The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while ∼2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (∼9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

Despite the importance of microbial communities for ecosystem services and human welfare, the relationship between microbial diversity and multiple ecosystem functions and services (that is, multifunctionality) at the global scale has yet to be evaluated. Here we use two independent, large-scale databases with contrasting geographic coverage (from 78 global drylands and from 179 locations across Scotland, respectively), and report that soil microbial diversity positively relates to multifunctionality in terrestrial ecosystems. The direct positive effects of microbial diversity were maintained even when accounting simultaneously for multiple multifunctionality drivers (climate, soil abiotic factors and spatial predictors). Our findings provide empirical evidence that any loss in microbial diversity will likely reduce multifunctionality, negatively impacting the provision of services such as climate regulation, soil fertility and food and fibre production by terrestrial ecosystems.

The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa. Our study narrows down the immense number of bacterial taxa to a "most wanted" list that will be fruitful targets for genomic and cultivation-based efforts aimed at improving our understanding of soil microbes and their contributions to ecosystem functioning.Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Recently, microbiologists have established the existence of biogeographic patterns among a wide range of microorganisms. The focus of the field is now shifting to identifying the mechanisms that shape these patterns. Here, we propose that four processes - selection, drift, dispersal and mutation - create and maintain microbial biogeographic patterns on inseparable ecological and evolutionary scales. We consider how the interplay of these processes affects one biogeographic pattern, the distance-decay relationship, and review evidence from the published literature for the processes driving this pattern in microorganisms. Given the limitations of inferring processes from biogeographic patterns, we suggest that studies should focus on directly testing the underlying processes.

Relationships between biodiversity and multiple ecosystem functions (that is, ecosystem multifunctionality) are context-dependent. Both plant and soil microbial diversity have been reported to regulate ecosystem multifunctionality, but how their relative importance varies along environmental gradients remains poorly understood. Here, we relate plant and microbial diversity to soil multifunctionality across 130 dryland sites along a 4,000 km aridity gradient in northern China. Our results show a strong positive association between plant species richness and soil multifunctionality in less arid regions, whereas microbial diversity, in particular of fungi, is positively associated with multifunctionality in more arid regions. This shift in the relationships between plant or microbial diversity and soil multifunctionality occur at an aridity level of ∼0.8, the boundary between semiarid and arid climates, which is predicted to advance geographically ∼28% by the end of the current century. Our study highlights that biodiversity loss of plants and soil microorganisms may have especially strong consequences under low and high aridity conditions, respectively, which calls for climate-specific biodiversity conservation strategies to mitigate the effects of aridification.© 2021. The Author(s).

The soil microbiome governs biogeochemical cycling of macronutrients, micronutrients and other elements vital for the growth of plants and animal life. Understanding and predicting the impact of climate change on soil microbiomes and the ecosystem services they provide present a grand challenge and major opportunity as we direct our research efforts towards one of the most pressing problems facing our planet. In this Review, we explore the current state of knowledge about the impacts of climate change on soil microorganisms in different climate-sensitive soil ecosystems, as well as potential ways that soil microorganisms can be harnessed to help mitigate the negative consequences of climate change.

Our planet teems with microorganisms that often present a skewed abundance distribution in a local community, with relatively few dominant species coexisting alongside a high number of rare species. Recent studies have demonstrated that these rare taxa serve as limitless reservoirs of genetic diversity, and perform disproportionate types of functions despite their low abundances. However, relatively little is known about the mechanisms controlling rarity and the processes promoting the development of the rare biosphere. Here, we propose the use of multivariate cut-offs to estimate rare species and phylogenetic null models applied to predefined rare taxa to disentangle the relative influences of ecoevolutionary processes mediating the assembly of the rare biosphere. Importantly, the identification of the factors controlling rare species assemblages is critical for understanding the types of rarity, how the rare biosphere is established, and how rare microorganisms fluctuate over spatiotemporal scales, thus enabling prospective predictions of ecosystem responses.Copyright © 2018 Elsevier Ltd. All rights reserved.

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 rRNA 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.© 2017 John Wiley & Sons Ltd.

Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the stability and functions of the rare microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate climate change and sampled the soils annually after harvesting the maize over the following 6 years (from 2005 to 2011). By sequencing microbial 16S ribosomal RNA gene amplicons, we found that changing climate regimes significantly altered the composition and dynamics of soil microbial communities. A continuous succession of the rare and abundant communities was observed. Rare microbial communities were more stable under changing climatic regimes, with lower variations in temporal dynamics, and higher stability and constancy of diversity. More nitrogen cycling genes were detected in the rare members than in the abundant members, including amoA, napA, nifH, nirK, nirS, norB and nrfA. Random forest analysis and receiver operating characteristics analysis showed that rare taxa may act as potential contributors to maize yield under changing climatics. The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances. With ongoing global climate change, exploring the succession process and functional changes of rare taxa may be important in elucidating the ecosystem stability and multifunctionality that are mediated by microbial communities.© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.

