Search

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]

Agricultural ecosystems are facing increasing environmental changes. Revealing ecological stability of belowground organisms is key to developing management strategies that maintain agricultural ecosystem services in a changing world. Here, we collected soils from adjacent pairs of maize and rice fields along large spatial scale across Eastern and Southeast China to investigate the importance of core microbiota as a predictor of resistance of soil microbiome (e.g. bacteria, fungi and protist) to climate changes and nutrient fertilization, and their effect on multiple ecosystem functions, representing key services for crop growth and health in agro‐ecosystems. Soil microbiome in maize soils exhibited stronger resistance than that in rice soils, by considering multiple aspects of the resistance index, for example, community, phylogenetic conservation and network complexity. Community resistance of soil microbiome showed a geographic pattern, with higher resistance at lower latitudes, suggesting their stronger resistance in warmer regions. Particularly, we highlighted the role of core phylotypes in enhancing the community resistance of soil microbiome, which was essential for the maintenance of multifunctionality in agricultural ecosystems. Our results represent a significant advance in linking core phylotypes to community resistance and ecosystem functions, and therefore forecasting agro‐ecosystems dynamics in response to ongoing environmental changes. These suggest that core phylotypes should be considered a key factor in enhancing agricultural sustainability and crop productivity under global change scenarios. [ABSTRACT FROM AUTHOR]

Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole‐soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0–300 cm) during natural succession in restored ex‐arable ecosystems, via high‐throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs. [ABSTRACT FROM AUTHOR]

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. [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]

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]

Summary: Soil functions and processes are driven by complex microbial interactions. It is, therefore, critical to understand the coexistence patterns of soil microbiota, especially in fragile alpine ecosystems. We identified biogeographic patterns in the network‐level topological features of the soil microbial co‐occurrence network in the Tibetan alpine grasslands, based on high‐throughput sequencing. We verified that soil pH was the most important environmental variable for predicting network‐level topological features of soil microbial co‐occurrence networks. Associations among soil microbiota were enhanced with increasing pH (5.17–8.92), and the network was the most stable at neutral pH. Moreover, node‐level topological features suggested that the archaeal operational taxonomic units, compared with bacterial operational taxonomic units, hold a central role in the co‐occurrence network. Network‐level topological features revealed closer connections among soil microbiota in the steppe ecosystem than in the meadow ecosystem. Therefore, our study demonstrated that soil pH served as a critical environmental filter that influenced the potential associations and ecological signature of soil microbiota in the Tibetan alpine grasslands. These findings provide a new perspective on the distinct biogeographic patterns of co‐occurrence networks, to explore the ecological role of soil microbiota and thus help manage soil bacterial and archaeal communities for provisioning alpine ecosystem services. [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]

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]

Elucidating the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances is essential for understanding the biodiversity-stability relationship and maintaining microbial diversity. Here, we explored the response patterns of abundant and rare bacterial taxa to disturbances by invasive plant growth and oil contamination in agricultural soils across a large spatial scale (latitude gradient = 18.62°–46.51°). Our meta-analysis based on existing Illumina sequencing datasets showed that abundant taxa persisted under the disturbances whereas rare taxa were more easily affected, indicating the higher resilience or resistance of abundant taxa to disturbances. The responses of abundant taxa were associated with mean annual temperature at the sampling sites, while rare taxa instead showed stochastic responses. There were significantly negative linear regressions between bacterial α -diversity and community dissimilarities (disturbed vs. undisturbed soils), suggesting stronger resilience or resistance in those bacterial communities with higher α -diversity. This resilience or resistance was mainly associated with the α -diversity of abundant taxa. Our network analysis showed that the disturbances substantially decreased the strength of the connections, loosened the co-occurrence relationships, and reshaped the complex bacterial interactions. In the undisturbed soils, abundant taxa were located in central positions within the network more often than were rare taxa, while these trends were reversed in the disturbed soils. Our results suggest that abundant taxa play a dominant role in the stability and maintenance of agro-soil bacterial communities, while rare taxa could greatly influence local bacterial interactions under environmental disturbances. Image 1 • Distinct responses of rare and abundant taxa to disturbances were observed. • Abundant taxa were more resilient or resistant to disturbances than rare taxa. • Abundant taxa dominate the stability of soil bacterial communities. • Rare taxa turn to heighten influence on bacterial interactions under disturbances. [ABSTRACT FROM AUTHOR]

