Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

Linking microbiomes with per- and poly-fluoroalkyl substances (PFASs) in soil ecosystems: Microbial community assembly, stability, and trophic phylosymbiosis

Microbiomes are vital in promoting nutrient cycling and plant growth in soil ecosystems. However, microbiomes face adverse effects from multiple persistent pollutants, including per- and poly-fluoroalkyl substances (PFASs). PFASs threaten the fertility and health of soil ecosystems, yet the response of microbial community stability and trophic transfer efficiencies to PFASs is still poorly understood. This study explored the spatial patterns of PFASs in topsoil environments from the West Taihu Lake Basin of China and links their presence to soil microbial community stability at compositional and functional levels. Our results revealed that PFBA (13.87%), PFTrDA (11.63%), PFDoA (11.02%), PFOA (10.99%), and PFOS (10.39%) contributed the most to the spatial occurrence of PFASs. Soil properties, including salinity (14.47%), uniformity (9.68%), dissolved inorganic carbon (8.62%), and clay content (8.18%), affected PFASs distribution the most. In soil microbiomes, eukaryotic taxa had wider niche breadths and stronger community stability than prokaryotes when exposed to PFASs (p < 0.05). The presence of PFBA and PFHpA inhibited the functional stability of archaeal and bacterial communities (p < 0.05). PFBA and PFPeA reduced the structural stability of heterotrophic bacteria and Myxobacteria, respectively (p < 0.05). Based on null modeling, PFPeA significantly regulated the assembly processes of most microbial sub-communities (p < 0.01). The trophic transferring efficiencies of autotrophic bacteria to metazoan organisms were directly stimulated by PFASs (p < 0.05), and the potential trophic transferring efficiencies of methanogenic archaea to protozoa were inhibited by PFASs (p < 0.05). This study highlighted the potential contributions of PFASs to soil microbial community stability and food webs during ecological soil management.

Plant traits and community composition drive the assembly processes of abundant and rare fungi across deserts

The difference in community assembly mechanisms between rare and abundant fungi in deserts remains unknown. Hence, we compared the distribution patterns of abundant and rare fungi, and assessed the factors driving their assembly mechanisms across major vegetation types (shrubby desert, semi-shrubby and dwarf semi-shrubby desert, dwarf semi-arboreous desert, and shrubby steppe desert) of Chinese deserts. We assessed abundant and rare fungal subcommunities base on the sequencing data of fungal ITS data. Abundant fungal assembly was more affected by neutral processes than the rare. Null model and VPA analysis indicated that heterogeneous selection dominated rare sub-communities, whereas abundant fungal assembly was mainly determined by heterogeneous selection, dispersal limitation and other, unknown processes together. As a result, abundant sub-communities exhibited a higher species turnover rate than the rare. Hierarchical partitioning analysis indicated that soil conditions and plant attributes drove the assembly processes of abundant and rare fungi, respectively. Meanwhile, the relative strength of different assembly processes differed significantly among four vegetation types. In addition, we found that plant functional traits and composition played more critical roles in shaping the assembly processes of rare fungi than those of abundant fungi. Taken together, our findings collectively suggest that rare and abundant fungi exhibit differential ecological patterns that are driven by distinct assembly processes in deserts. We emphasize that the assembly processes of abundant and rare fungi are dependent on different abiotic and biotic factors in desert ecosystems.

Dispersal limitation dominates the community assembly of abundant and rare fungi in dryland montane forests

The assembly mechanisms and drivers of abundant and rare fungi in dryland montane forest soils remain underexplored. Therefore, in this study, we compared the distribution patterns of abundant and rare fungi and explored the factors determining their assembly processes in a dryland montane forest in China. Stronger distance-decay relationships (DDRs) were found in abundant sub-communities than in rare sub-communities. In addition, abundant fungi exhibited greater presence and wider habitat niche breadth than rare fungi. Both the null model and variation partitioning analysis indicated that dispersal limitation and environmental selection work together to govern both abundant and rare fungal assembly, while dispersal limitation plays a dominant role. Meanwhile, the relative influence of dispersal limitation and environmental selection varied between abundant and rare sub-communities, where dispersal limitation showed greater dominance in abundant fungal assembly. Mantel tests demonstrated that soil pH and phosphorus played critical roles in mediating abundant and rare fungi assembly processes, respectively. Our findings highlight that the distinct biogeographic patterns of abundant and rare fungi are driven by different assembly mechanisms, and the assembly processes of abundant and rare fungi are determined by diverse ecological drivers in dryland montane forest soils.

Effects of Daqu Attributes on Distribution and Assembly Patterns of Microbial Communities and Their Metabolic Function of Artificial Pit Mud

Daqu provides functional microbiota and various nutrients for artificial pit mud (APM) cultivation. However, little is known about whether its attributes affect the microbiome and metabolome of APM. Here, two types of APM were manufactured by adding fortified Daqu (FD) and conventional Daqu (CD); they were comprehensively compared by polyphasic detection methods after being used for two years. The results showed that FD altered the prokaryotic communities rather than the fungal ones, resulting in increased archaea and Clostridium_sensu_stricto_12 and decreased eubacteria and Lactobacillus. Correlation analysis suggested that these variations in community structure promoted the formation of hexanoic acid, butyric acid, and the corresponding ethyl esters, whereas they inhibited that of lactic acid and ethyl lactate and thus improved the flavor quality of the APM. Notably, pH was the main driving factor for the bacterial community variation, and the total acid mediated the balance between the stochastic and the deterministic processes. Furthermore, the results of the network analysis and PICRUSt2 indicated that FD also enhanced the modularity and robustness of the co-occurrence network and the abundance of enzymes related to hexanoic acid and butyric acid production. Our study highlights the importance of Daqu attributes in APM cultivation, which are of great significance for the production of high-quality strong-flavor Baijiu.

Spatial variations of root-associated bacterial communities of alpine plants in the Qinghai-Tibet Plateau

Exploring the geospatial variation of root-associated microbiomes is critical for understanding plant-microbe-environment interactions and plant environmental adaptability. Root-associated bacterial communities from the three compartments [rhizosphere surrounding soil (RSS), rhizosphere soil (rhizosphere), and root endosphere (endophytic)] are influenced by multiple factors, including plant species and geographical locations. Nonetheless, these communities remain poorly understood under harsh conditions. In this study, we selected four dominant alpine plants on the Qinghai-Tibet Plateau (i.e., Elymus nutans, Festuca sinensis, Kobresia pygmaea, and Kobresia humilis) to investigate their root-associated bacterial communities across 11 geographical locations and determine the factors driving spatial variation. The results showed that the microbiota of the three compartments had significantly different community compositions, with more Pseudomonadaceae and Enterobacteriaceae present in the endosphere. Spatial variations in root endophytic microbiota were mainly governed by stochastic processes, which were different from the deterministic processes in the other two compartments. Meanwhile, the geographical location had greater effects on bacterial communities than plant species, and the spatial variation of α-diversity in the endosphere was much higher than that in the RSS and rhizosphere. We further found that the differentiation of bacterial diversity in the endosphere among sympatric plant species was enhanced by higher annual precipitation, lower soil nutrients (carbon and nitrogen), and pH. For example, the coefficient of variation of endosphere Pseudomonadaceae abundance was positively correlated with annual mean precipitation, whereas that of Enterobacteriaceae abundance was negatively correlated with soil pH. The co-occurrence network analysis identified a higher proportion of bacterial coexistence in the endosphere (70.9%) than in the RSS (49.5%) and rhizosphere soil (50.9%). Finally, we revealed the relative convergence of endophytic communities among sympatric plant species in the alpine grasslands.

