Microbial activities shape the biogeochemistry of the planet1,2 and macroorganism health3. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
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The metagenomes used in this paper are freely available from the SEED platform and are being made accessible from CAMERA and the NCBI Short Read Archive. The accession numbers are shown in Supplementary Table 1. The NCBI genome project IDs used in this study are: 28619, 28613, 28611, 28609, 28607, 28605, 28603, 28601, 28599, 28597, 28469, 28467, 28465, 28463, 28461, 28459, 28457, 28455, 28453, 28451, 28449, 28447, 28445, 28443, 28441, 28439, 28437, 28435, 28433, 28431, 28429, 28427, 28425, 28423, 28421, 28419, 28417, 28415, 28413, 28411, 28409, 28407, 28405, 28403, 28401, 28395, 28393, 28391, 28389, 28387, 28385, 28383, 28381, 28379, 28377, 28375, 28373, 28371, 28361, 28359, 28357, 28355, 28353 and 28351.
This project was supported by the Gordon and Betty Moore Foundation Marine Microbial Initiative, National Science Foundation grants (F.R. and D.L.V.), a Department of Commerce ATP grant (F.R.), a National Research Initiative Competitive Grant from the USDA Cooperative State Research, Education and Extension Service (B.W.), the National Institute of Allergy and Infectious Diseases, the National Institutes of Health and the Department of Health and Human Services (R.S.).
Author Contributions E.A.D. conceptualized the project, conducted the CDA and wrote the manuscript. R.A.E., R.O. and R.S. performed the bioinformatics. D.H. conducted the non-parametric statistical analysis. F.R. oversaw most of the metagenomic projects. All other authors collected the metagenomes and provided comments on the manuscript.
The file contains Supplementary Tables S1-S4 and Supplementary Figures S1-S6 with Legends. The Supplementary Tables present accession numbers and descriptions of metagenomes, phage and prophage content of each metagenome, the motility proteins present in the microbial and viral metagenomes and statistical comparisons of the proportions of metabolic processes across the nine biomes. The Supplementary Figures provide information about the geographic separation of samples, diversity versus sequences number, comparison of diversity between metagenomes and sequenced whole bacterial genomes, the fine-scale details about the sulfur metabolic processes, and two experiments that show the strength of the CDA across multiple groupings.