Determining the mechanisms underlying complex plant-microbe interactions and feedbacks is crucial for effective rhizoremediation of contaminated soils. Here, rhizosphere bacterial communities of 10 common legumes planted in arable and aged oil-contaminated soils for 90 days were used to degrade phenanthrene (PHE). Bacterial community structures were analyzed to reveal the mechanisms underlying the varying PHE degradation capacities. We found that bacterial β -diversity within the rhizospheres played a major role in predicting PHE degradation rates, and more complex bacterial communities exhibited higher PHE degradation capacities. The highest PHE degradation rates were obtained with bacterial communities of Coronilla varia and Vigna unguiculata planted in oil-contaminated soils (almost 80%). There were significant differences in bacterial community composition between arable and contaminated soils, and among different legumes rhizospheres and the unplanted soils, although minimal differences were observed in bacterial α -diversity. The potential degradation-related taxa were more abundant in bacterial communities from contaminated soils, indicating more effective PHE degradation than in arable soils. Network analysis revealed the vital ecological roles of the potential degradation-related taxa in the maintenance of complex associations among bacterial taxa. Oil contamination reduced the differences in bacterial community composition between rhizosphere soils with high and low PHE degradation rates. These results suggest that the formulation of effective rhizoremediation strategies ought to focus on more diverse and complex interactions between rhizosphere-inhabiting organisms from aged oil-contaminated soils through the selection of optimal plant-microbiota association. • We tested phenanthrene degradation by bacterial consortia from legume rhizospheres. • More complex bacterial consortia exhibited higher degradation capacities. • Degradation-enriched taxa were more abundant in consortia from contaminated soils. • Oil contamination led to a reduction in the specificity of plant-microbe interactions. [ABSTRACT FROM AUTHOR]

Abstract Large variation of CH 4 emissions from paddy and wetland ecosystems exists across different geographical locations in China. To obtain mechanistic understanding of this variation, we investigated the dynamics of methanogenesis over the course of glucose degradation in fourteen paddy field soils and five wetland soils collected from different regions of China. The results revealed that the maximal rate (2–3 mM per day) and the total amount (25–30 mM) of CH 4 produced were similar across soil samples. The lag phase of methanogenesis, however, differed substantially with the shortest lag phase of 4 days in a paddy soil from north China and the longest of 32 days in a soil from south China, and this difference reflected a general geographical trend among all soils tested. Nitrate was reduced completely within 4 days in all soils. The reduction of Fe(III) and sulfate was completed after 21 days and 29 days, respectively. The depletion time of Fe(III) and sulfate were positively correlated with the lag phase of methanogenesis. Competition for common substrates between methanogens and iron and sulfate reducers, however, does not explain this coincidence because a slow production of CH 4 was detected at the very beginning. It appears that the geographical variations in methanogenesis and the reduction of ferric iron and sulfate are related to the variation in soil pH but not to temperature, soil organic C and nutrient conditions in paddy and wetland soils across eastern China. Graphical abstract Unlabelled Image Highlights • Lag phase for soil methanogenesis increases from north to south in China. • Depletion time of Fe(III) and sulfate positively correlated with methanogenesis lag phase. • Geographical variations in methanogenesis are related to the soil pH variation. • Greater temperature response for soil methanogenesis from south to north in China [ABSTRACT FROM AUTHOR]

Natural wetlands and anthropogenic paddy fields are the dominant biogenic sources of atmospheric methane emission which have been speculated as the most probable sources for the increase of post-2006 atmospheric methane. Regional differences in CH 4 emission is possibly due to microbial biogeographic distribution. Here we collected soils from 19 wetlands from different regions in China. The methane production capacity (MPC) was measured for each soil samples and varied from 1.11 to 841.94 mg/kg dry soil. High throughput sequencing was employed to investigate the diversity and composition of bacterial, archaeal and methanogenic communities. Similar biogeographic patterns for bacterial, archaeal and methanogenic communities along the latitudinal gradient were observed, and the biogeographic assemblies of different microbial groups were driven by concurrent factors, including edaphic variables (total organic carbon, total phosphorus and pH) and climatic variables (annual frost days, mean annual temperature, direct solar radiation and mean annual precipitation). MPC was significantly correlated with TOC concentration, and in addition, various functional taxa were positively correlated with MPC ( P < 0.05), for example, Sphingomonas , Syntrophomonas , Methanospirillum and Methanoregula , indicating their potential contributions in the methanogenic process, and many of them were fermentative bacteria and methanogens. Network analysis showed that some syntrophs, sulfate-reducers and methanogens were tightly co-occurred in one module, suggesting their involvements in cross-linked functional processes. Our study implicated both temperature and substrate availability altered the biogeographic patterns of microbial community as well as methane production potential in Chinese wetlands. [ABSTRACT FROM AUTHOR]