Apex Predators Enhance Environmental Adaptation but Reduce Community Stability of Bacterioplankton in Crustacean Aquaculture Ponds

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

Seasonal Succession and Temperature Response Pattern of a Microbial Community in the Yellow Sea Cold Water Mass

Explaining the temporal dynamics of marine microorganisms is critical for predicting their changing pattern under environmental disturbances. Although the effect of temperature on microbial seasonality has been widely studied, the phylogenetic structure of the temperature response pattern and the extent to which temperature shift leads to disruptive community changes are still unclear. Here, we explored the microbial seasonal dynamics in the Yellow Sea Cold Water Mass (YSCWM) that occurs in summer and disappears in winter and tested the temperature thresholds and phylogenetic coherence in response to temperature change. The existence of YSCWM generates strong temperature gradients in summer and confers little temperature change during seasonal transition, thus representing a unique intermediate state. The microbial community of YSCWM is more similar to that in the previous YSCWM in winter than that outside YSCWM. Temperature alone explains >50% of the community variation, suggesting that a temperature shift can induce a nearly seasonality-level community variance in summer. Persistence of most previous winter YSCWM inhabitants in YSCWM leads to conservation in predicted functional potentials and cooccurrence patterns, indicating a decisive role of temperature in maintaining functionality. Evaluation of the temperature threshold reveals that a small temperature change can lead to significant community turnover, with most taxa negatively responding to an elevation in temperature. The temperature response pattern is phylogenetically structured, and closely related taxa show an incohesive response. Our study provides novel insights into microbial seasonality and into how marine microorganisms respond to temperature fluctuations. IMPORTANCE Microbial seasonality is driven by a set of covarying factors including temperature. There is still a lack of understanding of the details of the phylogenetic structure and susceptibility of microbial communities in response to temperature variation. Through examination of the microbial community in a seasonally occurring summer cold water mass, which experiences little temperature change during seasonal transition, we show here that the cold water mass leads to nearly seasonality-level variations in community composition and predicted functional profile in summer. Moreover, massive community turnover occurs within a small temperature shift, with most taxa decreasing in abundance in response to increased temperature, and contrasting response patterns are observed between phylogenetically closely related taxa. These results suggest temperature as the fundamental factor over other covarying factors in structuring microbial seasonality, providing important insights into the variation mode of the microbial community under temperature disturbances.

Deciphering the diversity patterns and community assembly of rare and abundant bacterial communities in a wetland system

Water microorganisms that have distinct contributions to community dynamics, including many rare taxa and few abundant taxa, are crucial to the wetland ecosystem functions. In this study, we comprehensively investigated the diversity patterns and assembly processes of rare and abundant taxa to strengthen our understanding of ecosystem function and diversity in a wetland system. The results showed that TN and NH₃-N were the most significant factors affecting the community structure in this wetland. Functional Annotation of Prokaryotic Taxa (FAPROTAX) revealed that functions associated with nitrogen removal were the most prevalent metabolic pathways in samples of regenerated wetland (RW). Co-occurrence network analysis revealed that nonrare taxa exhibited more interactions with rare taxa than with conspecifics and some microbial hubs belonged to rare taxa, which might play an instrumental role in maintaining the stability of the community structure. We found that the assembly of rare taxa with a lower niche breadth was mainly governed by homogeneous selection, implying that their higher sensitivity of these to environmental disturbances and changes in TN played significant roles in community assembly of rare taxa. In contrast, the assembly of abundant taxa with higher niche breadth was dominated by stochastic processes (undominated process and dispersal limitation) indicating that abundant taxa had greater responsibility for maintaining community structure when exposed to environmental fluctuations. These results broaden our understanding of the microbial structure, interactions and ecological assembly mechanisms underlying microbial dynamics in aquatic ecosystems, which are crucial for the management of microorganisms in the wetlands.

Nitrogen deficiency in soil mediates multifunctionality responses to global climatic drivers

Natural and anthropogenic processes that decrease the availability of nitrogen (N) frequently occur in soil. Losses of N may limit the multiple functions linked to carbon, N and phosphorous cycling of soil (soil multifunctionality, SMF). Microbial communities and SMF are intimately linked. However, the relationship between soil microbial communities and SMF in response to global changes under N deficiency has never been examined in natural ecosystems. Here, soil samples from nine temperate arid grassland sites were used to assess the importance of microbial communities as driver of SMF to climate change and N deficiency. SMF was significantly decreased by drought and drought-wetting cycles, independent of the availability of soil N. Interestingly, temperature changes (variable temperature and warming) significantly increased SMF in N-poor conditions. However, this was at the expense of decreased SMF resistance. Deterministic assembly-driven microbial α-diversity and particularly fungal α-diversity, but not β-diversity, were generally found to play key roles in maintaining SMF in N-poor soil, irrespective of the climate. The results have two important implications. First, the absence of the stability offered by β-diversity means N-poor ecosystems will be particularly sensitive to global climate changes. Second, fungi are more important than bacteria for maintaining SMF in N-poor soil under climate changes.

Homogeneous selection is stronger for fungi in deeper peat than in shallow peat in the low-temperature fens of China

Peatlands have accumulated enormous amounts of carbon over millennia, and climate changes threatens the release of this carbon into the atmosphere. Fungi are crucial drivers of global carbon cycling because they are the principal decomposer of organic matter in peatlands. However, the fungal community composition and ecological preferences in peat remain unclear, which restricts our ability to evaluate the role of the fungal community in peat biogeochemical functions. We investigated 54 soils from 6 low-temperature peatlands across China to fill this knowledge gap. The peat was divided into above-water table (AWT) and below-water table (BWT) layers based on the water table fluctuation. We investigated fungal community assembly processes and drivers for each peat layer. The results showed that fungal communities differed significantly among peat layers. The relative abundance of symbiotrophs was significantly higher in the AWT (17.4%) than in the BWT (9.0%), while the abundances of yeast and litter saprotrophs were obviously lower in the AWT than in the BWT. Our results revealed that the assemblage of both fungal taxonomic and phylogenetic communities was mainly governed by stochastic processes in both AWT (87.8%) and BWT (58.6%) layers. However, in the BWT, the relative importance of deterministic processes (28.4%) significantly increased, indicating a potential deterministic environmental selection induced by permanently anaerobic condition. Mean annual precipitation and mean annual temperature were the most critical drives for the assemblage of the fungal community in the BWT. These observations collectively indicate that fungal community assembly is depth-dependent, implying different community assembly mechanisms and ecological functions along the peat profile. These findings highlight the importance of climate driven deep peat fungal community composition assemblages and suggest the potential to project the changes in fungal diversity with ongoing climate change.

Soil microbial distribution and assembly are related to vegetation biomass in the alpine permafrost regions of the Qinghai-Tibet Plateau

It is generally believed that there is a vegetation succession sequence from alpine marsh meadow to desert in the alpine ecosystem of the Qinghai-Tibet Plateau. However, we still have a limited understanding about distribution patterns and community assemblies of microorganisms' response to such vegetation changes. Hence, across a gradient represented by three types of alpine vegetation from swamp meadow to meadow to steppe, the soil bacterial, fungal and archaeal diversity was evaluated and then associated with their assembly processes, and glacier foreland vegetation was also surveyed as a case out of this gradient. Vegetation biomass was found to decrease significantly along the vegetation gradient. In contrast to irregular shifts in alpha diversity, bacterial and fungal beta diversities that were dominated by species replacement components (71.07-79.08%) significantly increased with the decreasing gradient in vegetation biomass (P < 0.05). These trends of increase were also found in the extent of stochastic bacterial and fungal assembly. Moreover, an increase in microbial beta diversity but a decrease in beta nearest taxon index were observed along with increased discrepancy in vegetation biomass (P < 0.001). Stepwise regression analyses and structural equation models suggested that vegetation biomass was the major variable that was related to microbial distribution and community assembly, and there might be associations between the dominance of species replacements and stochastic assembly. These findings enhanced our recognition of the relationship between vegetation and soil microorganisms and would facilitate the development of vegetation-microbe feedback models in alpine ecosystems.

