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A central aim of community ecology is to understand how local species diversity is shaped. Agricultural activities are reshaping and filtering soil biodiversity and communities; however, ecological processes that structure agricultural communities have often overlooked the role of the regional species pool, mainly owing to the lack of large datasets across several regions. Here, we conducted a soil survey of 941 plots of agricultural and adjacent natural ecosystems (e.g., forest, wetland, grassland, and desert) in 38 regions across diverse climatic and soil gradients to evaluate whether the regional species pool of soil microbes from adjacent natural ecosystems is important in shaping agricultural soil microbial diversity and completeness. Using a framework of multiscales community assembly, we revealed that the regional species pool was an important predictor of agricultural bacterial diversity and explained a unique variation that cannot be predicted by historical legacy, large‐scale environmental factors, and local community assembly processes. Moreover, the species pool effects were associated with microbial dormancy potential, where taxa with higher dormancy potential exhibited stronger species pool effects. Bacterial diversity in regions with higher agricultural intensity was more influenced by species pool effects than that in regions with low intensity, indicating that the maintenance of agricultural biodiversity in high‐intensity regions strongly depends on species present in the surrounding landscape. Models for community completeness indicated the positive effect of regional species pool, further implying the community unsaturation and increased potential in bacterial diversity of agricultural ecosystems. Overall, our study reveals the indubitable role of regional species pool from adjacent natural ecosystems in predicting bacterial diversity, which has useful implication for biodiversity management and conservation in agricultural systems. [ABSTRACT FROM AUTHOR]

Flowering stage of soybean is an important agronomic trait, which is important for soybean yield, quality and adaptability, and is the external expression of integrating external environmental factors and endogenous signals of the plant itself. Cropping system can change soil properties and fertility, which in turn determine plant growth and yield. The microbial community is the key regulator of plant health and production performance. Currently, there is limited understanding of the effects of cropping systems on microbial community composition, ecological processes controlling community assembly in different soil-plant continuum compartments of soybean. Here, we hope to clarify the structure and assembly process of different soybean compartments bacterial community at flowering stage through our work. The results showed that intercropping decreased the species diversity of rhizosphere and phyllosphere, and phylloaphere microbes mainly came from rhizosphere. FAPROTAX function prediction showed that indicator species sensitive to intercropping and crop rotation were involved in nitrogen/phosphorus cycle and degradation process, respectively. In addition, compared to the continuous cropping, intercropping increased the stochastic assembly processes of bacterial communities in plant-associated compartments, while crop rotation increased the complexity and stability of the rhizosphere network and the deterministic assembly process. Our study highlights the importance of intercropping and crop rotation, as well as rhizosphere and phyllosphere compartments for future crop management and sustainable agricultural regulation of crop microbial communities. [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]

Understanding the ecological patterns of rhizosphere microbial communities is critical for propelling sustainable agriculture and managing ecosystem functions by exploiting microorganisms. However, this knowledge is still unclear, especially under host-associated large-scale and regarding the comparison between bacteria and fungi. We examined community assembly processes and community characters including environmental thresholds and co-occurrence patterns across the cultivatable area of Panax notoginseng for bacteria and fungi. Both are vital members of the rhizosphere but differ considerably in their life history and dispersal potentiality. Edaphic factors drove the parallel variations of bacterial and fungal communities. Although bacterial and fungal communities exhibited similar biogeographic patterns, the assembly of fungi was more driven by dispersal limitation than selection compared with bacteria. This finding supported the 'size-dispersal' hypothesis. pH and total nitrogen respectively mediated the relative importance of deterministic and stochastic processes in shaping bacterial and fungal communities. In addition, fungal communities exhibited potentially broader environmental thresholds and more modular co-occurrence patterns than bacteria (bacteria: 0.67; fungi: 0.78). These results emphasized the importance of dispersal limitation in structuring rhizosphere microbiota and shaping community features of ecologically distinct microorganisms. This study provides insights into the improved prediction and management of the key functions of rhizosphere microbiota. [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]

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]

Uncovering the plant‐soil feedback mechanisms underlying the assembly of belowground microbial communities is essential for terrestrial biodiversity conservation. However, little is known about the small‐scale spatial assembly processes of distinct soil microorganisms, especially during natural restoration of ex‐arable ecosystems.We examined the spatial structure of soil microbiomes in arable land and reforested soils to elucidate the underlying assembly processes at a small spatial scale. The analysis was based on a MiSeq sequencing database, detecting the diversity of archaeal, bacterial and fungal communities, simultaneously, from 300 soil samples along vertical and horizontal profiles during 30‐year reforestation.Compared with environmental filtering, dispersal limitation made crucial contributions to microbial community assembly. Archaeal and bacterial communities with a wider niche breadth were governed more by dispersal limitation than were fungal communities.The effect of dispersal limitation on archaeal and bacterial communities increased first and then decreased over time, while the effect on fungi temporally increased.Synthesis and applications. Our results highlight the variation of assembly processes governing distinct soil microbiomes during reforestation, with dispersal limitation playing a prominent role. This finding suggests that the increase in soil microbial diversity during natural restoration is mainly due to the stochastic influx and dispersal of microorganisms. This greater understanding of microbial community assembly can contribute to more targeted and efficient environmental management practices for the restoration of terrestrial ecosystems, for example, by promoting the restoration practices and shortening the restoration period. These practices may thus be incorporated into policies developed for effective biodiversity conservation, especially the restoration and maintenance of subsurface soil microbial diversity and associated functions. [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]

[Display omitted] • Homogeneous selection governs the assembly of rare biosphere in rhizosphere. • Dispersal limitation dominates the assembly of abundant taxa in rhizosphere. • Putative functions related to plant-microbe interaction were enriched in rare taxa. • Abundant taxa located in more central positions in co-occurrence network. Knowledge about the ecological patterns of abundant and rare bacteria in rhizosphere is still lacking. Through a large-scale sampling across the arable area of a medicinal plant Panax notoginseng , we examined the community assembly of abundant and rare rhizobacteria as well as their putative functions and co-occurrence patterns. At local level, the rare taxa exhibited significantly stronger phylogenetic clustering than the abundant taxa. At metacommunity level, both two subcommunities showed significant biogeographic patterns, but they were assembled by different ecological processes. Null model analysis showed that dispersal limitation (84.68%) governed the assembly of abundant subcommunity, whereas homogeneous selection (90.11%) dominated the dynamics of rare subcommunity. Although the putative functions indicated that the rare taxa potentially enriched more functional traits associated with plant-microbe interactions, the overall abundance profiles of putative pathways in two subcommunities exhibited significant collinearity. Additionally, the topological properties of abundant taxa in the co-occurrence network were significantly higher than those of rare taxa. We propose that stochasticity and determinism dominate the assembly of abundant and rare subcommunities, respectively. The abundant taxa may exhibit stronger environmental adaptability, while the rare taxa are more likely the result of rhizosphere effect. These findings also emphasize the importance of integrating phylogeny in ecological researches on plant-associated microbiota. [ABSTRACT FROM AUTHOR]