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Studying the functional heterogeneity of soil microorganisms at different spatial scales and linking it to soil carbon mineralization is crucial for predicting the response of soil carbon stability to environmental changes and human disturbance. Here, a total of 429 soil samples were collected from typical paddy fields in China, and the bacterial and fungal communities as well as functional genes related to carbon mineralization in the soil were analysed using MiSeq sequencing and GeoChip gene microarray technology. We postulate that CO2 emissions resulting from bacterial and fungal carbon mineralization are contingent upon their respective carbon consumption strategies, which rely on the regulation of interactions between biodiversity and functional genes. Our results showed that the spatial turnover of the fungal community was 2–4 times that of the bacterial community from hundreds of meters to thousands of kilometres. The effect of spatial scale exerted a greater impact on the composition rather than the functional characteristics of the microbial community. Furthermore, based on the establishment of functional networks at different spatial scales, we observed that both bacteria and fungi within the top 10 taxa associated with carbon mineralization exhibited a prevalence of generalist species at the regional scale. This study emphasizes the significance of spatial scaling patterns in soil bacterial and fungal carbon degradation functions, deepening our understanding of how the relationship between microbial decomposers and soil heterogeneity impacts carbon mineralization and subsequent greenhouse gas emissions. [ABSTRACT FROM AUTHOR]

Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18‐m depth profiles at 20–50‐cm intervals across contrasting aridity conditions in semi‐arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant‐derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa–taxa and bacteria–fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep‐soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria–fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole‐soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios. [ABSTRACT FROM AUTHOR]

Aim: Soil‐borne pathogens severely affect crop production, but the present distribution of agricultural soil‐borne pathogens and their response to global changes are unexplored at large spatial scales. Here, we examine the nationwide‐scale distribution patterns, dominant taxa and environmental drivers of fungal soil‐borne pathogens, and their response to warming, nutrient enrichment and their interaction. Location: China. Time period: July and August 2019. Major taxa studied: Fungal plant pathogens. Methods: Through nationwide field surveys of 711 top‐ and subsoil samples in 51 cropland locations, we investigated the distribution patterns, environmental drivers and dominant taxa of fungal plant pathogens. We then conducted a mesocosm experiment with soils collected at 40 survey locations to evaluate the response patterns of fungal pathogens to global changes, including warming, nutrient enrichment and their interaction. Results: We observed that the abundance and richness of potential soil‐borne pathogens were higher in the topsoil than in the subsoil. Mean annual temperature and mean annual precipitation as the main drivers had a stronger effect on the abundance, richness and community of pathogens in the topsoil than subsoil. Two phylotypes, belonging to genus Fusarium, were the dominant soil‐borne pathogens accounting for approximately one third of total abundance, and their abundances (e.g. relative and absolute abundance via quantitative polymerase chain reaction) were negatively correlated with precipitation and temperature. The mesocosm experiment simulating global changes further revealed that the abundance and richness distributions of soil pathogens predicted the direction of their response to global changes, with a positive response in pathogen‐poor soil and negative in pathogen‐rich soil. We further constructed spatial atlases of the dominant soil‐borne pathogens and their responses to global changes in agricultural fields. Main conclusions: Our findings suggest that the current distribution of potential soil‐borne pathogens is regulated by climate, which could affect their future dynamics and is vital to agricultural practices for pathogen control and crop production. [ABSTRACT FROM AUTHOR]

Background: The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments. Results: Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status. Conclusions: Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. CBzZNC2FEDswGcHctbDosa Video Abstract [ABSTRACT FROM AUTHOR]

Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats. [ABSTRACT FROM AUTHOR]