Sediment Bacteria and Phosphorus Fraction Response, Notably to Titanium Dioxide Nanoparticle Exposure

Titanium dioxide nanoparticle (TiO₂ NP) toxicity to the growth of organisms has been gradually clarified; however, its effects on microorganism-mediated phosphorus turnover are poorly understood. To evaluate the influences of TiO₂ NPs on phosphorus fractionation and the bacterial community, aquatic microorganisms were exposed to different concentrations of TiO₂ NPs with different exposure times (i.e., 0, 10, and 30 days). We observed the adhesion of TiO₂ NPs to the cell surfaces of planktonic microbes by using SEM, EDS, and XRD techniques. The addition of TiO₂ NPs resulted in a decrease in the total phosphorus of water and an increase in the total phosphorus of sediments. Additionally, elevated TiO₂ NPs enhanced the sediment activities of reductases (i.e., dehydrogenase [0.19–2.25 μg/d/g] and catalase [1.06–2.92 μmol/d/g]), and significantly decreased the absolute abundances of phosphorus-cycling-related genes (i.e., gcd [1.78 × 10⁴–9.55 × 10⁵ copies/g], phoD [5.50 × 10³–5.49 × 10⁷ copies/g], pstS [4.17 × 10²–1.58 × 10⁶ copies/g]), and sediment bacterial diversity. TiO₂ NPs could noticeably affect the bacterial community, showing dramatic divergences in relative abundances (e.g., Actinobacteria, Acidobacteria, and Firmicutes), coexistence patterns, and functional redundancies (e.g., translation and transcription). Our results emphasized that the TiO₂ NP amount—rather than the exposure time—showed significant effects on phosphorus fractions, enzyme activity, phosphorus-cycling-related gene abundance, and bacterial diversity, whereas the exposure time exhibited a greater influence on the composition and function of the sediment bacterial community than the TiO₂ NP amount. Our findings clarify the responses of phosphorus fractions and the bacterial community to TiO₂ NP exposure in the water–sediment ecosystem and highlight potential environmental risks of the migration of untreated TiO₂ NPs to aquatic ecosystems.

Long-term watermelon continuous cropping leads to drastic shifts in soil bacterial and fungal community composition across gravel mulch fields

Despite the known influence of continuous cropping on soil microorganisms, little is known about the associated difference in the effects of continuous cropping on the community compositions of soil bacteria and fungi. Here, we assessed soil physicochemical property, as well as bacterial and fungal compositions across different years (Uncropped control, 1, 6, 11, 16, and 21 years) and in the watermelon system of a gravel mulch field in the Loess Plateau of China. Our results showed that long-term continuous cropping led to substantial shifts in soil bacterial and fungal compositions. The relative abundances of dominant bacterial and fungal genera (average relative abundance > 1.0%) significantly varied among different continuous cropping years (P < 0.05). Structural equation models demonstrated that continuous cropping alter soil bacterial and fungal compositions mainly by causing substantial variations in soil attributes. Variations in soil pH, nutrient, salinity, and moisture content jointly explained 73% and 64% of the variation in soil bacterial and fungal compositions, respectively. Variations in soil moisture content and pH caused by continuous cropping drove the shifts in soil bacterial and fungal compositions, respectively (Mantel R = 0.74 and 0.54, P < 0.01). Furthermore, the variation in soil bacterial and fungal composition showed significant correlation with watermelon yield reduction (P < 0.01). Together, long-term continuous cropping can alter soil microbial composition, and thereby influencing watermelon yield. Our findings are useful for alleviating continuous cropping obstacles and guiding agricultural production.

Generalists and Specialists Determine the Trend and Rate of Soil Fungal Distance Decay of Similarity in a 20-ha Subtropical Forest

Fungi are an important component of microbial communities that serve a variety of important roles in nutrient cycling and are essential for plant nutrient uptake in forest soils. Distance decay of similarity (DDS) is one of the few ubiquitous phenomena in community ecology. However, the contribution of specialist and generalist fungal species in shaping DDS remains poorly investigated. Through removing operational taxonomic units (OTU) with low or high frequencies, we rigorously quantified the impact of specialists or generalists on the change in slope, initial similarity, and halving distance of DDS of undefined saprotroph, plant mutualist, and plant putative pathogen communities in a 20-ha subtropical evergreen forest plot in Yunnan Province, Southwest China. We hypothesized that (1) the soil fungal co-occurrence networks are different between the three fungal guilds; (2) specialists and generalists contribute to the spatial turnover and nestedness of beta diversity, respectively; and (3) the removal of specialists or generalists will have opposite effects on the change of slope, initial similarity, and halving distance of DDS. Co-occurrence network analysis showed that the undefined saprotroph network had a much more complicated structure than mutualist and pathogen networks. Ascomycota and Basidiomycota were the two most abundant phyla in soil fungal communities. We found that partly in line with our expectations, the change in initial similarity increased and decreased when removing specialists and generalists, respectively, but there was always one exception guild of out of the three communities for the change in slope and halving distance. We identified that such change was mainly due to the change in turnover and nestedness of beta diversity. Furthermore, the results show that species turnover rather than species nestedness drove fungal beta diversity across functional guilds for both specialists and generalists.

Rare bacterial biosphere is more environmental controlled and deterministically governed than abundant one in sediment of thermokarst lakes across the Qinghai-Tibet Plateau

Thermokarst lakes are widely distributed in cold regions as a result of ice-rich permafrost thaw. Disentangling the biogeography of abundant and rare microbes is essential to understanding the environmental influences, assembly mechanisms, and responses to climate change of bacterial communities in thermokarst lakes. In light of this, we assessed the abundant and rare bacterial subcommunities in sediments from thermokarst lakes across the Qinghai-Tibet Plateau (QTP). The operational taxonomic unit (OTU) richness was more strongly associated with location and climate factors for abundant subcommunities, while more strongly associated with physicochemical variables for rare subcommunities. The relative abundance of abundant and rare taxa showed opposite patterns with abundant taxa having greater relative abundance at higher latitude and pH, but at lower mean annual precipitation and nutrients. Both the abundant and rare subcommunities had a clear distribution pattern along the gradient of latitude and mean annual precipitation. Abundant subcommunities were dominantly shaped by dispersal limitation processes (80.9%), while rare subcommunities were shaped almost equally by deterministic (47.3%) and stochastic (52.7%) processes. The balance between stochastic and deterministic processes was strongly environmentally adjusted for rare subcommunities, while not associated with environmental changes for abundant subcommunities. The results shed light on biogeography patterns and structuring mechanisms of bacterial communities in thermokarst lakes, improving our ability to predict the influences of future climate change on these lakes.

Root attributes dominate the community assembly of soil fungal functional guilds across arid inland river basin

Plant attributes are increasingly acknowledged as key drivers shaping soil fungal communities, but considerable uncertainty exists over fungal community assembly mechanisms and their plant drivers based only on inferences from plant aboveground attributes. To date, empirical evidences of how root attributes are integrated into microbiome–plant linkages remain limited. Using 162 soil samples from a typical arid inland river basin in China, we assessed the drivers that regulate the distribution patterns and assembly processes of total, mycorrhizal, saprotrophic and pathotrophic fungi in surface (0–15 cm) and subsurface soils (15–30 cm). Total fungi and fungal functional guilds exhibited similar distribution patterns in arid inland river basins. Null-model and variance partitioning analysis revealed that the heterogeneous selection induced by root attributes, rather than dispersal limitation, predominated the fungal community assembly. Multiple regressions on matrices further demonstrated that specific root length were the most important predictors of fungal community assembly, which mediated the balance of assembly processes of soil fungal communities. Heterogeneous selection decreased for total, mycorrhizal and saprotrophic fungi, but increased for pathotrophic fungi with increasing specific root length. Additionally, fine-root biomass exerted important effects on fungal assembly processes in subsurface soil but not in surface soil, suggesting root attributes differently affected fungal community assembly between surface and subsurface soil. Collectively, our study highlights the importance of considering root attributes in differentiating the balance of stochastic and deterministic processes in microbial community assembly.

Evidence for saponin diversity-mycobiome links and conservatism of plant-fungi interaction patterns across Holarctic disjunct Panax species

Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant-mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant-fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant-fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant-fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.

