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Title: A communal catalogue reveals Earth’s multiscale microbial diversity

Journal Article · · Nature (London)
DOI:https://doi.org/10.1038/nature24621· OSTI ID:1411914
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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 researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE; W.M. Keck Foundation; National Science Foundation (NSF); Australian Research Council; National Oceanic and Atmospheric Administration (NOAA)
Contributing Organization:
The Earth Microbiome Project Consortium
Grant/Contract Number:
AC05-76RL01830; AC02-06CH11357
OSTI ID:
1411914
Alternate ID(s):
OSTI ID: 1467890
Report Number(s):
PNNL-SA-123888
Journal Information:
Nature (London), Vol. 551; ISSN 0028-0836
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 1285 works
Citation information provided by
Web of Science

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A Communal Catalogue Reveals Earth's Multiscale Microbial Diversity [Supplemental Data]
  • Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
  • Zenodo-Supplementary information for journal article at DOI: 10.1038/nature24621, 33 files (47.3 GB) https://doi.org/10.5281/zenodo.890000
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Figures / Tables (11)

Figure 1 | Environment type and provenance of samples.(p. 2)figure Figure 1 | Environment type and provenance of samples.
Figure 2 | Alpha-diversity, beta-diversity, and predicted average 16S rRNA gene copy number(p. 4)figure Figure 2 | Alpha-diversity, beta-diversity, and predicted average 16S rRNA gene copy number
Figure 3 | Nestedness of community composition(p. 5)figure Figure 3 | Nestedness of community composition
Figure 4 | Specificity of sequences and higher taxonomic groups for environment(p. 6)figure Figure 4 | Specificity of sequences and higher taxonomic groups for environment
Extended Data Figure 1 | Physicochemical properties of the EMP samples(p. 14)figure Extended Data Figure 1 | Physicochemical properties of the EMP samples
Extended Data Figure 2 | Sequence length, database effects, and beta-diversity patterns(p. 15)figure Extended Data Figure 2 | Sequence length, database effects, and beta-diversity patterns
Extended Data Figure 3 | Sequence length effects on observed diversity patterns(p. 16)figure Extended Data Figure 3 | Sequence length effects on observed diversity patterns
Extended Data Figure 4 | Tag sequence prevalence patterns(p. 17)figure Extended Data Figure 4 | Tag sequence prevalence patterns
Extended Data Figure 5 | Environmental effect sizes, sample classification, and correlation patterns(p. 19)figure Extended Data Figure 5 | Environmental effect sizes, sample classification, and correlation patterns
Extended Data Figure 6 | NODF scores of nestedness across samples by taxonomic level(p. 20)figure Extended Data Figure 6 | NODF scores of nestedness across samples by taxonomic level
Extended Data Figure 7 | Subsets and EMP trading cards(p. 21)figure Extended Data Figure 7 | Subsets and EMP trading cards

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