitats remain poorly understood. In this study, we investigated bacteria, fungi, protists, and metazoa across tunnels, reservoirs, and inverted siphon piping along the main and northern branches of the Yellow River Diversion Project into Shanxi, during spring, summer, and autumn. Our results showed that both seasonal factors and hydro-engineering facilities significantly influenced the composition and diversity of microbiota. Bacterial community composition remained relatively stable during water transport, while fungi, protists, and metazoa exhibited greater spatial variability and habitat specificity. Stochastic processes predominantly governed the community assembly of all microbial groups across all hydro-engineering habitats. The structural features of the main network modules within the co-occurrence networks of multi-trophic species were highly consistent across different seasons within the same habitat, indicating the stable adaptation of microbiota interactions to the same habitat. Patterns of intra-kingdom (within bacteria, fungi, protists, or metazoa) and inter-kingdom (between bacteria, fungi, protists, and metazoa) associations of microbiota in different habitats varied, reflecting specific adaptations of microorganisms to particular habitats and suggesting an important role for environmental filtering. Variance partitioning analysis revealed that environmental factors accounted for 34.21 % to 45.19 % of the variation in the four microbial taxa. Our findings reveal the ecological processes of microbial assembly and adaptation in large-scale water diversion projects, providing insights for project management and risk control.

Differences in Biogeographic Patterns and Mechanisms of Assembly in Estuarine Bacterial and Protist Communities

As transitional ecosystems between land and sea, estuaries are characterized by a unique environment that supports complex and diverse microbial communities. A comprehensive analysis of microbial diversity and ecological processes at different trophic levels is crucial for understanding the ecological functions of estuarine ecosystems. In this study, we systematically analyzed the diversity patterns, community assembly, and environmental adaptability of bacterial and protist communities using high-throughput sequencing techniques. The results revealed a higher alpha diversity for the bacteria than for protists, and the beta diversity pattern was dominated by species turnover in both communities. In addition, the two community assemblages were shown to be dominated by deterministic and stochastic processes, respectively. Furthermore, our results emphasized the influence of the local species pool on microbial communities and the fact that, at larger scales, geographic factors played a more significant role than environmental factors in driving microbial community variation. The study also revealed differences in environmental adaptability among different microbial types. Bacteria exhibited strong adaptability to salinity, while protists demonstrated greater resilience to variations in dissolved oxygen, nitrate, and ammonium concentrations. These results suggested differences in environmental adaptation strategies among microorganisms at different trophic levels, with bacteria demonstrating a more pronounced environmental filtering effect.

Soil carbon fractions drive microbial community assembly processes during forest succession

Forest succession is one of the foremost ecosystem restoration strategies, while soil microbes play essential roles in the processes by modulating carbon (C) cycling. The fraction of soil organic carbon (SOC) lead to shifts in the selective environment, which in turn contribute to changes in microbial assembly process. Here, by studying the microbial community during forest succession, the main role of SOC composition in determining soil microbial community structure and assembly process during forest succession was revealed in Changbai Mountains, China. We found that forest succession altered the structure and composition of bacterial and fungal communities and might be associated with potential changes in function. The null models indicated that forest succession enhanced the bacterial dispersal limitation process and weakened the fungal dispersal limitation processes. The labile SOC drove the microbial assembly processes by affecting microbial alpha diversity and keystone taxa, providing a new targeted therapy and an indicator of the soil microenvironment. This results highlighted the non-negligible role of labile SOC in determining microbial community assembly during long-term vegetation succession. Overall, this study could provide a perspective on the importance of the composition of SOC in shaping microbial differences and community assembly during forest succession, which cannot be overlooked in forest function studies.

Assembly of soil multitrophic community regulates multifunctionality via multifaceted biotic factors in subtropical ecosystems

Soil biodiversity underpins multiple ecosystem functions and services essential for human well-being. Understanding the determinants of biodiversity-ecosystem function relationships (BEFr) is critical for the conservation and management of soil ecosystems. Community assembly processes determine community diversity and structure. However, there remains limited systematic research on how the assembly processes of multiple organismal groups affect soil ecosystem functions through their influence on biodiversity and species interactions. Here, we analyzed 331 soil samples from different land-use types (cropland, forest, and grassland) in the Qinling-Daba Mountains to investigate the drivers, assembly processes, and network stability of multitrophic organisms. High-throughput sequencing was used to examine archaea, bacteria, fungi, algae, protozoa, and invertebrates, while enzyme activity assays were used to assess ecosystem multifunctionality related to nutrient provisioning. Our results indicated that biotic factors contributed to 62.81-94.97 % of α-diversity and 4.19-52.37 % of β-diversity in multitrophic organisms, even when considering the influence of abiotic factors. Protozoan α- and β-diversity most significantly explained the α- and β-diversity of bacteria, fungi, algae, and invertebrates in soil ecosystems, serving as important indicators for assessing soil multifunctionality and ecosystem health. Furthermore, the assembly processes in prokaryotes were primarily governed by stochasticity (>50 %), whereas those in eukaryotic groups were dominated by deterministic processes (<50 %). Diversity and network stability increased with greater stochasticity in bacterial communities where stochastic processes predominated. Conversely, in fungal and protozoan communities dominated by deterministic processes, diversity and network stability decreased as deterministic processes intensified. Importantly, stochastic processes in soil multitrophic assembly enhanced ecosystem multifunctionality by increasing α-diversity, β-diversity, and network stability. These findings provide valuable insights into the regulation of BEFr by multitrophic assembly processes. Future research should further explore the role of these assembly processes in soil ecosystem functioning under land-use change scenarios.