Broader environmental adaptation of rare rather than abundant bacteria in reforestation succession soil

Revealing the responses of rare and abundant bacteria to environmental change is crucial for understanding microbial community assembly and ecosystem function. However, both the environmental adaptability and the ecological assembly processes exhibited by rare and abundant soil bacteria remain poorly understood. Here we investigated the assembly processes of rare and abundant bacteria along a chronosequence of a 35-year reforestation succession (8, 17, and 35 years), particularly with regard to their environmental adaptations. Compared to the abundant taxa, the phylogenetic clustering of rare taxa was tighter but their environmental breadth wider. Homogeneous selection (65.8%) belonging to deterministic processes dominated the rare bacterial assembly, whereas homogenizing dispersal and undominated process (57.9%) belonging to stochastic processes governed the abundant taxa. Neutral processes had a significant impact on shaping the rare taxa compared to the abundant taxa. Rare taxa were environmentally less constrained than abundant taxa. Soil EC was the major determinant factor for the assembly processes of both rare and abundant taxa. Ecological assembly processes showed a significant negative correlation with rare bacterial functional redundancies, while they had a significant positive correlation with the abundant taxa. Microbial network modularity further demonstrated that rare taxa developed stronger environmental adaptation strategies than their abundant counterparts. Our study significantly advances the knowledge of the environmental adaptability of rare and abundant bacteria and emphasizes their key role in reforestation ecological succession soils.

Abundant and rare soil fungi exhibit distinct succession patterns in the forefield of Dongkemadi glacier on the central Qinghai-Tibet Plateau

Glaciers are retreating rapidly, exposing extensive new soil habitats in glacier forefields and providing unique areas for studying primary succession. However, understanding the variation patterns and assembly mechanisms of abundant and rare fungi subcommunities along the glacier-retreating chronosequence remains a knowledge gap, especially true for the vast Qinghai-Tibet Plateau (QTP). Here, we investigated fungal communities in the glacier forefield in Dongkemadi Glaicer on the central QTP. The results showed that fungal alpha diversity exhibited a clear increasing pattern in response to increasing of distance to glacier. The percentage of abundant OTUs decreased while the percentage of rare OTUs increased, suggesting that soil development is more beneficial to the rare taxa. The distributions of both abundant and rare subcommunities exhibited a clear spatial pattern along the distance to glacier, and might be strongly controlled by multiple environmental variables, including pH, soil moisture, vegetation status, soil organic carbon, total nitrogen, and soluble reactive phosphorus. Abundant and rare fungal subcommunities were structured in different assembly regimes. Dispersal limitation processes were dominant for both abundant and rare subcommunities but with a stronger contribution to abundant subcommunity assembly. Heterogeneous selection processes contributed higher and non-dominant processes contributed lower to abundant subcommunities than to rare subcommunities. The modular structure of the fungal co-occurrence network was highly localized along the soil chronosequence. By revealing distinct diversity patterns and community assembly mechanisms of abundant and rare fungal subcommunities, our study improved our understanding of ecological succession along the glacier-retreating chronosequence.

Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity—the backbone of the regulation of ecosystem services and “soil health” maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.

Rhizosphere Soil Microbial Community Under Ice in a High-Latitude Wetland: Different Community Assembly Processes Shape Patterns of Rare and Abundant Microbes

The rhizosphere soil microbial community under ice exhibits higher diversity and community turnover in the ice-covered stage. The mechanisms by which community assembly processes shape those patterns are poorly understood in high-latitude wetlands. Based on the 16S rRNA gene and ITS sequencing data, we determined the diversity patterns for the rhizosphere microbial community of two plant species in a seasonally ice-covered wetland, during the ice-covered and ice-free stages. The ecological processes of the community assembly were inferred using the null model at the phylogenetic bins (taxonomic groups divided according to phylogenetic relationships) level. Different effects of ecological processes on rare and abundant microbial sub-communities (defined by the relative abundance of bins) and bins were further analyzed. We found that bacterial and fungal communities had higher alpha and gamma diversity under the ice. During the ice-free stage, the dissimilarity of fungal communities decreased sharply, and the spatial variation disappeared. For the bacterial community, homogeneous selection, dispersal limitation, and ecological processes (undominated processes) were the main processes, and they remained relatively stable across all stages. For the fungal community, during the ice-covered stage, dispersal limitation was the dominant process. In contrast, during the ice-free stage, ecological drift processes were more important in the Scirpus rhizosphere, and ecological drift and homogeneous selection processes were more important in the Phragmites rhizosphere. Regarding the different effects of community assembly processes on abundant and rare microbes, abundant microbes were controlled more by homogeneous selection. In contrast, rare microbes were controlled more by ecological drift, dispersal limitation, and heterogeneous selection, especially bacteria. This is potentially caused by the low growth rates or the intermediate niche breadths of rare microbes under the ice. Our findings suggest the high diversity of microbial communities under the ice, which deepens our understanding of various ecological processes of community assembly across stages and reveals the distinct effects of community assembly processes on abundant and rare microbes at the bin level.

Soil Microbial Network Complexity Varies With pH as a Continuum, Not a Threshold, Across the North China Plain

There has been little study on the biogeographical patterns of microbial co-occurrence, especially in agricultural soils. Here we investigated the biogeographical patterns and major drivers of co-occurrence network topological structure, and the relative abundance of keystone taxa for soil bacterial and fungal communities using high-throughput sequencing on a set of 90 samples across a 1,092 km transect in wheat fields of the North China Plain (NCP). We found that pH was the most important environmental factor driving network topology and relative abundance of keystone taxa. For the metacommunity composed of both bacteria and fungi, and for the bacterial community alone, lower soil pH was associated with a more complex microbial network. However, the network for fungi showed no strong trend with soil pH. In addition, keystone taxa abundance was positively correlated with ecosystem function and stability, and best explained by pH. Our results present new perspectives on impacts of pH on soil microbial network structure across large scales in agricultural environments. This improved knowledge of community processes provides a step toward understanding of functioning and stability of agricultural ecosystems.

Differential microbial assembly processes and co-occurrence networks in the soil-root continuum along an environmental gradient

Microorganisms of the soil-root continuum play key roles in ecosystem function. The Loess Plateau is well known for its severe soil erosion and thick loess worldwide, where mean annual precipitation (MAP) and soil nutrients decrease from the southeast to the northwest. However, the relative influence of environmental factors on the microbial community in four microhabitats (bulk soil, rhizosphere, rhizoplane, and endosphere) in the soil-root continuum along the environmental gradient in the Loess Plateau remains unclear. In this study, we investigated 82 field sites from warm-temperate to desert grasslands across the Loess Plateau, China, to assess the bacterial diversity, composition, community assembly, and co-occurrence networks in the soil-root continuum along an environmental gradient using bacterial 16S recombinant DNA amplicon sequencing. We discovered that the microhabitats explained the largest source of variations in the bacterial diversity and community composition in this region. Environmental factors (e.g., MAP, soil organic carbon, and pH) impacted the soil, rhizosphere, and rhizoplane bacterial communities, but their effects on the bacterial community decreased with increased proximity to roots from the soil to the rhizoplane, and the MAP enlarged the dissimilarity of microbial communities from the rhizosphere and rhizoplane to bulk soil. Additionally, stochastic assembly processes drove the endosphere communities, whereas the soil, rhizosphere, and rhizoplane communities were governed primarily by the variable selection of deterministic processes, which showed increased importance from warm-temperate to desert grasslands. Moreover, the properties of the microbial networks in the rhizoplane community indicate more stable networks in desert grasslands, likely conferring the resistance of microbial communities in higher stress environments. Collectively, our results showed that the bacterial communities in the soil-root continuum had different sensitivities and assembly mechanisms along an environmental gradient. These patterns are shaped simultaneously by the intertwined dimensions of proximity to roots and environmental stress change in the Loess Plateau.