Afforestation is an effective approach to rehabilitate degraded ecosystems, but often depletes deep soil moisture. Presently, it is not known how an afforestation‐induced decrease in moisture affects soil microbial community and functionality, hindering our ability to understand the sustainability of the rehabilitated ecosystems. To address this issue, we examined the impacts of 20 years of afforestation on soil bacterial community, co‐occurrence pattern, and functionalities along vertical profile (0–500 cm depth) in a semiarid region of China's Loess Plateau. We showed that the effects of afforestation with a deep‐rooted legume tree on cropland were greater in deep than that of in top layers, resulting in decreased bacterial beta diversity, more responsive bacterial taxa and functional groups, increased homogeneous selection, and decreased network robustness in deep soils (120–500 cm). Organic carbon and nitrogen decomposition rates and multifunctionality also significantly decreased by afforestation, and microbial carbon limitation significantly increased in deep soils. Moreover, changes in microbial community and functionality in deep layer was largely related to changes in soil moisture. Such negative impacts on deep soils should be fully considered for assessing afforestation's eco‐environment effects and for the sustainability of ecosystems because deep soils have important influence on forest ecosystems in semiarid and arid climates. [ABSTRACT FROM AUTHOR]

Aim: Climate change is the foremost cause of terrestrial biodiversity decline, but the microbial communities from different habitats do not respond equally to environmental change. However, our understanding of the response patterns of microbial diversity to climate change remains limited in distinct agriculture ecosystems across large spatial scales. Here, we explore the response patterns of soil bacterial community structure and function to dry–wet cycles in dryland (maize) and paddy (rice) agricultural ecosystems throughout eastern China. Location: Eastern China. Time period: November 2019 to May 2020. Major taxa studied: Bacterial communities. Methods: Incubation experiments with dry–wet cycles were carried out on the soil samples collected from 25 paired maize and rice fields across eastern China. Bacterial community structure was estimated via high‐throughput sequencing techniques. We applied quantitative polymerase chain reaction to evaluate the effect of the dry–wet cycle on the change of functional genes. Phylogenetic signals were examined based on Blomberg's K to test the phylogenetic conservatism of maize and rice bacterial communities during dry–wet cycles. Results: Dry–wet cycles significantly decreased bacterial alpha diversity in both maize and rice soils, and bacterial communities from warmer regions were more sensitive to dry–wet cycles. The bacterial responses to dry–wet cycles were phylogenetically conserved, with greater phylogenetic conservation in the former. The abundance of functional genes that were related to carbon decomposition, nitrogen fixation, nitrification, denitrification and organophosphorus mineralization decreased during dry–wet cycles, and the resistances of such functional genes to disturbance were stronger in rice soils than in maize soils. In addition, the relative abundances of stable amplicon sequence variants during dry–wet cycles had a significant positive linear relationship with functional gene abundance in the maize and rice soils, indicating their essential roles in the stability of microbial function. Main conclusions: We conclude that soil bacterial community structure and function in dryland agricultural ecosystems are less stable and exhibit greater phylogenetic conservation in response to dry–wet cycles when compared with paddy fields. In addition, our study reveals, for the first time, the response patterns of bacterial communities to dry–wet cycles in dryland and wetland agroecosystems. [ABSTRACT FROM AUTHOR]

Interactions between plant hosts and their microbiotas are becoming increasingly evident, while the effects of plant communities on microbial communities in different geographic environments are poorly understood. Here, the differentiation of licorice plant ecotypes and the distribution of root‐associated microbiotas were investigated across five sampling sites in northwest China. The interactions between the environment, plant and microbial communities, and their effects on licorice root secondary metabolites, were elucidated. The plant community was clearly differentiated into distinct ecotypes based on genotyping‐by‐sequencing and was primarily driven by geographic distance and available soil nitrogen. The bulk soil and root‐associated microbiotas (rhizosphere soil and root endosphere) partially correlated with plant community, but all were significantly discriminated by plant clade. Moreover, these microbiotas were explained to different extents by distinct combinations of environment, geography, and plant community. Similarly, three structural equation models showed that licorice root secondary metabolites were complicatedly modulated by multiple abiotic and biotic factors, and were mostly explained by these factors in the rhizosphere model. Collectively, the results provide novel insights into the role of environment–plant–microbiota interactions in regulating root secondary metabolites. That should be accounted for when selecting appropriate licorice planting sites and management measures. [ABSTRACT FROM AUTHOR]