Revealing the biogeographies and ecologies of rare and abundant microorganisms is crucial to understand ecosystem diversity and function. In this study, we investigated the biogeographic assemblies and ecological diversity patterns of rare and abundant bacteria in long-term oil-contaminated soils at intervals of 46-360 km by performing high-throughput sequencing of 16S r RNA genes. The results clearly revealed distinct distribution patterns for rare and abundant bacteria in soil samples. Rare taxa were unevenly distributed; however, abundant taxa were ubiquitous across all samples. Both rare and abundant subcommunities showed significant distance-decay relationships, and their assemblies were driven by different factors. The rare subcommunity primarily exhibited a spatially structured distribution (i.e., stochastic processes), while edaphic factors (i.e., deterministic processes) largely contributed to the structure of the abundant subcommunity. A network analysis revealed closer relationships between abundant bacteria and their heightened influence on other co-occurrences in the community compared with rare species. In conclusion, rare microbial taxa may play potential roles in maintaining ecosystem diversity, although they do not appear to be central to microbial networks. Abundant microbes are vital for microbial co-occurrences in oil-contaminated soils, and high relative abundance and ubiquitous distribution suggest potential roles in the degradation of organic pollutants. [ABSTRACT FROM AUTHOR]

• Impact of neighboring plants on focal plant rhizobiome assemblages was studied. • Richness of neighboring plants and focal plant rhizobiome were decoupled. • Composition of above- not belowground plants and rhizobiome were coupled. • Neighboring plant identities were best predictors of rhizobiome assemblages. • These impacts were direct, or indirect by modulating bulk soil communities. The rhizosphere microbiome (i.e., rhizobiome) plays critical roles in modulating plant performance and fitness. Although plants in natural environments are inevitably affected by neighboring plants, less is known about how attributes of neighboring plant communities affect the rhizobiome of a focal plant. We evaluated the impacts of neighboring plant community attributes (e.g., above- and belowground plant species richness, identity, biomass and composition) on the richness and community composition of rhizosphere archaea, bacteria and fungi associated with Kobresia setchwanensis in an alpine meadow on the eastern Qinghai-Tibetan Plateau. We found that the richness of neighboring plant species both above- and belowground was poorly related to the rhizobiome richness of the focal plant. In contrast, the dissimilarity in aboveground rather than belowground plant community composition was positively correlated with the dissimilarity in the rhizobiome community composition. Aboveground plant community attributes posed stronger effects than belowground attributes on rhizobiome richness and community composition. The identities of neighboring plant species were the most important predictors of rhizobiome richness and community composition. Structural equation modeling further indicated that the effects of neighboring plant community attributes on the rhizobiome composition could be direct or indirect, by impacting bulk soil microbial communities. Our study provides empirical evidence that neighboring plant community attributes are important determinants of the rhizobiome communities of the focal plant in natural environments. [ABSTRACT FROM AUTHOR]

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S r RNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities. [ABSTRACT FROM AUTHOR]

Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s). [ABSTRACT FROM AUTHOR]

To improve the knowledge about the biogeographic patterns of bacteria in soils contaminated with crude oil, we studied the effects of local geochemical properties and geographic distance on bacterial community structure in oil contaminated soil in five oil refineries (46–360 km apart). The microbial structure was significantly affected by soil environmental factors such as pH, total petroleum hydrocarbons (TPH), total nitrogen, and cadmium level. Microbial alpha-diversity was positively correlated with pH but negatively correlated with TPH. Among sampling sites, the community dissimilarities increased with spatial distance. Variation of bacterial community was mostly attributed to simultaneous effects of spatial distance and environmental factors, and purely spatial distance contributed more to the variation. Microbial generalist OTUs were broadly distributed and dominant in contaminated soils. Their populations were in low proportion (15.75%), but they had high relative abundance (65.05%), and some were associated with TPH-degradation. Network analysis indicated that microbial communities had non-random co-occurrence patterns. Keystone taxa were Rubrivivax , Nitrospira , Methylotenera , Methyloversatilis and Acidaminobacter . Microbial taxa from the same module had strong ecological linkages and were involved in biological electron-transfer, C and N-cycles, and organic contaminant degradation. Our results indicate that the same microbial groups with TPH-degradation ability can be assembled from indigenous microorganisms in separate regions through long term exposure to contamination. [ABSTRACT FROM AUTHOR]

