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/emphttp://www.microbio.me/emp EMP Website: http://www.earthmicrobiome.org/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? ~5x10 30 ~1x10 23 How many stars in the observable universe?

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/)https://code.google.com/p/mixs-as-rdf/ - MaterialSample proposal for the DwC Standard

7. Other Methodological and Analytical Standards

8. EMP 10K  EMP has begun an analysis of the first ~10,000 samples  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  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. Reuben et al., 2013, PLOS ONE polar desert tundra warm desert temperate tropical temperate forest

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, Jarrad Marcelle, Daniel Smith, Iraxte Zarraonaindia, 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/emphttp://www.microbio.me/emp EMP Website: http://www.earthmicrobiome.org/http://www.earthmicrobiome.org/ Twitter: @gilbertjacka @gibbological

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

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