Summary: Soil biogeochemical processes are not only gauged by the dominant taxa in the microbiome but also depend on the critical functions of its 'rare biosphere' members. Here, we evaluated the biogeographical pattern of 'rare biosphere' propionate‐oxidizing syntrophs in 113 paddy soil samples collected across China. The relative abundance, activity and growth potential of propionate‐oxidizing syntrophs were analysed to provide a panoramic view of syntroph biogeographical distribution at the continental scale. The relative abundances of four syntroph genera, Syntrophobacter, Pelotomaculum, Smithella and Syntrophomonas were significantly greater at the warm low latitudes than at the cool high latitudes. Correspondingly, propionate degradation was faster in the low latitude soils compared with the high latitude soils. The low rate of propionate degradation in the high latitude soils resulted in a greater increase of the total syntroph relative abundance, probably due to their initial low relative abundances and the longer incubation time for propionate consumption. The mean annual temperature (MAT) is the most important factor shaping the biogeographical pattern of propionate‐oxidizing syntrophs, with the next factor being the soil's total sulfur content (TS). We suggest that the effect of MAT is related to the thermodynamic conditions, in which the endergonic constraint of propionate oxidation is leveraged with the increase of MAT. The TS effect is likely due to the ability of some propionate syntrophs to facultatively perform sulfate respiration. [ABSTRACT FROM AUTHOR]

Uncovering the linkages between community assembly and species diversity is a fundamental issue in microbial ecology. In this study, a large‐scale (transect intervals of 1257.6 km) cross‐biome soil survey was conducted, which ranged over agricultural fields, forests, wetlands, grasslands and desert, in the arid regions of northwest China. The aim was to investigate the biogeographic distribution, community assembly and species co‐occurrence of soil fungi. The fungal communities in agricultural soils exhibited a steeper distance–decay slope and wider niche breadths, and were more strongly affected by stochastic assembly processes, than fungi in other natural habitats. A strong relationship was revealed between soil fungal richness and community assembly in arid ecosystems, with the influence of stochastic assembly processes decreasing with increasing fungal richness. Moreover, aridity was the most important environmental factor influencing fungal richness, β‐diversity and species co‐occurrence patterns. Specifically, the predicted increase in arid conditions will probably reduce fungal richness and network complexity. These findings represent a considerable advance in linking fungal richness to mechanisms underlying the biogeographic patterns and assembly processes of fungal communities in arid ecosystems. These results can thus be used to forecast species co‐occurrence and diversities pattern of soil fungi under climate aridity and land‐use change scenarios. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Aim: A predictive understanding of the mechanisms underlying microbial biogeographical patterns is of great interest, particularly with respect to phylogenetic distributions of their ecological adaptations. Here, we test whether phylogenetic information can predict the biogeographical distributions, community assembly and species co‐occurrence of soil archaea. Location: Northern China. Time period: July and August 2017. Major taxa studied: Archaeal communities. Methods: By conducting a large‐scale (transect intervals of 1,257.6 km) study across agricultural field, forest, wetland, grassland and desert biomes, we applied the phylogenetic framework of niche conservatism to investigate archaeal biogeography, community assembly and network topology. We examined the phylogenetic signal based on Blomberg's K to test whether the environmental preference of a given archaeal taxon was related to the phylogeny, corresponding to the degree of phylogenetic conservatism for environmental niches across complex environmental gradients. We evaluated the assembly processes of archaeal communities based on null model and Sloan neutral model analyses. We then explored the major factors that influenced the species coexistence and assembly processes of soil archaeal communities. Results: Soil archaeal taxa exhibited strong climate‐related niche conservatism of ecological preferences. Mean annual precipitation (MAP) had the strongest phylogenetic signal, and this mediated both community assembly processes and species coexistence, with stronger deterministic assembly and less species coexistence in environments with lower precipitation. Phylogenetic diversity was closely linked to the balance of community assembly processes; that is, stochastic assembly processes were dominant in low‐diversity communities, whereas variable selection of deterministic processes promoted high phylogenetic diversity. Main conclusions: We conclude that strong phylogenetic niche conservatism of soil archaea drives their biogeographical distributions. Our findings represent a considerable advance in linking phylogenetic niche conservatism to soil archaeal biogeography, community assembly and species coexistence, and therefore forecasting soil archaeal evolutionary adaptations in response to ongoing environmental changes. [ABSTRACT FROM AUTHOR]