In observational studies, unbalanced observed covariates between treatment groups often cause biased inferences on the estimation of treatment effects. Recently, generalized propensity score (GPS) has been proposed to overcome this problem; however, a practical technique to apply the GPS is lacking. This study demonstrates how clustering algorithms can be used to group similar subjects based on transformed GPS. We compare four popular clustering algorithms:k-means clustering (KMC), model-based clustering, fuzzyc-means clustering and partitioning around medoids based on the following three criteria: average dissimilarity between subjects within clusters, average Dunn index and average silhouette width under four various covariate scenarios. Simulation studies show that the KMC algorithm has overall better performance compared with the other three clustering algorithms. Therefore, we recommend using the KMC algorithm to group similar subjects based on the transformed GPS. [ABSTRACT FROM PUBLISHER]

Environmental impacts of carbon nanomaterials (CNMs) have been attracting increasing concerns in recent years. Knowledge on how short-term exposure to CNMs influences soil microbial communities is available. However, little is known about the possible difference in effects of long-term versus short-term exposure of CNMs on soil microbial communities. In this study, we systematically compared effects of fullerene (C 60), single-walled carbon nanotubes (SW), and graphene (GR) on soil bacterial communities over short (30 d) and long (360 d) term exposure durations. Our findings revealed that short-term exposure to all CNMs significantly increased the alpha diversity of soil bacterial communities. SW and GR exposure for 360 d relative to that for 30 d more significantly decreased their alpha diversity. Compared to short-term exposure, a long term exposure to CNMs more strongly altered the beta diversity of soil bacterial communities. LEfSe analysis showed that, GR relative to C 60 and SW exposure more strongly altered soil bacterial community composition especially for long-term duration at various taxonomic levels; more taxa were also identified by LEfSe analysis as biomarkers upon long-term GR exposure. More OTUs were affected by long-term GR exposure. These differences resulted from both distinct physicochemical properties of various CNMs and their exposure durations. [Display omitted] • Long-term CNMs exposure more strongly altered the soil bacterial beta diversity. • Long-term exposure to CNMs more strongly impacted bacterial community composition. • Stronger impact of CNMs on community composition occurred at all taxonomic levels. • More taxa were identified by LEfSe analysis as biomarkers upon GR exposure for 360 d. • Abundance of soil bacterial OTUs changed as exposure duration of CNMs was prolonged. [ABSTRACT FROM AUTHOR]

Aim Location Time period Major taxa studied Methods Results Main conclusions Revealing the role of regional species pool size in community assembly rules is essential for extending the species‐pool framework to large‐scale community ecology, and thus for more comprehensive understanding of biodiversity formation. However, little has been done to couple the regional species‐pool effect into local ecological processes in soil fungal communities, which play essential roles in ecosystems worldwide. Here, we performed large‐scale soil surveys of fungal communities to examine the linkage between regional species pool size and Dispersal–Selection Relationships (DSRs), and their relations to community structure.China.July–August 2019.Fungal communities.By conducting the nationwide soil survey of ~1200 samples from various ecosystems across China, including agricultural, forest, grassland, and wetland soils, we examined the linkage between regional species pool size and DSRs, and their relationship to fungal community structure.We found that selection was negatively related to dispersal, which was consistent with the general view that the strength of selection is weakened by dispersal homogenization, and that this relationship was stronger in regions with larger species pools. Moreover, an increase in community dispersion was correlated with stronger effect size of DSRs, implying greater heterogeneity among fungal communities under larger species pools.Our study clearly illustrates the association of regional species pool size with local assembly rules and community formation of soil fungi across terrestrial ecosystems. [ABSTRACT FROM AUTHOR]