Marine heatwaves (MHWs) in the South China Sea (SCS) have dramatic impacts on local ecosystems, fisheries, and aquacultures. Our results show that SCS MHWs were strongly regulated by El Niño–Southern Oscillation (ENSO) with a distinct life cycle during 1982–2018. Based on the ENSO-associated sea surface temperature anomaly (SSTA) warming peaks in the SCS, we can classify SCS MHWs into three categories: El Niño-P1 during the first warming peak of El Niño from September to the following February, El Niño-P2 during the second warming peak of El Niño from the following June to September, and La Niña-P1 during the single warming peak of La Niña from the following February to May. The three types of SCS MHWs are all affected by the lower-level enhanced anticyclone over the western North Pacific (WNP), but their physical mechanisms are quite different. In El Niño-P1, SCS MHWs are mostly induced by enhanced net downward shortwave radiation and reduced latent heat flux loss over the southwestern and northern SCS, respectively. In El Niño-P2, SCS MHWs are primarily attributed to weaker entrainment cooling caused by a local enhanced anticyclone and stronger Ekman downwelling in the central-northern SCS. However, in La Niña-P1, SCS MHWs are mainly contributed by the reduced latent heat loss due to the weaker WNP anticyclone centered east of the Philippines on the pentad time scale. The distinct spatial distributions of MHWs show phase locking with ENSO-associated SCS SSTA warming, which provides a potential seasonal forecast of SCS MHWs according to the ENSO phase.

Changes in species composition across communities, i.e., β-diversity, is a central focus of ecology. Compared to macroorganisms, the β-diversity of soil microbes and its drivers are less studied. Whether the determinants of soil microbial β-diversity are consistent between soil depths and between abundant and rare microorganisms remains controversial. Here, using the 16S-rRNA of soil bacteria and archaea sampled at different soil depths (0–10 and 30–50 cm) from 32 sites along an aridity gradient of 1500 km in the temperate grasslands in northern China, we compared the effects of deterministic and stochastic processes on the taxonomic and phylogenetic β-diversity of soil microbes. Using variation partitioning and null models, we found that the taxonomic β-diversity of the overall bacterial communities was more strongly determined by deterministic processes in both soil layers (the explanatory power of environmental distance in topsoil: 25.4%; subsoil: 47.4%), while their phylogenetic counterpart was more strongly determined by stochastic processes (the explanatory power of spatial distance in topsoil: 42.1; subsoil 24.7%). However, in terms of abundance, both the taxonomic and phylogenetic β-diversity of the abundant bacteria in both soil layers was more strongly determined by deterministic processes, while those of rare bacteria were more strongly determined by stochastic processes. In comparison with bacteria, both the taxonomic and phylogenetic β-diversity of the overall abundant and rare archaea were strongly determined by deterministic processes. Among the variables representing deterministic processes, contemporary and historical climate and aboveground vegetation dominated the microbial β-diversity of the overall and abundant microbes of both domains in topsoils, but soil geochemistry dominated in subsoils. This study presents a comprehensive understanding on the β-diversity of soil microbial communities in the temperate grasslands in northern China. Our findings highlight the importance of soil depth, phylogenetic turnover, and species abundance in the assembly processes of soil microbial communities.

Microbial metabolism powers biogeochemical cycling in Earth's ecosystems. The taxonomic composition of microbial communities varies substantially between environments, but the ecological causes of this variation remain largely unknown. We analyzed taxonomic and functional community profiles to determine the factors that shape marine bacterial and archaeal communities across the global ocean. By classifying >30,000 marine microorganisms into metabolic functional groups, we were able to disentangle functional from taxonomic community variation. We find that environmental conditions strongly influence the distribution of functional groups in marine microbial communities by shaping metabolic niches, but only weakly influence taxonomic composition within individual functional groups. Hence, functional structure and composition within functional groups constitute complementary and roughly independent "axes of variation" shaped by markedly different processes.Copyright © 2016, American Association for the Advancement of Science.

Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and specificity (0.95-0.98) on simulated communities, which are 10-160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%). Interestingly, warming decreases 'drift' over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.

Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture - the most important environmental variable - had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that - despite considerable oscillation in space and time - the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.Copyright © 2020 Richter-Heitmann, Hofner, Krah, Sikorski, Wüst, Bunk, Huang, Regan, Berner, Boeddinghaus, Marhan, Prati, Kandeler, Overmann and Friedrich.

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater-surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater-surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds.

Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.