Although studies of biogeography in soil bacterial communities have attracted considerable attention, the generality of these patterns along with assembly processes and underlying drivers is poorly understood in the inner tissues of plants. Plant tissues provide unique ecological habitats for microorganisms, which play an essential role in plant performance. Here, we compared core bacterial communities among five soil–plant associated compartments of common bean across five sampling sites in China. Neutral and null modelling consistently suggested that stochastic processes dominated the core community assembly processes and escalated from the belowground compartments to the inner tissues of aerial plant parts. The multiple distance‐decay relationships also varied and had flattened patterns in the stem endosphere, which were shaped by distinct environmental factors in each compartment. Coexistence patterns also varied in topological features, in addition with the sparsest networks in the stem endosphere resulted from the interaction with the stochastic processes. This study considerably expanded our understanding of various biogeographic patterns, assembly processes, and the underlying mechanisms of core bacterial communities between aerial and belowground compartments of common bean. That will provide a scientific basis for the reasonable regulation of core bacterial consortia to get better plant performance. [ABSTRACT FROM AUTHOR]

Soil communities are intricately linked to ecosystem functioning, and a predictive understanding of how communities assemble in response to environmental change is of great ecological importance. Little is known about the assembly processes governing abundant and rare fungal communities across agro‐ecosystems, particularly with regard to their environmental adaptation. By considering abundant and rare taxa, we tested the environmental thresholds and phylogenetic signals for ecological preferences of fungal communities across complex environmental gradients to reflect their environmental adaptation, and explored the factors influencing their assembly based on the large‐scale soil survey in agricultural fields across eastern China. We found that the abundant taxa exhibited remarkably broader response thresholds and stronger phylogenetic signals for the ecological preferences across environmental gradients compared to the rare taxa. Neutral processes played a key role in shaping the abundant subcommunity compared to the rare subcommunity. Null model analysis revealed that the abundant subcommunity was less clustered phylogenetically and governed primarily by dispersal limitation, while homogeneous selection was the major assembly process in the rare subcommunity. Soil available sulfur was the major factor mediating the balance between stochastic and deterministic processes of both the abundant and rare subcommunities, as indicated by an increase in stochasticity with higher available sulfur concentration. Based on macroecological spatial scale datasets, our study revealed the potential broader environmental adaptation of abundant fungal taxa compared to rare fungal taxa, and identified the factors mediating their distinct community assembly processes in agricultural fields. These results contribute to our understanding of the mechanisms underlying the generation and maintenance of fungal diversity in response to global environmental change. [ABSTRACT FROM AUTHOR]

Summary: The factors determining stochastic and deterministic processes that drive microbial community structure, specifically the balance of abundant and rare bacterial taxa, remain underexplored. Here we examined biogeographic patterns of abundant and rare bacterial taxa and explored environmental factors influencing their community assembly processes in agricultural fields across eastern China. More phylogenetic turnover correlating with spatial distance was observed in abundant than rare sub‐communities. Homogeneous selection was the main assembly process for both the abundant and rare sub‐communities; however, the abundant sub‐community was more tightly clustered phylogenetically and was more sensitive to dispersal limitations than the rare sub‐community. Rare sub‐community of rice fields and abundant sub‐community of maize fields were more governed by stochastic assembly processes, which showed higher operational taxonomic unit richness. We propose a conceptual paradigm wherein soil pH and mean annual temperature mediate the assembly of the abundant and rare sub‐communities respectively. A higher soil pH leads to deterministic assembly of the abundant sub‐community. For the rare sub‐community, the dominance of stochasticity in low‐temperature regions indicates weaker niche‐based exclusion and the arrival of more evolutionary lineages. These findings suggest that the community assembly processes for abundant and rare bacterial taxa are dependent on distinct environmental variables in agro‐ecosystems. [ABSTRACT FROM AUTHOR]