Deserts are predicted to be one of the ecosystems most vulnerable to global climate change, with dramatic fluctuations of temperature and water, even over the span of a single day. These previous disturbances could influence the response of the soil microbiome and its functions to subsequent disturbances, which is known as legacy effect. However, how legacy effects shape the response of soil microbiome and its functions to environmental fluctuations (e.g. temperature and water availability) in desert ecosystems remains to be investigated.Here, we firstly exposed desert soils to drought, freezing or their combination, and then followed by a second disturbance, resulting in a temporally full factorial treatment.We found that environmental change legacies affected the response of soil multifunctionality, microbial abundance and richness to second drought and freezing, except for eukaryotic richness. Initial disturbances caused legacy effects on microbial composition and weakened their responses to later disturbances, and these effects were stronger for prokaryotes than eukaryotes. The attenuated response to later disturbances is largely due to that almost half of the taxa affected by the earlier disturbances were also affected by the second disturbances. The phylogenetic depth of these responses varied minimally among the types of disturbances but were more conserved for negative responses, indicating a result of historical adaptation. Moreover, the altered community composition was associated with functional changes in the disturbed soils.These findings will improve our understanding of the mechanisms underlying the legacy impacts of multiple environmental disturbances on desert microbial communities and strengthen our ability to develop management strategies for protection prior to disturbance events. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Across ecology, and particularly within microbial ecology, there is limited understanding how the generation and maintenance of diversity. Although recent work has shown that both local assembly processes and species pools are important in structuring microbial communities, the relative contributions of these mechanisms remain an important question. Moreover, the roles of local assembly processes and species pools are drastically different when explicitly considering the potential for saturation or unsaturation, yet this issue is rarely addressed. Thus, we established a conceptual model that incorporated saturation theory into the microbiological domain to advance the understanding of mechanisms controlling soil bacterial diversity during forest secondary succession. Conceptual model hypotheses were tested by coupling soil bacterial diversity, local assembly processes and species pools using six different forest successional chronosequences distributed across multiple climate zones. Consistent with the unsaturated case proposed in our conceptual framework, we found that species pool consistently affected α‐diversity, even while local assembly processes on local richness operate. In contrast, the effects of species pool on β‐diversity disappeared once local assembly processes were taken into account, and changes in environmental conditions during secondary succession led to shifts in β‐diversity through mediation of the strength of heterogeneous selection. Overall, this study represents one of the first to demonstrate that most local bacterial communities might be unsaturated, where the effect of species pool on α‐diversity is robust to the consideration of multiple environmental influences, but β‐diversity is constrained by environmental selection. [ABSTRACT FROM AUTHOR]

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. [ABSTRACT FROM AUTHOR]

Agrilus mali (Coleoptera: Buprestidae) is an invasive wood borer pest that has caused considerable damage to the Xinjiang wild fruit forest. In this study, we investigated the bacterial and fungal intestinal microbial communities of A. mali during different developmental stages, including larvae, pupae and newly eclosed adults or fed different diets (leaves of Malus halliana and Malus pumila) using Illumina MiSeq high-throughput sequencing technology. The results showed that microbial alpha diversity first increased and then decreased during the developmental stages, with the most dominant bacteria and fungi exhibiting the dynamic patterns “Decrease”, “Increase” and “Fluctuation”. With respect to the different diets, the bacterial communities were similar between the newly eclosed adults and adults fed M. pumila leaves, while the structure of the fungal communities showed great differences between newly eclosed adults and adults fed different diets. Through a co-correlation network analysis, we observed complex microbial interactions among bacterial and fungal taxa that were associated with potential diverse functions and intricate biological processes in the intestinal microbiota of A. mali. Overall, the results of this study demonstrated that the invasive insect A. mali harbours diverse, dynamic, and presumably multifunctional microbial communities, an understanding of which could improve our ability to develop more effective management approaches to control A. mali. [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]

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]

Rhizosphere microbes play key roles in plant growth and productivity in agricultural systems. One of the critical issues is revealing the interaction of agricultural management (M) and rhizosphere selection effects (R) on soil microbial communities, root exudates and plant productivity. Through a field management experiment, we found that bacteria were more sensitive to the M × R interaction effect than fungi, and the positive effect of rhizosphere bacterial diversity on plant biomass existed in the bacterial three two‐tillage system. In addition, inoculation experiments demonstrated that the nitrogen cycle‐related isolate Stenotrophomonas could promote plant growth and alter the activities of extracellular enzymes N‐acetyl‐ d‐glucosaminidase and leucine aminopeptidase in rhizosphere soil. Microbe‐metabolites network analysis revealed that hubnodes Burkholderia‐Caballeronia‐Paraburkholderia and Pseudomonas were recruited by specific root metabolites under the M × R interaction effect, and the inoculation of 10 rhizosphere‐matched isolates further proved that these microbes could promote the growth of soybean seedlings. Kyoto Encyclopaedia of Genes and Genomes pathway analysis indicated that the growth‐promoting mechanisms of these beneficial genera were closely related to metabolic pathways such as amino acid metabolism, melatonin biosynthesis, aerobactin biosynthesis and so on. This study provides field observation and experimental evidence to reveal the close relationship between beneficial rhizosphere microbes and plant productivity under the M × R interaction effect. Summary statement: This study reveals that bacterial communities in agriculture systems are more sensitive to the interactive effects of agricultural management (M) and rhizosphere selection (R) than fungal communities, and that rhizosphere bacterial diversity drives plant biomass enhancement. Root exudates recruit beneficial genera of bacteria to colonize the root surface and promote plant growth, and the growth‐promoting mechanisms are related to pathways such as amino acid metabolism, melatonin biosynthesis and aerobactin biosynthesis. [ABSTRACT FROM AUTHOR]