Soil fungal networks exhibit sparser interactions than bacterial networks in diseased banana plantations

Soil microorganisms play a crucial role in suppressing soil-borne diseases. Although the composition of microbial communities in healthy versus diseased soils is somewhat understood, the interplay between microbial interactions and disease incidence remains unclear. This study used 16S rRNA and fungal internal transcribed spacer (ITS) sequencing to investigate the bacterial and fungal community composition in three soil types: forest soil (Z), soil from healthy banana plantations (H), and soil from diseased banana plantations (D). Principal coordinate analysis revealed significant differences among the bacterial and fungal community structures of the three soil types. Compared with those in forest soil, bacterial and fungal diversities significantly decreased in diseased banana soil. Key microorganisms, including the bacteria Chloroflexi and Pseudonocardia and the fungi Mortierellomycota and Moesziomyces, were significantly increased in soil from diseased banana plantations. Redundancy analysis revealed that total nitrogen and available phosphorus were the primary drivers of the soil microbial community structure. The neutral community model posited that the bacterial community assembly in banana plantations is predominantly governed by stochastic processes, whereas the fungal community assembly in banana plantations is primarily driven by deterministic processes. Furthermore, co-occurrence network analysis revealed that the proportion of positive edges in the fungal network of soil from diseased banana plantations was 5.92 times lower than that in soil from healthy banana plantations, and its fungal network structure was sparse and simple. In conclusion, reduced interactions within the fungal network were significantly linked to the epidemiology of Fusarium wilt. These findings underscore the critical role of soil fungal communities in modulating pathogens.

IMPORTANCE

Soil microorganisms are pivotal in mitigating soil-borne diseases. The intricate mechanisms underlying the interactions among microbes and their impact on disease occurrence remain enigmatic. This study underscores that a reduction in fungal network interactions correlates with the incidence of soil-borne Fusarium wilt.

Are plant traits drivers of endophytic communities in seasonally flooded tropical forests?

PREMISE

In the Amazon basin, seasonally flooded (SF) forests offer varying water constraints, providing an excellent way to investigate the role of habitat selection on microbial communities within plants. However, variations in the microbial community among host plants cannot solely be attributed to environmental factors, and how plant traits contribute to microbial assemblages remains an open question.

METHODS

We described leaf- and root-associated microbial communities using ITS2 and 16 S high-throughput sequencing and investigated the stochastic-deterministic balance shaping these community assemblies using two null models. Plant ecophysiological functioning was evaluated by focusing on 10 leaf and root traits in 72 seedlings, belonging to seven tropical SF tree species in French Guiana. We then analyzed how root and leaf traits drove the assembly of endophytic communities.

RESULTS

While both stochastic and deterministic processes governed the endophyte assembly in the leaves and roots, stochasticity prevailed. Discrepancies were found between fungi and bacteria, highlighting that these microorganisms have distinct ecological strategies within plants. Traits, especially leaf traits, host species and spatial predictors better explained diversity than composition, but they were modest predictors overall.

CONCLUSIONS

This study widens our knowledge about tree species in SF forests, a habitat sensitive to climate change, through the combined analyses of their associated microbial communities with functional traits. We emphasize the need to investigate other plant traits to better disentangle the drivers of the relationship between seedlings and their associated microbiomes, ultimately enhancing their adaptive capacities to climate change.

Strengthened plant-microorganism interaction after topsoil removal cause more deterministic microbial assembly processes and increased soil nitrogen mineralization

Topsoil removal, among other restoration measures, has been recognized as one of the most successful methods to restore biodiversity and ecosystem functioning in European grasslands. However, knowledge about how removal as well as other restoration methods influence interactions between plant and microbial communities is very limited. The aims of the current study were to understand the impact of topsoil removal on plant-microorganism interactions and on soil nitrogen (N) mineralization, as one example of ecosystem functioning. We examined how three different grassland restoration methods, namely 'Harvest only', 'Topsoil removal' and 'Topsoil removal + Propagules (plant seed addition)', affected i) the interactions between plants and soil microorganisms, ii) soil microbial community assembly processes, and iii) soil N mineralization. We compared the outcome of these three restoration methods to initial degraded and target semi-natural grasslands in the Canton of Zurich, Switzerland. We were able to show that 'Topsoil removal' and 'Topsoil removal + Propagules', but not 'Harvest only', reduced the soil total N pool and available N concentration, but increased soil N mineralization and strengthened the plant-microorganism interactions. Microbial community assembly processes shifted towards more deterministic after both topsoil removal treatments. These shifts could be attributed to an increase in dispersal limitation and selection due to stronger interactions between plants and soil microorganisms. The negative relationship between soil N mineralization and microbial community stochasticity indicated that microbial assembly processes, to some extent, can be incorporated into model predictions of soil functions. Overall, the results suggest that topsoil removal may change the microbial assembly processes and thus the functioning of grassland ecosystems by enhancing the interaction between plants and soil microorganisms.

Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest

The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.

Community structure and assembly of myxomycetes in northern Chinese forests under geographic barriers

The study of myxomycete biogeography has a long-standing history and has consistently drawn scholarly interest. Nevertheless, studies focusing specifically on the spatial and temporal distribution patterns of myxomycete diversity are relatively limited, with even fewer investigating the mechanisms driving the generation and maintenance of myxomycete diversity. Therefore, this study selected two geographically distant sampling sites within northern Chinese forests to investigate myxomycete species composition, community structure, environmental drivers, and assembly patterns under geographic barriers. We established plots in the Altai Mountains (ALE) and the Greater Khingan Mountains (GKM), gathered bark and litter, and conducted 80-day moist chamber cultures of myxomycetes. Additionally, myxomycete specimens were collected in the field simultaneously to supplement the data set. This study collected 541 myxomycete specimens belonging to 73 species from 28 genera, spanning 12 families and eight orders. The ALE and the GKM had 20 identical species, accounting for 27% of the total species. Myxomycetes from both regions exhibited abundant occurrence 18 days after cultivation, with the quantity on bark substrates notably higher than on litter. Arcyria pomiformis and Comatricha elegans were the most common species in moist chamber cultures. Mantel test outcomes revealed that environmental factors had no significant impact on myxomycete community similarity between the two areas, aligning with findings from the neutral community model analysis, indicating a predominant influence of stochastic processes on myxomycete community structure in moist chamber cultures. This study represents the first application of a quantitative framework to analyze myxomycete community assembly cultivated in moist chambers.

