A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

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The spatial distribution of bacteria in bulk soil has been well studied, but little is known about the bacterial biogeography in the rhizosphere of crops. Here, we investigated bacterial distribution in bulk soil, loosely-and tightly-bound soils, from wheat fields distributed across 800,000 km 2 of the North China Plain. Bacterial community composition differed dramatically among bulk and rhizospheric soils, and bacterial diversity decreased with the root proximity. Soil pH correlated with bacterial community composition and diversity in three compartments. Bacterial community in tightly bound soil formed a hub-based network topology with higher transitivity and greater number of central nodes compared with loosely bound and bulk soils, potentially as a result of more direct ecological interactions between the members of the tightly bound soil compartment. Bulk and rhizospheric soils maintained similar compositional distance decay patterns (with equal decay rates), but distinct phylogenetic distance decay patterns (with steeper slope of tightly bound soil). Geographical distance described a relatively greater proportion of bacterial spatial distribution in tightly bound soil, compared with loosely bound soil and bulk soil. Deterministic processes dominated the assemblage of bacterial communities in all soil compartments, while phylogenetic clustering was weaker in tightly bound soil. Taken together, our results suggest distinct bacterial network structure and distribution patterns among bulk soil, loosely bound soil and tightly bound rhizospheric soil, which could possibly result in potential functional differentiation.

The diversity of eukaryotic macroorganisms such as animals and plants usually declines with increasing elevation and latitude. By contrast, the community structure of prokaryotes such as soil bacteria does not generally correlate with elevation or latitude, suggesting that differences in fundamental cell biology and/or body size strongly influence diversity patterns. To distinguish the influences of these two factors, soil eukaryotic microorganism community structure was investigated in six representative vegetation sites along an elevational gradient from forest to alpine tundra on Changbai Mountain in Northeast China, and compared with our previous determination of soil bacterial community structure along the same gradient. Using bar‐coded pyrosequencing, we found strong site differences in eukaryotic microbial community composition. However, diversity of the total eukaryotic microorganism community (or just the fungi or protists alone) did not correlate with elevation. Instead, the patterns of diversity and composition in the total eukaryotic microbial community (and in the protist community alone) were closely correlated with soil pH, suggesting that just as for bacteria, acidity is a particularly important determinant of eukaryotic microbial distributions. By contrast, as expected, plant diversity at the same sites declined along our elevational gradient. These results together suggest that elevational diversity patterns exhibited by eukaryotic microorganisms are fundamentally different from those of plants.

Summary Microbial elevational diversity patterns have been extensively studied, but their shaping mechanisms remain to be explored. Here, we examined soil bacterial and fungal diversity and community compositions across a 3.4 km elevational gradient (consists of five elevations) on Mt. Kilimanjaro located in East Africa. Bacteria and fungi had different diversity patterns across this extensive mountain gradient—bacterial diversity had a U shaped pattern while fungal diversity monotonically decreased. Random forest analysis revealed that pH (12.61% importance) was the most important factor affecting bacterial diversity, whereas mean annual temperature (9.84% importance) had the largest impact on fungal diversity, which was consistent with results obtained from mixed‐effects model. Meanwhile, the diversity patterns and drivers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fungal communities. Taken together, our study demonstrated that bacterial and fungal diversity and community composition responded differently to climate and edaphic properties along an extensive mountain gradient, and suggests that the elevational diversity patterns across microbial groups are determined by distinct environmental variables. These findings enhanced our understanding of the formation and maintenance of microbial diversity along elevation, as well as microbial responses to climate change in montane ecosystems.

The elevational diversity pattern for microorganisms has received great attention recently but is still understudied, and phylogenetic relatedness is rarely studied for microbial elevational distributions. Using a bar-coded pyrosequencing technique, we examined the biodiversity patterns for soil bacterial communities of tundra ecosystem along 2000–2500 m elevations on Changbai Mountain in China. Bacterial taxonomic richness displayed a linear decreasing trend with increasing elevation. Phylogenetic diversity and mean nearest taxon distance (MNTD) exhibited a unimodal pattern with elevation. Bacterial communities were more phylogenetically clustered than expected by chance at all elevations based on the standardized effect size of MNTD metric. The bacterial communities differed dramatically among elevations, and the community composition was significantly correlated with soil total carbon (TC), total nitrogen, C:N ratio, and dissolved organic carbon. Multiple ordinary least squares regression analysis showed that the observed biodiversity patterns strongly correlated with soil TC and C:N ratio. Taken together, this is the first time that a significant bacterial diversity pattern has been observed across a small-scale elevational gradient. Our results indicated that soil carbon and nitrogen contents were the critical environmental factors affecting bacterial elevational distribution in Changbai Mountain tundra. This suggested that ecological niche-based environmental filtering processes related to soil carbon and nitrogen contents could play a dominant role in structuring bacterial communities along the elevational gradient.

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