Biogeographic Patterns and Elevational Differentiation of Sedimentary Bacterial Communities across River Systems in China

Bacterial biodiversity is tightly correlated with ecological functions of natural systems, and bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning. However, the biogeographic pattern and elevational differentiation of sedimentary bacterial diversity have rarely been studied in cross-river systems at a continental scale. This study analyzed the biogeographic patterns and elevational differentiations of the entire, abundant, and rare bacterial (sub)communities as well as the underlying mechanisms across nine rivers that span distinct geographic regions and large elevational gradients in China. We found that bacterial rare and abundant subcommunities shared similar biogeographic patterns and both demonstrated strong distance-decay relationships, despite their distinct community compositions. However, both null model and variation partitioning analysis results showed that while environmental selection governed rare subcommunity assemblies (contribution: 51.9%), dispersal limitation (62.7%) controlled the assembly of abundant subcommunities. The disparity was associated with the broader threshold width of abundant taxa to water temperature and pH variations than rare taxa. Elevation-induced bacterial composition variations were more evident than latitude-induced ones. Some specific operational taxonomic units (OTUs), representing 16.4% of the total sequences, much preferentially and even exclusively lived in high-elevation or low-elevation habitats and demonstrated some adaptations to local conditions. Greater positive: negative link ratios in bacterial co-occurrence networks of low elevations than high elevations (P < 0.05) partly resulted from their harboring higher organic carbon: nitrogen ratios. Together, this study draws a biogeographic picture of sedimentary bacterial communities in a continental-scale riverine system and highlights the importance of incorporating elevation-associated patterns of microbial diversity into riverine microbial ecology studies. IMPORTANCE Bacterial diversity is tightly correlated with the nutrient cycling of river systems. However, previous studies on bacterial diversity are mainly constrained to one single river system, although microbial biogeography and its drivers exhibit strong spatial scale dependence. Moreover, elevational differentiations of bacterial communities across river systems have also rarely been studied. Bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning, and they share similar biogeographic patterns in some environments but not in others. Therefore, we explored the biogeography of the entire, abundant, and rare (sub)communities in nine rivers that cover a wide space range and large elevational gradient in China. Our results revealed that bacterial rare and abundant subcommunities shared similar biogeographic patterns but their assembly mechanisms were much different in these rivers. Moreover, bacterial communities showed evident differentiations between high elevations and low elevations. These findings will facilitate a better understanding of bacterial diversity features in river systems.

Distinct strategies of the habitat generalists and specialists in sediment of Tibetan lakes

Microbial metacommunities normally comprise generalists and specialists. Uncovering the mechanisms underlying the diversity patterns of these two sub-communities is crucial for aquatic biodiversity maintenance. However, little is known about the ecological assembly processes and co-occurrence patterns of the habitat generalists and specialists across large spatial scales in plateau lake sediments, particularly regarding their environmental adaptations. Here, we investigated assembly processes of the habitat generalists and specialists in sediment of Tibetan lakes and their role in the stability of metacommunity co-occurrence network. Our results showed that the habitat generalists exhibited broader environmental thresholds and closer phylogenetic clustering than specialist counterparts. In contrast, the specialists exhibited stronger phylogenetic signals of ecological preferences compared with the habitat generalists. Stochastic processes dominated the habitat generalist (63.2%) and specialist (81.3%) community assembly. Sediment pH was the major factor mediating the balance between stochastic and deterministic processes in the habitat generalists and specialists. In addition, revealed by network analysis, the habitat specialists played a greater role in maintaining the stability of metacommunity co-occurrence network. The insights gained from this study can be helpful to understand the mechanisms underlying maintenance of sediment microbial diversity in plateau lakes. This article is protected by copyright. All rights reserved.

Pharmaceutical Pollution in Aquatic Environments: A Concise Review of Environmental Impacts and Bioremediation Systems

The presence of emerging contaminants in the environment, such as pharmaceuticals, is a growing global concern. The excessive use of medication globally, together with the recalcitrance of pharmaceuticals in traditional wastewater treatment systems, has caused these compounds to present a severe environmental problem. In recent years, the increase in their availability, access and use of drugs has caused concentrations in water bodies to rise substantially. Considered as emerging contaminants, pharmaceuticals represent a challenge in the field of environmental remediation; therefore, alternative add-on systems for traditional wastewater treatment plants are continuously being developed to mitigate their impact and reduce their effects on the environment and human health. In this review, we describe the current status and impact of pharmaceutical compounds as emerging contaminants, focusing on their presence in water bodies, and analyzing the development of bioremediation systems, especially mycoremediation, for the removal of these pharmaceutical compounds with a special focus on fungal technologies.

Changes in assembly processes of soil microbial communities in forest-to-cropland conversion in Changbai Mountains, northeastern China

In response to human-induced changes in the environment, it is crucial to assess the underlying factors of the impacts of forest conversion on ecosystem function. However, research is limited on bacteria and fungi diversity, functional properties, and community assembly mechanisms in response to forest-to-cropland conversion. We categorized soil bacterial and fungal communities from primary forest, secondary forest, and cropland in Changbai Mountains, China. We found that forest-to-cropland conversion altered the structure and composition of bacterial and fungal communities and might be associated with potential changes in function. The null models indicated that the conversion from forest to cropland enhanced the bacterial dispersal limitation process and weakened the fungal dispersal limitation processes. Furthermore, ecological drift dominates the ecological processes of cropland fungi. Both edaphic properties (the content of C: N ratio, available phosphorus, nitrate) significantly impacted on soil bacterial and fungal community structures. In addition, there were significant functional variations in the fungal community between forest-to-cropland. The ectomycorrhizal and saprotrophic fungi showed increased abundance in the forest microbial communities, whereas the endophytic and pathogenic fungal abundance was increased in cropland soil. Taken together, our data illustrate the differences in the response of bacteria and fungi to forest-to-cropland conversion in temperate forest areas and deepen our understanding of the effects of forest conversion on microbial functions and community assembly processes.

Response of Fungal Sub-Communities in a Maize-Wheat Rotation Field Subjected to Long-Term Conservation Tillage Management

Conservation tillage is an advanced agricultural technology that seeks to minimize soil disturbance by reducing, or even eliminating tillage. Straw or stubble mulching in conservation tillage systems help to increase crop yield, maintain biodiversity and increase levels of exogenous nutrients, all of which may influence the structure of fungal communities in the soil. Currently, however, the assembly processes and co-occurrence patterns of fungal sub-communities remain unknown. In this paper, we investigated the effects of no-tillage and straw mulching on the composition, assembly process, and co-occurrence patterns of soil fungal sub-communities in a long-term experimental plot (15 years). The results revealed that combine straw mulching with no-tillage significantly increased the richness of fungi but not their diversity. Differential abundance analysis and principal component analysis (PCA) indicated that tillage management had a greater effect on the fungal communities of abundant and intermediate taxa than on the rare taxa. Available phosphorus (AP) and total nitrogen (TN) were the major determinants of fungal sub-communities in NT treatment. The abundant fungal sub-communities were assembled by deterministic processes under medium strength selection, while strong conservation tillage strength shifts the abundant sub-community assembly process from deterministic to stochastic. Overall, the investigation of the ecological network indicated that no-tillage and straw mulching practices decreased the complexity of the abundant and intermediate fungal networks, while not significantly influencing rare fungal networks. These findings refine our knowledge of the response of fungal sub-communities to conservation tillage management techniques and provide new insights into understanding fungal sub-community assembly.

Environmental stress-discriminatory taxa are associated with high C and N cycling functional potentials in dryland grasslands

Increasing environmental stress strongly affects soil microbial communities, but the responses of the microbial assembly and the functional potential of the dominant microbial community in the presence of environmental stress in drylands are still poorly understood. Here, we undertook a broad appraisal of the abundance, diversity, similarity, community assembly, network properties and functions of soil microbiomes in 82 dryland grasslands along environmental gradients. We found that the bacterial and fungal diversity and community similarity showed different sensitivities to environmental stress (decreased mean annual precipitation (MAP) and soil nutrient levels and increased soil pH), and MAP was the most important factor influencing microbial community patterns. In addition, the dominant subcommunity of both bacteria and fungi was more sensitive to environmental stress than the nondominant subcommunity. Although increasing environmental stress decreased microbial phylogenetic clustering, it had no effects on the stochastic and deterministic assembly process balance. Moreover, we identified 101 bacterial and 34 fungal environmental stress-discriminatory taxa that were sensitive to environmental stress, and these bacterial markers showed a high correlation with the abundance of carbon (C) and nitrogen (N) cycling-related genes, whereas the taxa classified as connectors in the network were mainly correlated with C degradation genes. Our study shows that the different responses of bacteria and fungi to environmental stress bring challenges to predicting microbial function, but a relatively small number of taxa play an important role in driving C and N cycling-related functional genes, indicating that identifying an organism's phenotypic characteristics or traits of key taxa may improve our knowledge of the microbial response to ongoing global changes.