Disentangling the assembly patterns and drivers of microbial communities during thermal stratification and mixed periods in a deep-water reservoir

Effect of periodic thermal stratification in deep-water reservoirs on aquatic ecosystems has been a research hotspot. Nevertheless, there is limited information on the response patterns of microbial communities to environmental changes under such specialized conditions. To fill this gap, samples were collected from a typical deep-water reservoir during the thermal stratification period (SP) and mixed period (MP). Three crucial questions were answered: 1) How microbial communities develop with stratified to mixed succession, 2) how the relative importance of stochastic and deterministic processes to microbial community assembly, shifted in two periods, and 3) how environmental variables drive microbial co-occurrence networks and functional group alteration. We used Illumina Miseq high-throughput sequencing to investigate the dynamics of the microbial community over two periods, constructed molecular ecological networks (MENs), and unraveled assembly processes based on null and neutral models. The results indicated that a total of 33.9 % and 27.7 % of bacterial taxa, and 23.1 % and 19.4 % of fungal taxa were enriched in the stratified and mixed periods, respectively. Nitrate, water temperature, and total phosphorus drove the variation of microbial community structure. During the thermal stratification period, stochastic processes (dispersal limitation) and deterministic processes (variable selection) dominated the assembly of bacterial and fungal communities, followed by a shift to stochastic processes dominated by dispersal limitation in two communities. The MENs results revealed that thermal stratification-induced environmental stresses increased the complexity of microbial networks but decreased its robustness, resulting in more vulnerable ecological networks. Therefore, this work provides critical ecological insights for the longevity and sustainability of water quality management in an artificially regulated engineered system.

Pinewood nematode induced changes in the assembly process of gallery microbiomes benefit its vector beetle's development

Microbiomes play crucial roles in insect adaptation, especially under stress such as pathogen invasion. Yet, how beneficial microbiomes assemble remains unclear. The wood-boring beetle Monochamus alternatus, a major pest and vector of the pine wilt disease (PWD) nematode, offers a unique model. We conducted controlled experiments using amplicon sequencing (16S rRNA and ITS) within galleries where beetles and microbes interact. PWD significantly altered bacterial and fungal communities, suggesting distinct assembly processes. Deterministic factors like priority effects, host selection, and microbial interactions shaped microbiome composition, distinguishing healthy from PWN-infected galleries. Actinobacteria, Firmicutes, and Ophiostomataceae emerged as potentially beneficial, aiding beetle's development and pathogen resistance. This study unveils how nematode-induced changes in gallery microbiomes influence beetle's development, shedding light on microbiome assembly amid insect-pathogen interactions. Insights gleaned enhance understanding of PWD spread and suggest novel management strategies via microbiome manipulation.IMPORTANCEThis study explores the assembly process of gallery microbiomes associated with a wood-boring beetles, Monochamus alternatus, a vector of the pine wilt disease (PWD). By conducting controlled comparison experiments and employing amplicon approaches, the study reveals significant changes in taxonomic composition and functional adaptation of bacterial and fungal communities induced by PWD. It identifies deterministic processes, including priority effects, host selection, and microbial interactions, as major drivers in microbiome assembly. Additionally, the study highlights the presence of potentially beneficial microbes such as Actinobacteria, Firmicutes, and Ophiostomataceae, which could enhance beetle development and resistance to pathogens. These findings shed light on the intricate interplay among insects, microbiomes, and pathogens, contributing to a deeper understanding of PWD prevalence and suggesting innovative management strategies through microbiome manipulation.

Assembly and maintenance of phyllosphere microbial diversity during rubber tree leaf senescence

Phyllosphere microorganisms execute important ecological functions including supporting host plant growth, enhancing host resistance to abiotic stresses, and promoting plant diversity. How leaf developmental stages affect plant-microbiome interactions and phyllosphere microbial community assembly and diversity is poorly understood. In this study, we utilized amplicon sequencing of 16S rRNA and ITS genes to investigate the composition and diversity of microbial communities across different leaf developmental stages of rubber trees. Our findings reveal that endophytic microbial communities, particularly bacterial communities, are more influenced by leaf senescence than by epiphytic communities. The high abundance of metabolism genes in the endosphere of yellow leaves contributes to the degradation and nutrient relocation processes. Nutrient loss leads to a higher abundance of α-Proteobacteria (r-selected microorganisms) in the yellow leaf endosphere, thereby promoting stochastic community assembly. As leaves age, the proportion of microorganisms entering the inner layer of leaves increases, consequently enhancing the diversity of microorganisms in the inner layer of leaves. These results offer insights into the mechanisms governing community assembly and diversity of leaf bacteria and fungi, thereby advancing our understanding of the evolving functions of microbial communities during leaf senescence in general, and for an important tropical crop species in particular.

The enhanced neutral process with decreasing cell size: a study on phytoplankton metacommunities from the glacier-fed river of Qinghai-Xizang Plateau

The cell size of phytoplankton is an important defining functional trait that can serve as a driver and sentinel of phytoplankton community structure and function. However, the study of the assembly patterns and drivers of phytoplankton metacommunities with different cell sizes has not been widely carried out. In this study, we systematically investigated the biodiversity patterns, drivers, and assembly processes of the three phytoplankton cell sizes (micro: 20-200 μm; nano: 2-20 μm; pico: 0.2-2 μm) in the Za'gya Zangbo River from the source to the estuary using 18S rDNA amplicon sequencing. The results demonstrated that the alpha diversity and co-occurrence network complexity for all three sizes of phytoplankton increased to a peak downstream of the glacier sources and then decreased to the estuary. The nanophytoplankton subcommunity consistently had the highest alpha diversity and co-occurrence network complexity. On the other hand, total beta diversity followed a unimodal trend of decreasing and then increasing from source to estuary, and was dominated by species replacement components. In addition, deterministic processes driven mainly by physiochemical indices (PCIs) and biogenic elements (BGEs) dominated the assembly of micro- and nanophytoplankton subcommunities, whereas stochastic processes driven by geographical factors (GGFs) dominated the assembly of picophytoplankton subcommunities. The results explained the contradictions in previous studies of phytoplankton community assembly processes in highland aquatic ecosystems, elucidating the different contributions of deterministic and stochastic processes, and the complexity of compositional mechanisms in shaping the assembly of micro-, nano-, and picophytoplankton in this highland glacial river.

IMPORTANCE

The cell size of phytoplankton is a key life-history trait and key determinant, and phytoplankton of different cell sizes are differentially affected by ecological processes. However, the study of the assembly patterns and drivers of phytoplankton metacommunities with different cell sizes has not been widely carried out. We provide an in-depth analysis of phytoplankton community diversity across three cell sizes in the glacier-fed river, describing how the pattern of phytoplankton communities differs across cell sizes in response to geochemical gradients. The results show that the smaller phytoplankton (picophytoplankton) are relatively more influenced by dispersal-based stochastic processes, whereas larger ones (microphytoplankton and nanophytoplankton) are more structured by selection-based deterministic processes.

Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers

The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.

Characterization of bacterial community dynamics dominated by salinity in lakes of the Inner Mongolian Plateau, China

Microorganisms in lakes are sensitive to salinity fluctuations. Despite extensive prior research on bacterial communities, our understanding of their characteristics and assembly mechanisms in lakes, especially in desert lakes with different salinities. To address this issue, we collected three samples from freshwater lakes, six from brackish lakes, and five from salt lakes in the Badanjilin Desert. The 16S rRNA gene sequencing was applied to investigate the bacterial interactions with rising salinity, community coexistence patterns, and assembly mechanisms. Our findings suggested that the increased lake salinity significantly reduces the bacterial community diversity and enhanced the community differentiation. Significant variations were observed in the contribution of biomarkers from Cyanobacteria, Chloroflexi, and Halobacterota to the composition of the lake bacterial communities. The bacterial communities in the salt lakes exhibited a higher susceptibility to salinity limitations than those in the freshwater and brackish lakes. In addition, the null modeling analyses confirmed the quantitative biases in the stochastic assembly processes of bacterial communities across freshwater, brackish, and saline lakes. With the increasing lake salinity, the significance of undominated and diffusion limitation decreased slightly, and the influence of homogenizing dispersal on community assembly increased. However, the stochasticity remained the dominant process across all lakes in the Badanjilin Desert. The analysis of co-occurring networks revealed that the rising salinity reduced the complexity of bacterial network structures and altered the interspecific interactions, resulting in the increased interspecies collaboration with increasing salinity levels. Under the influence of salinity stress, the key taxon Cyanobacteria in freshwater lakes (Schizothrix_LEGE_07164) was replaced by Proteobacteria (Thalassobaculum and Polycyclovorans) in brackish lakes, and Thermotogota (SC103) in salt lakes. The results indicated the symbiotic patterns of bacterial communities across varying salinity gradients in lakes and offer insights into potential mechanisms of community aggregation, thereby enhancing our understanding of bacterial distribution in response to salinity changes.

Smaller microorganisms outcompete larger ones in resistance and functional effects under disturbed agricultural ecosystems

Body size is a key ecological trait of soil microorganisms related to their adaptation to environmental changes. In this study, we reveal that the smaller microorganisms show stronger community resistance than larger organisms in both maize and rice soil. Compared with larger organisms, smaller microorganisms have higher diversity and broader niche breadth to deploy survival strategies, because of which they are less affected by environmental selection and thus survive in complex and various kinds of environments. In addition, the strong correlation between smaller microorganisms and ecosystem functions reflects their greater metabolic flexibility and illustrates their significant roles in adaptation to continuously changing environments. This research highlights the importance of body size in maintaining stability of the soil microbiome and forecasting agroecosystem dynamics under environmental disturbances.

Fertilization regime changes rhizosphere microbial community assembly and interaction in Phoebe bournei plantations

Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat. KEY POINTS: • Fertilization altered the key taxa and microbial interaction • Organic fertilizer facilitated the turnover of rhizosphere microbial communities • Stochasticity governed soil fungal and bacterial community assembly.

Body size: A hidden trait of the organisms that influences the distribution of antibiotic resistance genes in soil

Body size is a key life-history trait of organisms, which has important ecological functions. However, the relationship between soil antibiotic resistance gene (ARG) distribution and organisms' body size has not been systematically reported so far. Herein, the impact of organic fertilizer on the soil ARGs and organisms (bacteria, fungi, and nematode) at the aggregate level was analyzed. The results showed that the smaller the soil aggregate size, the greater the abundance of ARGs, and the larger the body size of bacteria and nematodes. Further analysis revealed significant positive correlations of ARG abundance with the body sizes of bacteria, fungi, and nematodes, respectively. Additionally, the structural equation model demonstrated that changes in soil fertility mainly regulate the ARG abundance by affecting bacterial body size. The random forest model revealed that total phosphorus was the primary soil fertility factor influencing the body size of organisms. Therefore, these findings proposed that excessive application of phosphate fertilizers could increase the risk of soil ARG transmission by increasing the body size of soil organisms. This study highlights the significance of organisms' body size in determining the distribution of soil ARGs and proposes a new disadvantage of excessive fertilization from the perspective of ARGs.

Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety 'Jingu 21' (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species.

Biotic and abiotic factors interplay in structuring the dynamics of microbial co-occurrence patterns in tropical mountainsides

Ecological interactions are important for maintaining biodiversity and ecosystem functions. Particularly in stream biofilms, little is known about the distributional patterns of different taxonomic groups and their potential interactions along elevational gradients. Here, we investigated the bacterial and fungal community structures of stream biofilms across elevational gradients on Mount Kilimanjaro, and explored patterns of their distribution, diversity, community structures, and taxa co-occurrence. We found that fungal and bacterial richness were more convergent at higher elevations, while their community structures became significantly more divergent. Inferred network complexity and stability significantly decreased with increasing elevation for fungi, while an opposite trend was observed for bacteria. Further quantitative analyses showed that network structures of bacteria and fungi were more divergent as elevation increased. This pattern was strongly associated with shifts in abiotic factors, such as mean annual temperatures, water PO43--P, and stream width. By constructing bipartite networks, we showed the fungal-bacterial network to be less redundant, more clustering, and unstable with increasing elevation. Abiotic factors (e.g., temperatures and stream width) and microbial community properties (i.e., structure and composition) significantly explained the dynamic changes in fungal-bacterial network properties. Taken together, this study provides evidence for the interplay of biotic and abiotic factors structuring potential microbial interactions in stream biofilms along a mountainside elevational gradient.