Pennisetum sinese is a good forage grass with high biomass production and crude proteins. However, little is known about the endophytic fungi diversity of P. sinese, which might play an important role in the plant's growth and biomass production. Here, we used high throughput sequencing of the Internal Transcribed Spacer (ITS) sequences based on primers ITS5-1737 and ITS2-2043R to investigate the endophytic fungi diversity of P. sinese roots at the maturity stage, as collected from four provinces (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China). The ITS sequences were processed using QIIME and R software. A total of 374,875 effective tags were obtained, and 708 operational taxonomic units (OTUs) were yielded with 97% identity in the five samples. Ascomycota and Basidiomycota were the two dominant phyla in the five samples, and the genera Khuskia and Heydenia were the most abundant in the FJ and XJ samples, respectively, while the most abundant tags in the other three samples could not be annotated at the genus level. In addition, our study revealed that the FJ sample possessed the highest OTU numbers (242) and the NS sample had the lowest (86). Moreover, only 22 OTUs were present in all samples simultaneously. The beta diversity analysis suggested a division of two endophytic fungi groups: the FJ sample from the south of China and the other four samples from north or northwest China. Correlation analysis between the environmental factors and endophytic fungi at the class level revealed that Sordariomycetes and Pucciniomycetes had extremely significant positive correlations with the total carbon, annual average precipitation, and annual average temperature, while Leotiomycetes showed an extremely significant negative correlation with quick acting potassium. The results revealed significant differences in the root endophytic fungi diversity of P. sinese in different provinces and might be useful for growth promotion and biomass production in the future. [ABSTRACT FROM AUTHOR]

Revealing soil microbial community assembly and associated influencing factors is essential for understanding the diversity and functioning of terrestrial ecosystems. Yet how soil microbial communities respond to environmental factors and plant traits in natural shrub ecosystems has received little attention. Therefore, we explored the diversity and assembly mechanisms of soil bacterial and fungal communities across four ecoregions of natural shrubland in Shaanxi Province, northeastern China. Soil chemical properties, climatic variable, and plant growth traits of dominant shrub species were analyzed to determine their relationships with local soil microbial communities. The results indicated that soil bacteria and fungi in the four ecoregions had divergent diversity patterns. The microbial community composition was significantly affected by soil pH, nutrients, and mean annual precipitation. Bacterial community assembly was mainly driven by variable selection (a deterministic process) in the Loess Plateau and the southern slope of Qinling Mountains, or by stochastic processes in the Mu Us Desert and the northern slope of Qinling Mountains. Fungal community assembly was primarily influenced by variable selection in different ecoregions, except for the Mu Us Desert. A highly connected subnetwork of microorganisms did not exist in the desert, but in the southern mountain slope the microbial network did harbor remarkably critical nodes. Bacterial keystone taxa that belonged to Chloroflexi were most relevant to shrub biomass traits. Our findings have implications for predicting the structure of microbial communities in shrubland soils in response to environmental change and their potential impact on plant growth. This study could improve our understanding of soil bacterial and fungal diversity and community assembly patterns in natural shrublands. • Divergent patterns of bacterial and fungal diversity characterized shrubland ecoregions. • Soil pH, organic carbon, nitrogen, and precipitation affected microbial community composition. • Distinct assembly processes shaped bacterial and fungal communities in the Mu Us Desert. • Bacterial keystone taxa contributed to biomass traits of dominant shrub species. [ABSTRACT FROM AUTHOR]