This article discusses a study conducted in the Ziwuling region, which has experienced 160 years of secondary succession. The research focuses on the role of labile organic carbon (OC) fractions in shaping microbial community assembly during this succession. The study finds that deterministic processes, particularly homogeneous selection, are crucial in microbial community assembly. The research also identifies key microbial taxa that drive community assembly and shows that their abundance decreases over time. The findings emphasize the significance of labile OC fractions and microbial community dynamics in ecosystem function. Additionally, the study reveals that labile SOC is the primary driver of microbial community assembly, with labile organic carbon fractions having a greater impact than stable organic carbon. The researchers also observe that soil bacteria influence fungal community assembly and that bacterial alpha diversity plays a role in driving fungal assembly. Overall, the study underscores the importance of labile organic carbon in determining microbial community assembly during long-term vegetation succession. [Extracted from the article]

Nodulation outer proteins secreted via type 3 secretion systems are involved in the process of symbiosis between legume plants and rhizobia. To study the function of NopT in symbiosis, we mutated nopT in Mesorhizobium amphore CCNWGS0123 (GS0123), which can nodulate black locust (Robinia pseudoacacia). The nopT mutant induced higher levels of jasmonic acid, salicylic acid, and hydrogen peroxide accumulation in the roots of R. pseudoacacia compared with wild-type GS0123. The Δ nopT mutant induced higher disease-resistant gene expression 72 hours post-inoculation (hpi), whereas GS0123 induced higher disease-resistant gene expression earlier, at 36 hpi. Compared with the nopT mutant, GS0123 induced the up-regulation of most genes at 36 hpi and the down-regulation of most genes at 72 hpi. Proteolytically active NopT_GS0123 induced hypersensitive responses when expressed transiently in tobacco leaves (Nicotiana benthamiana). Two NopT_GS0123 targets in R. pseudoacacia were identified, ATP-citrate synthase alpha chain protein 2 and hypersensitive-induced response protein. Their interactions with NopT_GS0123 triggered resistance by the plant immune system. In conclusion, NopT_GS0123 inhibited the host plant immune system and had minimal effect on nodulation in R. pseudoacacia. Our results reveal the underlying molecular mechanism of NopT function in plant–symbiont interactions. [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]

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]

Purpose: The root-associated microbiota is essential to plant health, fitness and productivity, but the effect of plant domestication on the ecological process of microbial community assembly is unclear. Methods: High-throughput sequencing of the 16S rRNA genes was employed to investigated the the diversity, ecological assembly process and cooccurrence relationship of the bacterial communities of multiple root compartment niches (root zone, rhizosphere, and root endosphere) between wild and landrace accessions grown in three soil types. Results: Our results showed that the domestication effect on bacterial community increased from the root zone to the rhizosphere and endosphere, while the soil type effect decreased. Compared with wild soybean, the root endosphere bacterial community of the landraces was more sensitive to soil environmental change. The deterministic process dominated the assembly of the bacterial community in the rhizosphere and root endosphere, and its relative contribution was higher in the landraces than in wild soybeans. In the two root compartments, the increased root system selection pressure in the landraces was indicated by a greater loss of bacteria at the same taxon level and lower bacterial diversity. Furthermore, the family Oxalobacteraceae and the class Actinobacteria were identified as important root-associated biomarker taxa for wild soybeans, while Enterobacteriaceae was such for the landraces. Conclusions: Our findings provide crucial empirical evidence for the host selection and enrichment process of the microbial community under local domestication and are of great significance in understanding the coevolution of hosts and microbiota, which will aid in manipulating microbiota for future crop breeding. [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]