Compositional Changes and Co-Occurrence Patterns of Planktonic Bacteria and Microeukaryotes in a Subtropical Estuarine Ecosystem, the Pearl River Delta

Planktonic microorganisms in aquatic ecosystems form complex assemblages of highly interactive taxa and play key roles in biogeochemical cycles. However, the microbial interactions within bacterial and microeukaryotic communities, and the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances in the river estuary remain unknown. Here, 16S and 18S rRNA gene sequencing were used to investigate the compositional changes and the co-occurrence patterns of bacterial and microeukaryotic communities. The results showed that the rare taxa in the bacterial communities were more prevalent than those in the microeukaryotic communities and may influence the resilience and resistance of microorganisms to environmental variations in estuarine ecosystems. The environmental variations had strong effects on the microeukaryotic communities and their assembly mechanisms but not on the bacterial communities in our studied area. However, based on co-occurrence network analyses, the bacterial communities had stronger links and more complex interactions than microeukaryotic communities, suggesting that bacterial networks may help improve the buffering capacities of the estuarine ecosystem against environmental change. The keystone taxa of bacteria mainly belonged to rare subcommunities, which further illustrates that rare taxa may play fundamental roles in network persistence. Overall, these results provide insights into the microbial responses of aquatic ecosystems to environmental heterogeneity.

Wheat yellow mosaic enhances bacterial deterministic processes in a plant-soil system

Understanding the mechanisms that govern microbial community assembly across soil-plant continuum is crucial for predicting the response of ecosystems to environmental changes. However, the impact of the health status of plant on microbial assembly across this continuum still remain poorly understood. Here, we investigated how wheat yellow mosaic (WYM), caused by the wheat mosaic virus transmitted by Polymyxa graminis, affected microbial assembly across soil (bulk soil, rhizosphere soil), and plant (roots and leaves) continuum in a winter wheat (Triticum aestivum L.) system in northern China, using null model analysis. The results showed that deterministic processes dominated the bacterial community assembly, whereas stochastic processes were primarily responsible for the assembly of the fungal communities. With increasing levels of WYM, deterministic processes were greatly enhanced for bacterial community assembly, accompanied by a decrease in community niche breadth. Intensified competition between bacteria and fungi and increased soil total nitrogen (TN) and soil organic carbon (SOC) contents were mainly responsible for the enhanced deterministic processes for bacterial community assembly. Random forest modeling indicated a strong potential of rhizosphere bacterial community assembly for predicting the pathological conditions of wheat. Structural equation modeling showed that disease level was positively correlated with SOC and TN contents, competitions between bacteria and fungi, and the contribution of variable selection processes to the bacterial community assembly in the wheat rhizosphere. Our study revealed the ecological mechanisms underlying the associations between microbial communities and soil-borne disease, and highlighted the significance of microbial community assembly for maintaining soil and plant health.

Assembly of functional microbial communities in paddy soil with long-term application of pig manure under rice-rape cropping system

Organic farming is considered an efficient approach to improve soil fertility for sustainable agriculture. However, its soil micro-ecological effects and functions in intensive rice cropping systems are still obscure. Twelve soil samples were collected from a field experiment with four treatments such as M0 (no pig manure), M1 (1.6 t ha^-1 pig manure), M2 (3.2 t ha^-1 pig manure) and M3 (4.8 t ha^-1 pig manure) after eight rice-oilseed rape rotation. Soil chemical property, enzyme activity and abundant/rare bacterial or fungal communities were analyzed to investigate the effect of conversion to organic farming with continuous pig manure application on soil microbiota. Stochastic processes controlled the assembly of abundant taxa, and deterministic processes dominated rare taxa. The composition and network construction of bacterial and fungal communities were significantly affected by pig manure, with changes in soil property and enzyme activity. Based on partial least squares path modeling (PLS-PM), pig manure application affected bacteria construction and enzyme activities by increasing soil carbon (C) and nitrogen (N). In summary, long-term pig manure application promotes specific microbial associations known to be involved in degrading complex organic compounds, and improving soil fertility such as soil enzyme activities. This research provides insight into understanding the processes behind changes in bacterial and fungal communities in paddy soil after conversion to organic farming.

Linking soil fungi to bacterial community assembly in arid ecosystems

Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.

Similar geographic patterns but distinct assembly processes of abundant and rare bacterioplankton communities in river networks of the Taihu Basin

Bacterioplankton play an important role in the biogeochemical cycling in rivers. The dynamics of hydrologic conditions in rivers were believed to affect geographic pattern and assembly process of these microorganisms, which have not been widely investigated. In this study, the geographic pattern and assembly process of bacterioplankton community in river networks of the Taihu Basin were systematically explored using amplicon sequencing of the 16S rRNA gene. The results showed that the diversity, structure,  and taxonomic composition of bacterioplankton community all exhibited significant temporal variation during wet, normal, and dry seasons (p<0.01). The neutral community model and null model were applied to reveal the assembly process of bacterioplankton community. The stochastic process and deterministic process both shaped the bacterioplankton community with greater influence of deterministic process. In addition, the abundant and rare bacterioplankton communities were comparatively analyzed. The abundant and rare bacterioplankton communities exhibited similar temporal dynamics (principal coordinates analysis) and spatial variations (distance-decay relationship), indicating similar geographic patterns. Meanwhile, distinct assembly processes were observed for the abundant and rare bacterioplankton communities. Stochastic process (dispersal limitation) shaped the abundant bacterioplankton community while deterministic process (heterogeneous selection) dominated the assembly process of rare bacterioplankton community. Mantel test, redundancy analysis, and correlation analysis together indicated that pH and dissolved oxygen were the major environmental attributes that affected thestructure and assembly process of bacterioplankton community. These results expanded our understanding of the geographic pattern, assembly process, and driving factors of bacterioplankton community in river networks and provided clues for the underlying mechanisms.

Contrasting assembly mechanisms and drivers of soil rare and abundant bacterial communities in 22-year continuous and non-continuous cropping systems

Despite many studies on the influence of cropping practices on soil microbial community structure, little is known about ecological patterns of rare and abundant microbial communities in response to different tobacco cropping systems. Here, using the high-throughput sequencing technique, we investigated the impacts of two different cropping systems on soil biochemical properties and the microbial community composition of abundant and rare taxa and its driving factors in continuous and rotational tobacco cropping systems in the mountain lands of Yunnan, China. Our results showed that distinct co-occurrence patterns and driving forces for abundant and rare taxa across the different cropping systems. The abundant taxa were mainly constrained by stochastic processes in both cropping systems. In contrast, rare taxa in continuous cropping fields were mainly influenced by environmental perturbation (cropping practice), while governed by deterministic processes under rotational cropping. The α-diversity indices of rare taxa tended to be higher than those of the abundant ones in the two cropping systems. Furthermore, the network topologies of rare taxa were more complex than those of the abundant taxa in the two cropping systems. These results highlight that rare taxa rather than abundant ones play important roles in maintaining ecosystem diversity and sustaining the stability of ecosystem functions, especially in continuous cropping systems.

Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem

Soil microbes are an essential component of terrestrial ecosystems and drive many biogeochemical processes throughout the soil profile. Prior field studies mainly focused on the vertical patterns of soil microbial communities, meaning their temporal dynamics have been largely neglected. In the present study, we investigated the vertical and temporal patterns of soil bacterial and archaeal communities in a wheat-soybean rotation agroecosystem at a depth of millions of sequences per sample. Our results revealed different vertical bacterial and archaeal richness patterns: bacterial richness was lowest in the deep soil layer and peaked in the surface or middle soil layer. In contrast, archaeal richness did not differ among soil layers. PERMANOVA analysis indicated that both bacterial and archaeal community compositions were significantly impacted by soil depth but unaffected by sampling time. Notably, the proportion of rare bacteria gradually decreased along with the soil profile. The rare bacterial community composition was the most important indicator for soil nutrient fertility index, as determined by random forest analysis. The soil prokaryotic co-occurrence networks of the surface and middle soil layers are more connected and harbored fewer negative links than that of the deep soil layer. Overall, our results highlighted soil depth as a more important determinant than temporal variation in shaping the soil prokaryotic community and interspecific interactions and revealed a potential role of rare taxa in soil biogeochemical function.

