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

How many microbes on Earth?

~5x1030

~1x1023

How many stars in the observable universe?

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!

Metadata Standards

MIMARKS Environmental Packages

http://gensc.org/gc_wiki/index.php/MIMARKS

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

Other Methodological and Analytical Standards

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

Reuben et al., 2013, PLOS ONE

polar desert

tundrawarm desert

temperate

tropical

temperate forest

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

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/emp EMP Website: http://www.earthmicrobiome.org/ Twitter: @gilbertjacka @gibbological

English Channel

Bog Lakes

Lake Mendota

Great Lakes

Maureen Coleman and Mark Anderson

Taxonomic Annotation Standards

16S

16S & 18S

Manually-curated full-length rRNA gene databases