• A large-scale survey shows the distribution of micronutrients in paddy and maize soils across eastern China. • The available iron, copper and manganese are higher in paddy soils than those in maize soils. • The micronutrient availability in the paddy and maize soils is driven by organic matter content and soil pH. • The available iron is decoupled with environment and total metal in paddy fields. • Soil micronutrients need to be further improved in the northwest region in maize soils. Micronutrient deficiencies, known as 'hidden hunger', harm the growth and development of plants and people alike. However, less attention has been paid to soil micronutrients, the main source of micronutrients for plants and humans, than macronutrients (e.g. N and P availability). Understanding the geographic distribution of soil micronutrients across different agricultural fields is critical to support crop production and quality. Here we investigated the micronutrient composition (total and available copper, iron, manganese and zinc) of parallel 114 maize and rice fields in major crop production regions of eastern China. We found that available iron, copper and manganese were significantly higher in paddy soils than in maize soils, and total zinc was significantly higher in maize soils than in paddy soils. There was geospatial variation in the composition of micronutrients across latitudinal gradients and crop types. Soil organic matter and pH drove geographic variation of available micronutrient concentrations and ratio of total to available micronutrient, which were specific to micronutrient and crop type. Available Fe was decoupled with environment and total metal in paddy fields. Our study sheds light on the distribution patterns and environmental drivers of soil micronutrients in eastern China, and provides theoretical guidance for agricultural practice and fertilization management. [ABSTRACT FROM AUTHOR]

Protists are essential for nutrient cycling and plant performance in diverse ecosystems. However, the biogeographic patterns and driving forces (i.e. abiotic or biotic factors) of protistan communities remain poorly understood in agricultural ecosystems. Here, the biogeographic patterns of soil protists were assessed in adjacent pairs of maize and rice fields across eastern China. By combining our results with previously published datasets, we presented the first evidence that the α - and β -diversity of protists were highly structured by bacterial diversity in maize soils and fungal diversity in rice soils, respectively. Consistently, network analyses showed higher connectedness of protists to bacteria in maize soils, but higher connectedness of protists to fungi in rice soils. In addition, bacteria were more correlated with protistan consumers in maize soils, whereas fungi were more associated with protistan phototrophs. Protists in rice soils with lower diversity displayed broader environmental breadth and stronger phylogenetic conservatism than those in maize soils. Taken together, our results provides novel insights into the importance of biotic factors (trophic interrelationships) in driving the biogeographic patterns of soil protistan community in distinct agricultural ecosystems. • Biotic factors strongly affect the protistan biogeography in agricultural ecosystems. • Higher connectedness of protists to bacteria in maize soils. • Higher connectedness of protists to fungi in rice soils. • Protists displayed broader environmental breadthin rice soilsthan in maize soils. [ABSTRACT FROM AUTHOR]

It is critical to establish response thresholds for fungal communities to global environmental change and assess the relationship between fungal diversity and nutrient cycling in soils. However, these have not yet been evaluated in agro-ecosystems. Here we report the findings of a survey across eastern China on the soil fungi and physicochemical properties in adjacent maize and rice fields. The results revealed a wider range of environmental thresholds for soil fungi in rice than maize fields. We found that the dominant fungal taxa only accounted for 0.6% of all taxa, but constituted >50% of total fungi. Based on their habitat preferences, distinct distribution maps between maize and rice fields were constructed, which indicated niche differentiation of soil fungi between dry and waterlogged soils. Rice fields showed higher fungal richness in low latitude regions, consistent with latitudinal richness patterns found in natural terrestrial ecosystems; however, no such trend was observed in maize fields. Fungal richness was positively correlated with nutrient cycling in rice soils and fungal beta diversity with nutrient cycling in maize soils. These findings provide response thresholds for fungal community change across environmental gradients, advancing our understanding of soil fungal diversity patterns in agricultural ecosystems. Differences between wetland and dryland should be taken into consideration when formulating sustainable management plans and baselines for assessments of future global change and resilience of agricultural fields., Competing Interests: Declaration of competing interest The authors declare no conflicts of interest., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.