Dryland ecosystems are sensitive to perturbations and generally slow to recover post disturbance. The microorganisms residing in dryland soils are especially important as they contribute to soil structure and nutrient cycling. Disturbance can have particularly strong effects on dryland soil structure and function, yet the natural resistance and recovery of the microbial components of dryland soils has not been well documented. In this study, the recovery of surface soil bacterial communities from multiple physical and environmental disturbances is assessed. Samples were collected from three field sites in the vicinity of Moab, UT, United States, 6 to 7 years after physical and climate disturbance manipulations had been terminated, allowing for the assessment of community recovery. Additionally, samples were collected in a transect that included three habitat patches: the canopy zone soils under the dominant shrubs, the interspace soils that are colonized by biological soil crusts, and edge soils at the plot borders. Field site and habitat patch were significant factors structuring the bacterial communities, illustrating that sites and habitats harbored unique soil microbiomes. Across the different sites and disturbance treatments, there was evidence of significant bacterial community recovery, as bacterial biomass and diversity were not significantly different than control plots. There was, however, a small number of 16S rRNA gene amplicon sequence variants that distinguished particular treatments, suggesting that legacy effects of the disturbances still remained. Taken together, these data suggest that dryland bacterial communities may possess a previously unappreciated potential to recover within years of the original disturbance.

Microbes are the unseen majority in soil and comprise a large portion of life's genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogen-fixing bacteria are responsible for c. 5-20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.

<p id="p00005"><strong>Aims</strong> Extreme drought exacerbates the expansion of desert areas around the world. Microbial diversity is associated with multiple ecosystem functions in the desert. Evaluating the response of fungal communities to extreme drought is essential for our understanding of regional desertification caused by drought in a temperate desert.</p><p id="p00010"><strong>Methods</strong> Based on three-year (D3) and ten-year (D10) drought plots established in the Gurbantunggut Desert, we investigated the effect of extreme drought on the diversity and ecological network of fungal communities.</p><p id="p00015"><strong>Results</strong> Our results demonstrated that in both the D3 and D10 plots, the droughts had no significant influence on the Chao1 and Shannon diversity indexes of the whole and abundant fungi, while the rare fungal Shannon diversity index significantly increased. Both extreme drought treatments had a noticeable effect on community composition of whole, abundant and rare fungi, with stronger effect on rare fungi (ANOSIM, <i>R</i> = 0.378-0.595, <i>P</i> &lt; 0.01) than that on the abundant fungi (ANOSIM, <i>R</i> = 0.282-0.555, <i>P</i> &lt; 0.01), suggesting that abundant fungi were more resistant to drought than rare taxa. Moreover, beta-diversity of the whole, abundant, and rare fungi decreased significantly in D3 and D10 treatments, suggesting that extreme drought served as an ecological filter on fungal community assembly. Molecular ecological network analysis revealed that in both the D3 and D10 plots there was a reduced fungal network complexity, suggesting that extreme drought reduced the interactions among fungal communities. In addition, abundant fungi had higher node topological parameters (<i>P</i> &lt; 0.05), indicating that abundant fungi were important for maintaining fungal species interactions under extreme drought conditions.</p><p id="p00020"><strong>Conclusion</strong> Extreme drought significantly altered fungal community composition and weakened the interactions among fungal communities in a temperate desert. Furthermore, rare fungi were sensitive to extreme drought, contributing to reducing the lag in the response to fungal communities, and abundant fungi, as the core microflora in fungal networks, were crucial to sustaining the stability of fungal communities and interactions among species under extreme drought conditions.</p>

评估极端干旱对温带荒漠土壤真菌群落的影响有助于进一步认识干旱导致的区域荒漠化特征。本研究利用在古尔班通古特沙漠建立的干旱三年和干旱十年样地, 分析了长期极端干旱对温带荒漠土壤真菌群落和生态网络的影响。结果显示, 干旱三年与干旱十年处理对总真菌和丰富真菌的Chao1和Shannon多样性指数均无显著性影响, 而对稀有真菌的Shannon多样性指数有显著促进作用; 干旱三年和干旱十年处理显著影响总真菌、丰富和稀有真菌的群落组成, 且极端干旱对稀有真菌群落变异的影响(ANOSIM, R = 0.378-0.595, P &lt; 0.01)大于对丰富真菌的影响(ANOSIM, R = 0.282-0.555, P &lt; 0.01), 表明丰富真菌具有更强的干旱抵抗力; 另外, 极端干旱显著降低了总真菌、丰富和稀有真菌的&#x003b2;多样性, 表明极端干旱具有生态过滤作用。分子生态网络结果显示, 干旱三年与干旱十年处理降低了荒漠土壤真菌群落网络复杂性, 表明极端干旱减弱了真菌物种间的相互作用; 相比稀有真菌, 丰富真菌具有更高的节点拓扑参数(P &lt; 0.05), 表明丰富真菌对维持极端干旱下的真菌物种间相互作用的重要性。综上所述, 极端干旱显著改变了荒漠表层土壤真菌群落组成, 减弱了真菌物种间的相互作用; 稀有真菌敏感响应极端干旱, 有利于减缓荒漠土壤真菌群落响应的滞后性; 丰富真菌作为网络的核心菌群, 对维持极端干旱下的真菌群落稳定性以及物种间的相互作用很关键。