Background: Leguminous crops could fix atmospheric nitrogen through their symbiotic and non-symbiotic associations with different microbes to survive and maintain nutrient in soils that are deficient in nitrogen. Only limited number of lateral roots of the legume prefers to formulate nodules. So far, it is unclear whether microbial communities in lateral roots with/without nodules are different, and whether the selection of microbiome among different types of lateral roots of a plant is a random process or is strictly controlled by the host plant. Methods: We investigated the diversity and community structure of prokaryotic and eukaryotic microorganisms inhabiting in lateral roots with and without nodules of soybean via high-throughput 16S rDNA and 18S rDNA amplicon sequencing. In addition, quantitative microbial element cycling method was applied to estimate the functional genes that are related to carbon, nitrogen, phosphorus, sulfur cycling and methane metabolism. Results: Microbiome in rhizosphere of lateral roots with nodules had significantly lower α-diversity and higher co-occurrence network complexity, compared to those of lateral roots without nodules. The neutral model analysis demonstrated that microbial community of lateral roots with nodules in rhizosphere soil were less affected by neutral process than that of lateral roots without nodules. In addition, we identified a keystone ecological cluster (Module #1) of the rhizosphere cross-kingdom network that positively correlated with multiple functional gene copies, suggesting that the microbial taxa in Module #1 could play important roles in nutrient cycling of rhizosphere microenvironment. Conclusions: Overall, our study revealed the differences in microbial communities in the lateral roots with/without the nodule of root systems and identified a keystone ecological cluster positively linking with multiple functional cycling. [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]

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]

The generalized doubly robust estimator is proposed for estimating the average treatment effect (ATE) of multiple treatments based on the generalized propensity score (GPS). In medical researches where observational studies are conducted, estimations of ATEs are usually biased since the covariate distributions could be unbalanced among treatments. To overcome this problem, Imbens [The role of the propensity score in estimating dose-response functions, Biometrika 87 (2000), pp. 706–710] and Fenget al.[Generalized propensity score for estimating the average treatment effect of multiple treatments,Stat. Med. (2011), in press. Available at:http://onlinelibrary.wiley.com/doi/10.1002/sim.4168/abstract] proposed weighted estimators that are extensions of a ratio estimator based on GPS to estimate ATEs with multiple treatments. However, the ratio estimator always produces a larger empirical sample variance than the doubly robust estimator, which estimates an ATE between two treatments based on the estimated propensity score (PS). We conduct a simulation study to compare the performance of our proposed estimator with Imbens’ and Fenget al.’s estimators, and simulation results show that our proposed estimator outperforms their estimators in terms of bias, empirical sample variance and mean-squared error of the estimated ATEs. [ABSTRACT FROM PUBLISHER]

In recognition of the impacts of climate change and air pollution, a special issue was prepared to address the response and adaptation of agricultural ecosystems to global changes. A total of thirteen papers were published, delving into the mechanisms underlying the effects on crops and agroecosystems and adding important insights into the modeling and adaptation of agroecosystems to global change through optimized management practices. This collection of papers has a broad relevance to numerous areas in agriculture, ecology, and environmental and earth sciences. • A special issue dedicated to 'agricultural ecosystems response and adaptation to global changes'. • A total of thirteen papers were published. • Studies concerned ozone, precipitation, warming, management, and modelling. • This Editorial discusses the content of the publications included in the special issue. [ABSTRACT FROM AUTHOR]

Grasslands have an important global role in biological methane (CH 4) oxidation and therefore it is crucial to understand the key factors determining the assembly of high-affinity methanotroph populations and explore mechanisms that regulate CH 4 oxidation activity in these ecosystems. This study explored the linkage between high-affinity methanotroph community assembly processes and CH 4 oxidation potential across three grassland types in Inner Mongolia with or without livestock grazing. We found the largest proportion of deterministic selection in temperate desert grasslands, but it was increasingly structured by stochastic dispersal in temperate meadow and temperate typical grasslands. The distance decay relationship (DDR) and variation partitioning analysis (VPA) showed the strongest relationship and highest proportion of environmental factors in desert grasslands, followed by meadow and typical grasslands. Mean annual precipitation (MAP), environmental factors (moisture content, soil organic matter), and microbial traits (abundance, diversity and normalized stochasticity ratio) were significantly related with CH 4 oxidation activity. Multiple statistical analyses consistently indicated the key role of MAP in shaping high-affinity methanotroph community diversity, composition, co-occurrence networks, assembly processes and CH 4 oxidation activity. We found an association of increasing stochastic assembly and high-affinity methanotroph diversity with decreasing CH 4 oxidation potential. This study revealed the mechanisms governing high-affinity methanotroph community assembly processes and integrates high-affinity methanotroph community assembly with CH 4 oxidation activity in grassland soils. [Display omitted] ● The proportion of determinism was highest in desert than other grasslands. ● MAP was key factor regulating methanotrophs community and their activity. ● Stochastic assembly processes are dominant in high-diversity communities. ● CH 4 oxidation potential decreased with the increase of stochastic assembly. [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]