Spatial variations impact the soil fungal communities of Larix gmelinii forests in Northeast China

Soil fungi play a critical role in the biogeochemical cycles of forest ecosystems. Larix gmelinii is a strong and important timber tree species, which forms close associations with a wide range of soil fungi. However, the temporal-spatial disparity effects on the assembly of soil fungal communities in L. gmelinii forests are poorly understood. To address these questions, a total of 120 samples, including 60 bulk soil and 60 root samples, were collected from Aershan and Genhe in July (summer) and October (autumn)2021. We obtained 7,788 operational taxonomic units (OTUs) after merging, filtering, and rarefying using high-throughput sequencing. The dominant phyla are Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota. There were 13 dominant families, among which the families with average relative abundance more than 5% included Thelephoraceae, Mortierellaceae, Archaeorhizomycoaceae, and Inocybaceae. In the functional guilds, symbiotrophic fungi had a relative advantage in the identified functions, and the relative abundances of pathotrophic and saprotrophic fungi varied significantly between sites. There were 12 families differentially expressed across compartments, 10 families differentially expressed between seasons, and 69 families were differentially expressed between sites. The variation in alpha diversity in the bulk soil was greater than that in the rhizosphere soil. Among the three parts (compartment, season, and site), the site had a crucial effect on the beta diversity of the fungal community. Deterministic processes dominated fungal community assembly in Genhe, whereas stochastic processes dominated in Aershan. Soil physicochemical properties and climatic factors significantly affected fungal community structure, among which soil total nitrogen and pH had the greatest effect. This study highlights that spatial variations play a vital role in the structure and assembly of soil fungal communities in L. gmelinii forests, which is of great significance for us in maintaining the health of the forests.

Deterministic assembly of grassland soil microbial communities driven by climate warming amplifies soil carbon loss

Perturbations in soil microbial communities caused by climate warming are expected to have a strong impact on biodiversity and future climate-carbon (C) feedback, especially in vulnerable habitats that are highly sensitive to environmental change. Here, we investigate the impact of four-year experimental warming on soil microbes and C cycling in the Loess Hilly Region of China. The results showed that warming led to soil C loss, mainly from labile C, and this C loss is associated with microbial response. Warming significantly decreased soil bacterial diversity and altered its community structure, especially increasing the abundance of heat-tolerant microorganisms, but had no effect on fungi. Warming also significantly increased the relative importance of homogeneous selection and decreased "drift" of bacterial and fungal communities. Moreover, warming decreased bacterial network stability but increased fungal network stability. Notably, the magnitude of soil C loss was significantly and positively correlated with differences in bacterial community characteristics under ambient and warming conditions, including diversity, composition, network stability, and community assembly. This result suggests that microbial responses to warming may amplify soil C loss. Combined, these results provide insights into soil microbial responses and C feedback in vulnerable ecosystems under climate warming scenarios.

Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates

Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.

The size and diversity of microbes determine carbon use efficiency in soil

Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Polysaccharide preferred minority-dominant community assembly and exoenzyme enrichment in transparent exopolymer particles: Implication for global carbon cycle in water

The ubiquitous transparent exopolymer particles (TEPs) are an important organic carbon pool and an ideal microhabitat for bacteria in aquatic environments. They play a crucial role in the global carbon cycle. Organic matter transformation and carbon turnover in TEPs strongly depend on the assembly of their associated bacterial communities and enzyme activity. However, the mechanisms of bacterial community assembly and their potential effects on the organic carbon cycle in TEPs are still unclear. In this study, we comparatively explored the community assembly of TEP-associated bacteria and bacterioplankton from surface freshwater using metagenomics. It was found that the bacterial community assembly in TEPs followed a minority-dominant rule and was governed by homogeneous selection. Pseudomonadota and Actinomycetota, which are responsible for polysaccharide degradation, serve as taxon-specific biomarkers among the abundant and diverse bacteria in TEPs. The network of TEP-associated bacteria displayed stronger robustness than that of bacterioplankton. Bin 76 (majorly Acinetobacter) was the overwhelmingly dominant taxa in TEPs, whereas there was no clearly dominant taxa in TEP-free water. Exoenzyme analysis showed that 64 out of 71 identified polysaccharide hydrolases were markedly linked with the dominant bin 76 in TEPs, while no such linkage was observed for bacterioplankton. Generally, Acinetobacter, which is capable of utilizing polysaccharides, is preferred to be assembled in TEPs together with high polysaccharide hydrolase activity. This may significantly accelerate the turnover of organic carbon in the giant global TEP pool. These findings are important for a deep understanding of the carbon cycle in water.

Trophic relationships between protists and bacteria and fungi drive the biogeography of rhizosphere soil microbial community and impact plant physiological and ecological functions

Rhizosphere microorganisms play a vital role in enhancing plant health, productivity, and the accumulation of secondary metabolites. Currently, there is a limited understanding of the ecological processes that control the assembly of community. To address the role of microbial interactions in assembly and for functioning of the rhizosphere soil microbiota, we collected rhizosphere soil samples from Anisodus tanguticus on the Tibetan Plateau spanning 1500 kilometers, and sequenced the bacteria, fungi, archaea, and protist communities. We observed a significant but weak distance-decay relationship in the microbial communities of rhizosphere soil. Our comprehensive analysis of spatial, abiotic, and biotic factors showed that trophic relationships between protists and bacteria and fungi predominantly influenced the alpha and beta diversity of bacterial, fungal, and protistan communities, while abiotic factors had a greater impact on archaeal communities, including soil pH, available phosphorus, total phosphorus and mean annual temperature. Importantly, microbial interactions had a more significant influence on Anisodus tanguticus physiological and ecological functions compared to individual microorganisms. Network analyses revealed that bacteria occupy a central position of the co-occurrence network and play a crucial role of connector within this community. The addition of protists increased the stability of bacterial, fungal, and archaeal networks. Overall, our findings indicate that trophic relationships play an important role in assembly and for functioning of the rhizosphere soil microbiota. Bacterial communities serve as a crucial link between different kingdoms of microorganisms in the rhizosphere community. These findings help us to fully harness the beneficial functions of rhizosphere microorganisms for plants and achieve sustainable use of biological resources.

Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function

How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.