Aridity Threshold Induces Abrupt Change of Soil Abundant and Rare Bacterial Biogeography in Dryland Ecosystems

Aridity, which is increasing worldwide due to climate change, affects the biodiversity and functions of dryland ecosystems. Whether aridification leads to gradual (or abrupt) and systemic (or specific) changes in the biogeography of abundant and rare microbial species is largely unknown. Here, we investigated stress-adaptive changes (aridity-driven, ranging from 0.65 to 0.94) and biogeographic patterns of abundant and rare bacterial communities in different habitats, including agricultural field, forest, wetland, grassland, and desert, in desert oasis transition zones in northern China. We observed abrupt changes at the breakpoint of aridity values (0.92), characterized by diversity (α-diversity and β-diversity), species coexistence, community assembly processes, and phylogenetic niche conservatism. Specifically, when aridity was <0.92, increasing aridity led to more deterministic assembly and species coexistences for the abundant subcommunity, whereas the reverse was observed for the rare subcommunity. The phylogenetic niche conservatism for both subcommunities increased slowly with aridity. When aridity was >0.92, the systemic responses of abundant and rare taxa changed dramatically in a consistent direction, such that both subcommunities rapidly tended to have a more deterministic assembly, species coexistence, and stronger phylogenetic niche conservatism with increasing aridity. In addition, the change rates of abundant taxa were higher than those of rare taxa, indicating the more sensitive responses of abundant taxa along aridity variation. This finding has important implications for understanding the impact of aridity on the structure and function of abundant and rare soil taxa and how diversity maintenance is associated with soil microbiota responding to global change. The abrupt threshold of soil bacteria found can be used for buffering and for building effective adaptation and mitigation measures aimed at maintaining the capacity of drylands for basic ecosystem functioning.

IMPORTANCE Aridity, which is increasing worldwide due to climate change, affects the biodiversity and functions of dryland ecosystems. We provided the first statistical evidence for abrupt changes of species coexistence, ecological processes, and niche conservation of abundant and rare soil bacteria triggered by diversity to abrupt increases in aridity. The abrupt threshold of soil bacterial community response to aridity is spatially heterogeneous at the local scale and should be specified according to local conditions for buffering and for building effective adaptation and mitigation measures aimed at maintaining the capacity of drylands for basic ecosystem functioning.

Nitrogen rather than phosphorus driving the biogeographic patterns of abundant bacterial taxa in a eutrophic plateau lake

Eutrophication of freshwater lakes is an important cause of global water pollution. In this study, the composition and biogeographic distribution of both abundant and rare sedimentary bacterial taxa and their relationship with nutrients were assessed in Erhai Lake, a subtropical plateau lake. Proteobacteria (48.3%) and Nitrospirae (11.7%) dominated the composition of abundant taxa, while the rare taxa were dominated by Proteobacteria (25.8%) and Chloroflexi (14.1%). The abundant bacterial taxa had strong energy metabolism, whereas the rare bacterial taxa had strong xenobiotics biodegradation and metabolism. These results indicated different compositions and functions existed between abundant and rare taxa. Total nitrogen (TN) was the most influential factor shaping the biogeographic patterns of both abundant and rare taxa. Phosphorus was not the deterministic factor, although nitrogen and phosphorus were the main contributors to eutrophication. Total organic carbon and pH also contributed to the biogeographic patterns of both abundant and rare taxa. In the eutrophic plateau lake sediments, abundant taxa, rather than rare taxa, played a dominant role in maintaining the community structure and ecological function of the bacterial community. The TN gradient was an important factor that affected the biogeographic distribution and assembly processes of abundant taxa. This study sheds light on the role of TN in shaping the biogeographic distribution and assembly processes of abundant taxa in eutrophic lakes.

Perfluorinated compounds (PFCs) in regional industrial rivers: Interactions between pollution flux and eukaryotic community phylosymbiosis

Perfluorinated compounds (PFCs) pose serious threats to aquatic ecosystems, especially their microbial communities. However, little is known about the phylosymbiosis of aquatic fungal and viridiplantae communities in response to PFC accumulation. We quantified the distribution of 14 PFCs in rivers and found that PFBA was dominant in the transition from water to sediment. High through-put sequencing revealed that phyla Ascomycota, Basidiomycota, Anthophyta, and Chlorophyta were the predominant in eukaryotic community. The effects of PFCs on spatial community coalescence at taxonomic and phylogenetic levels (p < 0.05) were revealed. Fungal community coalescence triggered the spatial assembly of fungal and viridiplantae communities in riverine environments (p < 0.05). Null modeling indicated that PFBA, PFTrDA and PFOS, etc, mediated phylogenetic assembly (p < 0.05) and stochastic processes (86.67-100%) maintain phylogenetic turnover in the fungal community. Meanwhile, variable selection (27.78-54.44%) explained the viridiplantae community assemblage. Finally, we identified fungal genera Hannaella, Naganishia, Purpureocillium and Stachybotrys as indicators for PFC pollution (p < 0.001). These results help explain the effects of PFCs on riverine ecological remediation.

Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems

Belowground biodiversity supports multiple ecosystem functions and services that humans rely on. However, there is a dearth of studies exploring the determinants of the biodiversity-ecosystem function (BEF) relationships, particularly in intensely managed agricultural ecosystems. Here, we reported significant and positive relationships between soil biodiversity of multiple organism groups and multiple ecosystem functions in 228 agricultural fields, relating to crop yield, nutrient provisioning, element cycling, and pathogen control. The relationships were influenced by the types of organisms that soil phylotypes with larger sizes or at higher trophic levels, for example, invertebrates or protist predators, appeared to exhibit weaker or no BEF relationships when compared to those with smaller sizes or at lower trophic levels, for example, archaea, bacteria, fungi, and protist phototrophs. Particularly, we highlighted the role of soil network complexity, reflected by co-occurrence patterns among multitrophic-level organisms, in enhancing the link between soil biodiversity and ecosystem functions. Our results represent a significant advance in forecasting the impacts of belowground multitrophic organisms on ecosystem functions in agricultural systems, and suggest that soil multitrophic network complexity should be considered a key factor in enhancing ecosystem productivity and sustainability under land-use intensification.

Soil pH and moisture govern the assembly processes of abundant and rare bacterial communities in a dryland montane forest

The assembly mechanisms and ecological drivers of abundant and rare bacterial subcommunities in dryland montane forest ecosystems remain unclear. Here, we compared the biogeographic patterns of rare and abundant bacterial subcommunities and examined the ecological drivers governing their assembly processes in a dryland montane forest of China. Our results showed that a stronger relationship existed between phylogenetic turnover and spatial distance in rare subcommunities compared with that in abundant subcommunities. Null model analysis indicated that abundant subcommunities were predominantly controlled by dispersal limitation, whereas variable selection controlled rare bacterial assembly. More importantly, the balance between deterministic and stochastic processes for abundant and rare subcommunities was regulated by soil pH and soil moisture content, respectively, rather than aridity. Increasing soil moisture decreased the importance of deterministic processes for rare bacterial assembly. In abundant subcommunities, the dominance of stochastic processes was higher in neutral pH soils. Our findings suggested that divergent assembly mechanisms underlying distinct biogeographic patterns in rare and abundant bacterial subcommunities in dryland montane forests, and the assembly mechanisms of abundant and rare bacterial subcommunities were mediated by differentiated environmental factors. Our study provides a new understanding of the generation and maintenance of soil biodiversity in dryland ecosystems.

Linking rare and abundant phoD-harboring bacteria with ecosystem multifunctionality in subtropical forests: From community diversity to environmental adaptation

Environmental factor-driven bacterial diversity could be an indicator for evaluating ecosystem multifunctionality (EMF). However, little is known about interconnections between EMF and the community diversity of rare and abundant phoD-harboring bacteria responsible for organic phosphorus mineralization. Illumina MiSeq sequencing and multiple statistical analyses were used to evaluate diversity maintenance of rare and abundant phoD-harboring bacteria at both taxonomic and phylogenetic levels and their contributions to soil EMF in the subtropical Shennongjia primeval forest. We found that rare phoD-harboring bacteria exhibited higher community diversity and broader environmental breadths than abundant ones, while abundant phoD-harboring bacteria showed closer phylogenetic clustering and stronger phylogenetic signals of ecological preferences than rare ones. Stochastic processes dominated community assemblies of rare and abundant phoD-harboring bacteria, and temperature was an important environmental variable adjusting the balance between stochastic and deterministic processes. The taxonomic α-diversity of rare phoD-harboring bacteria showed larger contribution to soil EMF than that of abundant ones, while the phylogenetic α-diversity of abundant phoD-harboring bacteria contributed significantly more than that of rare ones. Our findings enrich knowledge of the environmental adaptation of rare and abundant phoD-harboring bacteria, and highlight linkages between soil EMF and the diversity of rare and abundant phoD-harboring bacteria at both the taxonomic and phylogenetic levels.

Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil

Soil microorganisms, which intricately link to ecosystem functions, are pivotal for the ecological restoration of heavy metal-contaminated soil. Despite the importance of rare and abundant microbial taxa in maintaining soil ecological function, the taxonomic and functional changes in rare and abundant communities during in situ chemical stabilization of cadmium (Cd)-contaminated soil and their contributions to the restoration of ecosystem functions remain elusive. Here, a 3-year field experiment was conducted to assess the effects of five soil amendments (CaCO₃ as well as biochar and rice straw, individually or in combination with CaCO₃) on rare and abundant microbial communities. The rare bacterial community exhibited a narrower niche breadth to soil pH and Cd speciation than the abundant community and was more sensitive to environmental changes altered by different soil amendments. However, soil amendments had comparable impacts on rare and abundant fungal communities. The assemblies of rare and abundant bacterial communities were dominated by variable selection and stochastic processes (dispersal limitation and undominated processes), respectively, while assemblies of both rare and abundant fungal communities were governed by dispersal limitation. Changes in soil pH, Cd speciation, and soil organic matter (SOM) by soil amendments may play essential roles in community assembly of rare bacterial taxa. Furthermore, the restored ecosystem multifunctionality by different amendments was closely related to the recovery of specific keystone species, especially rare bacterial taxa (Gemmatimonadaceae and Haliangiaceae) and rare fungal taxa (Ascomycota). Together, our results highlight the distinct responses of rare and abundant microbial taxa to soil amendments and their linkage with ecosystem multifunctionality.

IMPORTANCE Understanding the ecological roles of rare and abundant species in the restoration of soil ecosystem functions is crucial to remediation of heavy metal-polluted soil. Our study assessed the efficiencies of five commonly used soil amendments on recovery of ecosystem multifunctionality and emphasized the relative contributions of rare and abundant microbial communities to ecosystem multifunctionality. We found great discrepancies in community composition, assembly, niche breadth, and environmental responses between rare and abundant communities during in situ chemical stabilization of Cd-contaminated soil. Application of different soil amendments triggered recovery of specific key microbial species, which were highly related to ecosystem multifunctionality. Together, our results highlighted the importance of rare bacterial as well as rare and abundant fungal communities underpinning restoration of soil ecosystem multifunctionality during the Cd stabilization process.

Leaf surface microtopography shaping the bacterial community in the phyllosphere: evidence from 11 tree species

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

High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling

Salinization is considered a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Here, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered both bacterial alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, total nitrogen (TN), and soil organic matter (SOM) were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased, indicating that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. MiSeq sequencing of 16S rRNA genes revealed that the abundance and composition of the nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for a salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbes respond to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m^-1). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized the bacterial network. Moreover, variable selection (61% to 66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance for managing saline soils and maintaining a healthy ecosystem.

Preferences for core microbiome composition and function by different definition methods: Evidence for the core microbiome of Eucommia ulmoides bark

The core microbiome, as a unique group of microorganisms, is an emerging research hotspot that provides a new opportunity to improve growth and production of a host. However, the subjectivity associated with the concept of "core microbiome" means there is currently no uniform definition method for the core microbiome. In this study, the strengths and limitations of four commonly used definition methods for the core microbiome were explored from composition to function based on the 16S rRNA gene dataset of Eucommia ulmoides bark from 25 different biogeographical regions in China. There were differences in the composition of the core microbiomes defined by the different methods. The four definition methods of phylogeny, membership, composition, and network connection contained 274, 10, 5, and 5 core OTUs (operational taxonomic units), respectively. In contrast, the core microbiomes defined by different methods displayed similarities in function. In addition, different definition methods showed varying preferences for abundant taxa, intermediate taxa, and rare taxa. Some core taxa defined by the definition method of phylogeny were significantly associated with pharmacologically active ingredients of E. ulmoides bark. The findings of this study suggest that although the core microbiomes defined by different methods have preferences in composition and function, the term refers to a group of microbes that are particularly notable and important for host-associated microbiomes. Therefore, we propose: (I) The definition method of the core microbiome should be selected according to the ecological problems faced; (II) A combination of multiple methods may comprehensively reveal the core microbiome at different levels of the host, and may also facilitate understanding of the ecological and evolutionary processes that govern host-microbe interactions.

Land-use conversion from open field to greenhouse cultivation differently affected the diversities and assembly processes of soil abundant and rare fungal communities

Soil fungal communities, consisting of a few abundant taxa but many rare taxa, play critical roles in terrestrial ecosystem functioning. However, little is known about ecological processes governing the assembly of abundant and rare sub-communities in response to agricultural intensification, which can threaten soil biodiversity. Here, we performed a regional-scale survey of soil fungal community assembly in different land-use types with an increasing gradient of agricultural intensity, i.e., open field cultivation of main crops (CF) or vegetables (VF), and greenhouse cultivation of vegetables (VG). Results showed that greenhouse cultivation decreased the alpha diversity and spatial turnover rate of soil fungal community. The abundant sub-community was more sensitive to land-use conversion than the rare sub-community. Partitioning the Bray-Curtis dissimilarity found that balanced variation in abundance (i.e., the substitution of individuals by the same number of individuals of a different species), rather than abundance gradients (i.e., one assemblage is a subset of another), accounted for the major shift in fungal beta diversity. Moreover, greenhouse cultivation reduced potential inter-species interactions, and the rare sub-community plays an important role in fungal co-occurrence network. Conversions from CF to VF or VG promoted deterministic processes, which was, to a large extent, associated with changes in soil physicochemical properties. However, conversion from VF to VG decreased deterministic processes. Compared with the rare sub-community, the abundant sub-community with wider niche breadths was more influenced by stochastic processes. Changes in the assembly processes induced by land-use conversion differed between abundant and rare sub-communities. Overall, abundant and rare sub-communities exhibited differential responses to land-use conversion and rare taxa might play a crucial role in maintaining the stability of fungal community.

Adaptation of Soil Fungal Community Structure and Assembly to Long- Versus Short-Term Nitrogen Addition in a Tropical Forest

Soil fungi play critical roles in ecosystem processes and are sensitive to global changes. Elevated atmospheric nitrogen (N) deposition has been well documented to impact on fungal diversity and community composition, but how the fungal community assembly responds to the duration effects of experimental N addition remains poorly understood. Here, we aimed to investigate the soil fungal community variations and assembly processes under short- (2 years) versus long-term (13 years) exogenous N addition (∼100 kg N ha^–1 yr^–1) in a N-rich tropical forest of China. We observed that short-term N addition significantly increased fungal taxonomic and phylogenetic α-diversity and shifted fungal community composition with significant increases in the relative abundance of Ascomycota and decreases in that of Basidiomycota. Short-term N addition also significantly increased the relative abundance of saprotrophic fungi and decreased that of ectomycorrhizal fungi. However, unremarkable effects on these indices were found under long-term N addition. The variations of fungal α-diversity, community composition, and the relative abundance of major phyla, genera, and functional guilds were mainly correlated with soil pH and NO₃^––N concentration, and these correlations were much stronger under short-term than long-term N addition. The results of null, neutral community models and the normalized stochasticity ratio (NST) index consistently revealed that stochastic processes played predominant roles in the assembly of soil fungal community in the tropical forest, and the relative contribution of stochastic processes was significantly increased by short-term N addition. These findings highlighted that the responses of fungal community to N addition were duration-dependent, i.e., fungal community structure and assembly would be sensitive to short-term N addition but become adaptive to long-term N enrichment.

Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata)

BACKGROUND

Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress.

RESULTS

We find that the response of the wild rice microbiome to drought was divided into aboveground-underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased 'dispersal limitation', and enhanced 'drift'.

CONCLUSIONS

Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.