A communal catalogue reveals Earth’s multiscale microbial diversity

Abstract

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...

Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring

“…Other metagenomics studies have investigated the microbiome in soil, extreme environments, and the ocean (Rinke et al, 2013; Sunagawa et al, 2015; Thompson et al, 2017). Although highly important for human health, airborne metagenomics are disproportionally understudied due to technological difficulties such as a) low density of microorganisms in the air, b) lack of an efficient method of retrieving information from such microorganisms, and c) bioinformatics challenges (Behzad et al, 2015).…”

SEDE-GPS: socio-economic data enrichment based on GPS information

“…In part, this is due to the fact that the samples and lakes included in this analysis are limited in number and are geographically close to each other [22, 24, 25, 36]. Therefore, for a more thorough analysis, larger datasets from more variable sites would be neccessary, as currently only available from large-scale environmental sequencing efforts such as the Earth Microbiome Project [37] or the 1000 Springs Project [28, 38]. Nevertheless, on the basis of the results presented here, experiments can be designed in order to illuminate the mechanistic and causal relationships between environmental features and microbial biodiversity.…”

pH as a Primary Control in Environmental Microbiology: 1. Thermodynamic Perspective

“…Among these factors, pH emerges as a primary control (Chen et al, 2004;Kemmitt et al, 2006;Bethke et al, 2011;Zhalnina et al, 2015). pH correlates strongly with microbial communities across a wide range of biogeochemical conditions (Thompson et al, 2017). In addition, variations in environmental pH also induce significant responses of metabolic activities of natural communities (Kotsyurbenko et al, 2004;Ye et al, 2012).…”