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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]

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]

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]

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]

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]

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]

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]

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: The dynamics of microbial diversity in response to biotic and abiotic disturbances provide a sensitive indicator for evaluating the potential stability and degradation of soils in agro‐ecosystems. To determine the effect on soil bacterial communities of disturbances by plant growth (Robinia pseudoacacia) and oil contamination, we sequenced 16S rRNA genes using MiSeq technology. A greenhouse experiment was conducted using 21 agro‐soils from 19 provinces in China. Abiotic and biotic disturbances, including treating the soils with sterile water, crude oil, and/or an invasive plant, altered the bacterial community structure in the soils, increased bacterial richness, and reduced bacterial dispersion. Oil contamination exerted stronger effects on the bacterial α‐ and β‐diversity than plant growth. The different responses of bacterial communities and the core microbiome indicated that the disturbances shifted the prevalent soil microbial groups in agro‐ecosystems. Among different sampling sites, community dissimilarity increased with spatial distance. Edaphic factors (deterministic processes) exerted the primary influence on the assembly of soil microbiomes in agricultural fields, whereas geographic factors (stochastic processes) were less influential. The bacterial communities in agro‐soils from warmer regions were more sensitive to the disturbances. This study provides new insight into the alteration of soil microbiota by plant growth and oil contamination in agro‐ecosystems across a large spatial scale. [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]

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]

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]

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]