Grazing weakens the linkages between plants and soil biotic communities in the alpine grassland

Livestock grazing alters the diversity and composition of plants and soil biota in grassland ecosystems. However, whether and how grazing affects plant-soil biota interactions are limited. Here, we performed a field investigation on the Tibetan grasslands to determine the relationships between plant community properties (biomass, diversity and richness) and soil biota (abundance, diversity and composition of bacteria, fungi and nematodes) in the long-term yak grazing and ungrazed plots, and responses of plant-soil biota linkages to grazing in alpine meadows and alpine swampy meadows were compared. The results found that grazing did not cause significant changes in plant community properties but increased the soil water content. Further, grazing weakened plant-soil microbes/nematode relationships in alpine meadows. The bacterial and fungal abundances were correlated with plant belowground biomass and Simpson index in the ungrazed plots of alpine meadows, while the correlation was not significant under grazing. Bacterial composition was correlated with plant richness only in the ungrazed meadows. Plant-soil nematode linkages were more sensitive to grazing than plant-microbes linkages. Grazing decoupled the relationships between the abundances of nematode trophic groups and plant aboveground biomass, richness and Simpson index in alpine meadows, while the decoupling phenomenon is less evident in alpine swampy meadows. The SEM results indicate that grazing altered the plant above- and belowground biomass to affect the soil nematode community, while influenced soil microbes only through alterations of plant belowground biomass. The findings highlight the importance of grazing in influencing the interactions between aboveground plant communities and soil biological communities in Tibetan grasslands.

Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave

Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.

Differences in soil microbial community structure and assembly processes under warming and cooling conditions in an alpine forest ecosystem

Global climate change affects the soil microbial community assemblages of many ecosystems. However, little is known about the effects of climate warming on the structure of soil microbial communities or the underlying mechanisms that influence microbial community composition in alpine forest ecosystems. Thus, our ability to predict the future consequences of climate change is limited. In this study, with the use of PVC pipes, the in situ soils of the rush-tip long-bud Abies georgei var. smithii forest at 3500 and 4300 m above sea level (MASL) of the Sygera Mountains were incubated in pairs for 1 year to simulate climate cooling and warming. This shift corresponds to a change in soil temperature of ±4.7 °C. Findings showed that climate warming increased the complexity of bacterial networks but decreased the complexity of fungal networks. Climate cooling also increased the complexity of bacterial networks. However, in fungal communities, climate cooling increased the number of nodes but decreased the total number of edges. Stochastic processes acted as the drivers of bacterial community composition, with climate warming leading the shift from deterministic to stochastic drivers. Fungal communities were more sensitive to climate change than bacterial communities, with soil temperature (ST) and soil water content (SWC) acting as the main drivers of change. By contrast, soil bacterial communities were more closely related to soil conditions than fungal communities and remained stable after a year of soil transplantation. In conclusion, fungi and bacteria had different response patterns, and their responses to climate cooling and warming were asymmetric. This work is expected to contribute to our understanding of the response to climate change of soil microbial communities in alpine forests and our prediction of the functions of soil microbial ecosystems in alpine forests.

Lacustrine plastisphere: Distinct succession and assembly processes of prokaryotic and eukaryotic communities and role of site, time, and polymer types

Microplastics as a carrier can promote microbial diffusion, potentially influencing the ecological functions of microbial communities in aquatic environments. However, our understanding of the assembly mechanism of microbial communities on different microplastic polymers in freshwater lakes during succession is still insufficient, especially for the eukaryotes. Here, the colonization time, site, and polymer types of microplastics were comprehensively considered to investigate the composition and assembly of prokaryotic and eukaryotic communities and their driving factors during the lacustrine plastisphere formation. Results showed that the particle-associated microorganisms in water were the main source of the plastisphere prokaryotes, while the free-living microorganisms in water mainly accounted for the plastisphere eukaryotes. The response of prokaryotic communities to different microplastic polymers was stronger than eukaryotic communities. The assembly of plastisphere prokaryotic communities was dominated by homogenizing processes (mainly homogenous selection), while the assembly of eukaryotic communities was dominated by differentiating processes (mainly dispersal limitation). Colonization time was an important factor affecting the composition of prokaryotic and eukaryotic communities during the formation of the plastisphere. The Chao1 richness of prokaryotic communities in the plastisphere increased with the increase of colonization time, whereas the opposite was true in eukaryotic communities. This differential response of species diversity and composition of prokaryotic and eukaryotic communities in the plastisphere during dynamic succession could lead to their distinct assembly processes. Overall, the results suggest that distinct assembly of microbial communities in the plastisphere may depend more on specific microbial sub-communities and colonization time than polymer types and colonization site.

Long-term application of nitrogen and phosphorus fertilizers changes the process of community construction by affecting keystone species of crop rhizosphere microorganisms

Keystone species of microbial communities play a very important role in community structure and ecosystem function; however, the effect of long-term nitrogen (N) and phosphorus (P) fertilizers on key taxa and the mechanisms of community construction of rhizosphere microbial communities remain unclear. In this study, the effect of nine fertilization treatments (N0P0, N0P1, N0P2, N1P0, N1P1, N1P2, N2P0, N2P1, and N2P2) on soil microbial community diversity, keystone species, and construction methods in the crop rhizosphere were studied in a loess hilly area after 26 years of fertilization. The results showed that fertilization significantly increased the nutrient contents of the rhizospheric soil and root system and significantly affected microbial community composition (based on the Bray-Curtis distance) and community construction process (β-nearest taxon index: βNTI). The decrease in the abundance of oligotrophic bacteria (from phyla Acidobacteriota and Chloroflexi) in the keystone species of bacterial communities shifted the community construction process from homogenizing dispersal to variable selection process and was significantly regulated by soil factors (total P and carbon-N ratio). However, the decrease in the abundance of keystone species (from phylum Basidiomycota) in the fungal communities did not have a significant effect on community construction, which was mainly affected by root characteristics (root N content and soluble sugar). This study found that long-term N and P fertilization changed the keystone species composition of bacterial communities by affecting the nutrient content of the rhizospheric soil, such as total P, so that the construction mode of communities changed from a stochastic to a deterministic process, and the N2 fertilization, especially the N1P2 treatment was better for increasing network stability (modularity and clustering coefficient).

