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The Earth Microbiome Project: Planetary Scale Systems Ecology

The Earth Microbiome Project: Planetary Scale Systems Ecology. Sean M. Gibbons , Antonio González, Emmanuel Prestat , Jai Rideout , J. Gregory Caporaso , Rob Knight, Janet Jansson , and Jack A. Gilbert Download EMP Data : http://www.microbio.me/emp

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The Earth Microbiome Project: Planetary Scale Systems Ecology

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  1. The Earth Microbiome Project: Planetary Scale Systems Ecology Sean M. Gibbons, Antonio González, Emmanuel Prestat, Jai Rideout, J. Gregory Caporaso, Rob Knight, Janet Jansson, and Jack A. Gilbert Download EMP Data: http://www.microbio.me/emp EMP Website: http://www.earthmicrobiome.org/ Twitter: @gilbertjacka @gibbological November 1, 2013 Argonne National Laboratory Institute for Genomic and Systems Biology

  2. How many microbes on Earth? ~5x1030 How many stars in the observable universe? ~1x1023

  3. What have we accomplished so far? • Collaborators: 139 • 60,000 samples pledged • 15,000 environmental samples being processed • 20,304 completed for 16S rRNA analyses. • Biomes Represented: 42 • Total 16S rRNA Sequences: 1,713,425,117 • Public data analysis led by EMP working group • Incredibly diverse set of metadata!

  4. Metadata Standards

  5. MIMARKS Environmental Packages http://gensc.org/gc_wiki/index.php/MIMARKS

  6. MIMARKS Environmental Packages http://gensc.org/gc_wiki/index.php/MIMARKS Genomic Biodiversity Working Interest Group - MIxS as RDF (https://code.google.com/p/mixs-as-rdf/) - MaterialSample proposal for the DwC Standard

  7. Other Methodological and Analytical Standards

  8. EMP 10K • Recently finished the largest OTU picking run ever attempted…that we know of • 13,000 samples & 1.2 billion 16S reads • Run on Amazon EC2 M2.4xlarge spot instances using StarCluster • 11,000 processor consumed • 560 Gb – 1.3 Tb of RAM • 1.2 Tb of hard disc space • EMP has begun an analysis of the first ~10,000 samples • Results • ~10 million OTUs (97% identity) • 5,594,412 non-singleton OTUs • Questions/Goals • Novel Phyla/diversity • Phylogenetic overlap between and within biomes • Significant evidence for endemism, or allopatry • How much sampling is needed to sufficiently characterize an environment? • Who are the keystone species for different environments? Generalists vs. specialists? • Provide a framework for placing local datasets into a global context

  9. temperate forest temperate polar desert tropical tundra warm desert Reuben et al., 2013, PLOS ONE

  10. Get Involved! • Membership defined by participation • Send us your samples • Why would the EMP help you address your hypotheses? What will your data contribute to the EMP? • If you provide MIxS-compliant metadata, we sequence your samples! $$ • Help analyze data through github

  11. Acknowledgements • Argonne National Laboratory: Jack Gilbert,Sarah Owens, JarradMarcelle, Daniel Smith, IraxteZarraonaindia, Simon Lax, Kim Handley, Peter Larsen, Nicole Scott, and Chris Marshall • University of Chicago: Maureen Coleman, Jacob Waldbauer, Rick Stevens • University of Colorado at Boulder: Rob Knight, Antonio Gonzáles • Northern Arizona University: Greg Caporaso, Jai Rideout • Berkeley National Laboratory: Janet Jansson, Emmanuel Prestat • Graduate Program in Biophysical Sciences: Michele Wittels, Adam Hammond, Tobin Sosnick, Julie Feder * Graduate Funding: EPA STAR Fellowship Thanks for your attention! Questions? Download EMP Data: http://www.microbio.me/emp EMP Website: http://www.earthmicrobiome.org/ Twitter: @gilbertjacka@gibbological

  12. Maureen Coleman and Mark Anderson Bog Lakes Lake Mendota English Channel Great Lakes

  13. Taxonomic Annotation Standards Manually-curated full-length rRNA gene databases 16S 16S & 18S

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