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]

An increasing number of anthropogenic pressures can have negative effects on biodiversity and ecosystem functioning. However, our understanding of how soil microbial communities and functions in response to multiple global change factors (GCFs) is still incomplete, particularly in less frequently disturbed subsoils. In this study, we examined the impact of different levels of GCFs (0–9) on soil functions and bacterial communities in both topsoils (0–20 cm) and subsoils (20–40 cm) of an agricultural ecosystem, and characterized the intrinsic factors influencing community resistance based on microbial life history strategy. Our experimental results showed a decline in soil multifunctionality, bacterial diversity, and community resistance as the number of GCFs increased, with a more drastic reduction in community resistance of subsoils. Specifically, we observed a significantly positive relationship between the oligotroph/copiotroph ratio and community resistance in subsoils, which was also verified by the negative correlation between 16S rRNA operon (rrn) copy number and community resistance. Structural equation modeling further revealed the direct effects of community resistance in promoting the ecosystem functioning, regardless of top- and subsoils. Therefore, these results suggested that subsoils may recruit more oligotrophic microbes to enhance their originally weaker community resistance under multiple GCFs, which was essential for maintaining sustainable agroecological functions and services. Overall, our study represents a significant advance in linking microbial life history strategy to the resistance of belowground microbial community and functionality. [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. Unlabelled Image • We report a systematic large-scale survey of soil fungi and environmental data. • Soil fungi show wider range of environmental thresholds in rice than maize fields. • Soil fungi show distinct continental atlases between maize and rice fields. • Fungal diversities are respectively associated with multi-nutrients cycling. [ABSTRACT FROM AUTHOR]

Aims: Licorice (Glycyrrhiza uralensis Fisch.) is a crucial medicinal herb as it accumulates glycyrrhizin and liquiritin in roots. Licorice root-associated bacterial communities shaped by soil characteristics are supposed to regulate the accumulation of root secondary metabolites. Methods: The soil characteristics, root secondary metabolites, and root-associated bacterial communities were analyzed in licorice plants of different ages to explore their temporal dynamics and interaction mechanisms. Results: Temporal variation in soil characteristics and root secondary metabolites was distinct. The alpha-diversity of root-associated bacterial communities decreased with root proximity, and the community composition was clustered in the rhizosphere. Different taxa that were core-enriched from the dominant taxa in the bulk soil, rhizosphere soil, and root endosphere displayed varied time–decay relationships. Soil total potassium (TK) as a key factor regulated the temporal variation in some individual taxa in the bulk and rhizosphere soils; these taxa were associated with the adjustment of root secondary metabolites across different TK levels. Conclusions: Licorice specifically selects root-associated core bacteria over the course of plant development, and TK is correlated with root secondary metabolites and individual core-enriched taxa in the bulk and rhizosphere soils, which may have implications for practical licorice cultivation. [ABSTRACT FROM AUTHOR]

Sourdough is widely used for the preparation of traditional sourdough breads in Europe and as an important inoculum for steamed buns prepared in Asian countries, especially China. This study aims to characterize Chinese traditional sourdoughs in terms of their taxonomic compositions, physicochemical characteristics, bacterial diversity and functional features. Thirty geographically diverse sourdoughs were collected from three regions across China. High-throughput sequencing and bioinformatics were used to characterize the bacterial diversity of the sourdoughs from the different sampling sites. The results showed that the West group was significantly different from the North and South groups in the dominant genera (mainly Lactobacillus , Pediococcus and Leuconostoc ) and metabolic pathways (metabolism of terpenoids and polyketides, MTP, and xenobiotics biodegradation and metabolism, XBM), whereas samples from the North and South groups were not significantly different from each other. This is the first report of the genus Clostridium in sourdough and the first report of metabolic pathways related to MTP and XBM in sourdough. This research provides a thorough description and analysis of the relationship between bacterial diversity and geographic region in sourdough. [ABSTRACT FROM AUTHOR]