Distribution, assembly, and interactions of soil microorganisms in the bright coniferous forest area of China's cold temperate zone

The bright coniferous forest area in the cold temperate zone of China is a terrestrial ecosystem primarily dominated by low mountain Larix gmelinii trees. Limited information is available regarding the assembly mechanisms and interactions of microbial communities in the soil in this region. This study employed high-throughput techniques to obtain DNA from myxomycetes, bacteria, and fungi in the soil, evaluated their diversity in conjunction with environmental factors, associated them with the assembly process, and explored the potential interaction relationships between these microorganisms. The findings of our study showed that environmental factors had a more significant influence on the α and β diversity of bacteria compared to myxomycetes and fungi. Microbial communities were influenced by environmental selection and geographical diffusion, although environmental selection appeared to have a more significant impact than geographical diffusion. Our study suggested that different microorganisms exhibited unique evolutionary patterns and may have different assembly modes within phylogenetic groups. Myxomycetes and fungi exhibited a similar assembly process that was mainly influenced by stochastic dispersal limitation and drift. In contrast, bacteria's assembly process was primarily influenced by stochastic drift and deterministic homogeneous selection. The community of myxomycetes and fungi is greatly influenced by spatial distribution and random events, while bacteria have a relatively stable population composition in specific regions and may also be subject to environmental constraints. Finally, this study revealed that Humicolopsis cephalosporioides, a fungus that exclusively resided in cold environments, may play a critical role as a keystone species in maintaining molecular ecological networks and was considered a core member of the microbiome.

Community- and genome-based evidence for a shaping influence of redox potential on bacterial protein evolution

Despite deep interest in how environments shape microbial communities, whether redox conditions influence the sequence composition of genomes is not well known. We predicted that the carbon oxidation state (ZC) of protein sequences would be positively correlated with redox potential (Eh). To test this prediction, we used taxonomic classifications for 68 publicly available 16S rRNA gene sequence data sets to estimate the abundances of archaeal and bacterial genomes in river & seawater, lake & pond, geothermal, hyperalkaline, groundwater, sediment, and soil environments. Locally, ZC of community reference proteomes (i.e., all the protein sequences in each genome, weighted by taxonomic abundances but not by protein abundances) is positively correlated with Eh corrected to pH 7 (Eh7) for the majority of data sets for bacterial communities in each type of environment, and global-scale correlations are positive for bacterial communities in all environments. In contrast, archaeal communities show approximately equal frequencies of positive and negative correlations in individual data sets, and a positive pan-environmental correlation for archaea only emerges after limiting the analysis to samples with reported oxygen concentrations. These results provide empirical evidence that geochemistry modulates genome evolution and may have distinct effects on bacteria and archaea. IMPORTANCE The identification of environmental factors that influence the elemental composition of proteins has implications for understanding microbial evolution and biogeography. Millions of years of genome evolution may provide a route for protein sequences to attain incomplete equilibrium with their chemical environment. We developed new tests of this chemical adaptation hypothesis by analyzing trends of the carbon oxidation state of community reference proteomes for microbial communities in local- and global-scale redox gradients. The results provide evidence for widespread environmental shaping of the elemental composition of protein sequences at the community level and establish a rationale for using thermodynamic models as a window into geochemical effects on microbial community assembly and evolution.

Distinct distribution patterns and functional potentials of rare and abundant microorganisms between plastisphere and soils

The increasing application of plastic film has caused the "white pollution" of farmlands in greenhouses. To date, most studies on the ecology of the plastisphere have focused on the whole microbial community, with few on the rare and abundant taxa, especially in the terrestrial ecosystems. To understand the plastisphere rare and abundant taxa of bacterial and fungal communities, we collected residues of plastic film from plastic-covered soils in the greenhouse. The plastisphere was significantly different from surrounding soils in terms of alpha- and beta-diversities of abundant and rare taxa. Such discrepancies were greater in rare taxa than in abundant taxa. Besides, the enrichment of soil-borne plant pathogenic fungi in the plastisphere implied that plastic film residues can act as vectors for pathogen transmission. In the plastisphere, the stochastic process governed the assemblies of rare taxa, while deterministic assemblies dominated that of abundant taxa. However, in surrounding soils, the stochastic process played a larger role in abundant taxa as compared to rare taxa. The plastisphere showed a network of less complexity, more competitive connections, and more modules compared to surrounding soils, and rare taxa played greater roles than abundant taxa. There existed obvious discrepancies in the microbial functions between surrounding soils and plastisphere, including carbon, sulfur, nitrogen, and phosphorus cycling, and rare taxa contribute large proportions to the above cycling processes. Altogether, the findings advance our understanding of ecological mechanisms of abundant and rare taxa in the plastisphere in terrestrial ecosystems.

A meta-analysis reveals that geographical factors drive the bacterial community variation in Chinese lakes

The biogeographical distribution of plants and animals has been extensively studied, however, the biogeographical patterns and the factors that influence bacterial communities in lakes over large scales are yet to be fully understood, even though they play critical roles in biogeochemical cycles. Here, bacterial community compositional data, geographic information, and environmental factors were integrated for 326 Chinese lakes based on previously published studies to determine the underlying factors that shape bacterial diversity among Chinese lakes. The composition of bacterial communities significantly varied among the three primary climatic regions of China (Northern China, NC; Southern China, SC; and the Tibetan Plateau, TIP), and across two different lake habitats (waters and sediments). Sediment bacterial communities exhibited significantly higher alpha-diversity and distance-decay relationships compared to water communities. The results indicate that the "scale-dependent patterns" of controlling factors, primarily influenced by geographical factors, become increasingly pronounced as the spatial scale increases. At a national scale, geographical factors exerted a dominant influence on both the water and sediment communities across all lakes, as geographical barriers restrict the dispersal of individuals. At smaller spatial scales, temperature-driven selection effects played a greater role in shaping water bacterial community variation in the NC, SC, and TIP, while geographical factors had a stronger association with sediment bacterial community variation in the lakes of the three regions. This synthesis offers novel insights into the ecological factors that determine the distribution of bacteria in Chinese lakes.

Spatial distribution patterns across multiple microbial taxonomic groups

Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria). Our results showed that the entire community generally fitted the DDR patterns (P < 0.001), this was also true at the kingdom level (P < 0.001, with the exception of the fungal community), and for most individual phyla (47/75) in both ecosystems and with soil depth. Meanwhile, these results presented a general trend that the community turnover rate of nontidal soils was higher than tidal soils (P < 0.05), and that the rate of topsoil was also higher than that of subsoil (P < 0.05). Additionally, microbial spatial turnover rates displayed a negative relationship with body sizes in nontidal topsoil (R² = 0.29, P = 0.009), suggesting that the smaller the body size of microorganisms, the stronger the spatial limitation was in this environment. However, in tidal soils, the body size effect was negligible, probably owing to the water's fluidity. Moreover, community assembly was judged to be deterministic, and heterogeneous selection played a dominant role in the different environments. Specifically, the spatial distance was much more influential, while the soil salinity in these ecosystems was the major environmental factor in selecting the distributions of microbial communities. Overall, this study revealed that microbial community compositions at different taxonomic levels followed relatively consistent distribution patterns and mechanisms in this coastal area.

Interconnected versus unconnected microorganisms: Does it matter in anaerobic digestion functioning

Microorganisms in anaerobic digestion (AD) are essential for wastes/pollutants treatment and energy recovery. Due to microbial enormous diversity, developing effective perspectives to understand microbial roles therein is urgent. This study conducted AD of swine manure, used an ensemble-based network analysis to distinguish interconnected, unconnected, copresence (positively interconnected) and mutual-exclusion (negatively interconnected) microorganisms within microbial communities, and explored their importance towards AD performances, using amplicon sequencing of 16S rRNA and 16S rRNA gene. Our analyses revealed greater importance of interconnected than unconnected microorganisms towards CH₄ production and AD multifunctionality, which was attributed to higher niche breadth, deterministic community assembly, community stability and phylogenetic conservatism. The diversity was higher in unconnected than interconnected microorganisms, but was not linked to AD performances. Compared to copresence microorganisms, mutual-exclusion microorganisms showed greater and equal importance towards CH₄ production and AD multifunctionality, which was attributed to their roles in stabilizing microbial communities. The increased feedstock biodegradability, by replacing part of manure with fructose or apple waste, hardly affected the relative importance of interconnected versus unconnected microorganisms towards CH₄ production or AD multifunctionality. Our findings develop a new framework to understand microbial roles, and have important implications in targeted manipulation of critical microorganisms in waste-treatment systems.

Distinct Ecological Processes Mediate Domain-Level Differentiation in Microbial Spatial Scaling

The spatial scaling of biodiversity, such as the taxa-area relationship (TAR) and distance-decay relationship (DDR), is a typical ecological pattern that is followed by both microbes and macrobes in natural ecosystems. Previous studies focusing on microbes mainly aimed to address whether and how different types of microbial taxa differ in spatial scaling patterns, leaving the underlying mechanisms largely untouched. In this study, the spatial scaling of different microbial domains and their associated ecological processes in an intertidal zone were comparatively investigated. The significant spatial scaling of biodiversity could be observed across all microbial domains, including archaea, bacteria, fungi, and protists. Among them, archaea and fungi were found with much stronger DDR slopes than those observed in bacteria and protists. For both TAR and DDR, rare subcommunities were mainly responsible for the observed spatial scaling patterns, except for the DDR of protists and bacteria. This was also evidenced by extending the TAR and DDR diversity metrics to Hill numbers. Further statistical analyses demonstrated that different microbial domains were influenced by different environmental factors and harbored distinct local community assembly processes. Of these, drift was mainly responsible for the compositional variations of bacteria and protists. Archaea were shaped by strong homogeneous selection, whereas fungi were more affected by dispersal limitation. Such differing ecological processes resulted in the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling and provides novel mechanistic insights into the diversity patterns of microbes that belong to different trophic levels. IMPORTANCE As the most diverse and numerous life form on Earth, microorganisms play indispensable roles in natural ecological processes. Revealing their diversity patterns across space and through time is of essential importance to better understand the underlying ecological mechanisms controlling the distribution and assembly of microbial communities. However, the diversity patterns and their underlying ecological mechanisms for different microbial domains and/or trophic levels require further exploration. In this study, the spatial scaling of different microbial domains and their associated ecological processes in a mudflat intertidal zone were investigated. The results showed different spatial scaling patterns for different microbial domains. Different ecological processes underlie the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling to provide novel mechanistic insights into the diversity patterns of microorganisms that belong to different trophic levels.

Drivers of nematode diversity in forest soils across climatic zones

Nematodes are the most abundant multi-cellular animals in soil, influencing key processes and functions in terrestrial ecosystems. Yet, little is known about the drivers of nematode abundance and diversity in forest soils across climatic zones. This is despite forests covering approximately 30% of the Earth's land surface, providing many crucial ecosystem services but strongly varying in climatic conditions and associated ecosystem properties across biogeographic zones. Here, we collected nematode samples from 13 forests across a latitudinal gradient. We divided this gradient into temperate, warm-temperate and tropical climatic zones and found that, across the gradient, nematode abundance and diversity were mainly influenced by soil organic carbon content. However, mean annual temperature and total soil phosphorus content in temperate zones, soil pH in warm-temperate zones, and mean annual precipitation in tropical zones were more important in driving nematode alpha-diversity, biomass and abundance. Additionally, nematode beta-diversity was higher in temperate than in warm-temperate and tropical zones. Together, our findings demonstrate that the drivers of nematode diversity in forested ecosystems are affected by the spatial scale and climatic conditions considered. This implies that high resolution studies are needed to accurately predict how soil functions respond if climate conditions move beyond the coping range of soil organisms.

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters

Community and diversity shifts of bacteria and microeukaryotes with strong environmental and spatial variations have been unveiled in the Pearl River Estuary (PRE) and northern coastal part of South China Sea (SCS). However, it is not clear what the determining factors shape the microbial community and how the biotic interactions respond to the estuarine and oceanic environment. Here, we established the multiple regression models (MRM) and co-occurrence networks on microbial communities in PRE and SCS habitats. The results showed that there were significant differences of the abiotic factors affecting the bacterial and microeukaryotic communities between PRE and SCS habitats. Salinity explained the largest variations to the microbial community dissimilarities in PRE. Whereas spatial and environmental factors determined the microbial community dissimilarities in SCS. Positive relations between parasitic lineages (e.g. Perkinsea and Cercozoa) and algal taxa (Dinophyceae, Cryptophyta, Chlorophyta and Ochrophyta) dominated in the PRE network. While parasites Syndiniales positively correlated with other Syndiniales and protists in SCS. Strong positive associations among autotrophic and heterotrophic groups were revealed in both niches. Therefore, the biotic interactions are also important and may be responsible for the unexplained variations of the abiotic factors from MRM models. Microbial network in the PRE estuarine water had weakened resistance to environmental disturbances, while the SCS network had greater capacity to maintain network stability. This study shed light on the different mechanisms of abiotic and biotic factors in shaping the compositions of bacteria and microeukaryotes between PRE and SCS niches, and highlights the weakening effect of environmental disturbances on the microbial network stability.