Microbial Earth Project

Microbial Earth Project (MEP) proposal

Project Title: MEP – Microbial Earth Project

Project Lead: Nikos C. Kyrpides, nckyrpides@lbl.gov, DOE Joint Genome Institute, Prokaryote Super Program Head

Team members (Steering Committee)

Jonathan Eisen (University of California, Davis)
George Garrity (Names for Life, USA)
Philip Hugenholtz (Australian Centre for Ecogenomics Research, Australia)
Hans-Peter Klenk (DSMZ, Germany)
Nikos C. Kyrpides (DOE-Joint Genome Institute, USA)
William B. Whitman (University of Georgia)
Tanja Woyke (DOE-Joint Genome Institute, USA)

In addition to the Steering Committee there is an Advisory Committee (under construction) as well as working groups for i) type strain management; ii) metadata collection and management; and iii) strain growth and DNA isolation.

Elevator pitch The Microbial Earth project is an international effort to generate a comprehensive catalog from genome sequences of the type strains of all archaeal and bacterial species with a validly published name. The name of the project comes from the recognition that Earth is a predominantly a microbial planet.

Project Summary It is now widely recognized that microorganisms are the driving force of all life on the planet. Indeed, “all life turns of microbial life” (1) since microbes, catalyze unique transformations in the biogeochemical cycles of the biosphere; they maintain basic components of the earth’s atmosphere and global ecosystems (i.e. the carbon, nitrogen, and sulphur cycles rest on microbial activity); they represent by far the largest portion of life’s genetic diversity both in terms of species numbers as well as biomass (2); their history represents the history of cellular life itself (they are the oldest and most biochemicaly diverse organisms). Non-surprisingly then, while microbiology has become central to Biology’s future, microbial genomics are providing the new foundation upon which we now rest our understanding of the origins and dynamics of all microbial life.

In 2007, The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was initiated by the JGI with the goal of generating a comprehensive genomic encyclopedia of all the validly named bacterial and archaeal species. A pilot project of sequencing 250 strains was launched at the time with two major goals: (a) to provide evidence to support the use of the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes.

The goals of the pilot project have already been successfully accomplished leading the way for the next phase of the project which was the sequencing of 1,000 type strains in one year. The 1,000 microbial genomes (KMG) project was funded from the Community Sequencing Program (CSP) at the DOE-JGI on 2012, representing the Phase-I of the GEBA project, while a second proposal of similar scale (KMG-II) was funded again from the CSP program for 2013. The ultimate goal is to have at least one representative genome sequence of every bacterial and archaeal type strain.

Project initiation date The project started in Spring 2010 with a presentation by Nikos C. Kyrpides during the GSC-9 workshop at JCVI and a year later with a successful CSP proposal to DOE-JGI for sequencing 1,000 microbial genomes.

What will this project aim to contribute to the GSC? The project provides to GSC and the wider community a large set of highly standardized short genome reports including all at the time of publication available metadata for i) the organism whose genome was sequenced; ii) sequencing and annotation process; and iii) genome content. It contributes a significant number of peer-reviewed genome reports to GSC’s Stand Genomic Sci.

Have you spoken about the project already within GSC? The project was first presented at the GSC-9 workshop, JCVI, April 2010.

Which existing projects, if any, does this one replace/complement/subsume/expand? The project expands on the Genomic Encyclopedia of Bacteria and Archaea, a pilot project performed at JGI since 2007. It is unique in its kind by the strictly phylogeny-driven selection of sequencing targets, its size (thousands of genomes) and coverage of the whole range of prokaryotic diversity. The fairly large number of publications produced by MEP has a good potential to draw the attention of microbiologists to the need of reporting metadata and to standardization matter.

How does this project fit into GSC’s mission statement? The project fits into the GSC’s mission statement because it focuses on capturing and exchanging metadata related to genome-sequenced organisms, genome sequencing procedures and genome content. Through the significant number of publications it helps to set standards for short genome reports which are already accepted by other authors outside the project.

Will you start a GSC working group? GSC working group Microbial Earth already exists, with several committees (see #3) (http://wiki.gensc.org/index.php?title=Microbial_Earth).

How do you wish to further engage the GSC? The GSC is asked to provide contacts and consult us particularly regarding the further development of standards that must be kept in sync with other GSC-established checklists (e.g. MIxS). Through the frequent publications the MEP is tightly linked to SIGS. Contacts to the Genomic Biodiversity Working Group should be strengthened for strategic planning of future sequencing targets.

Do you already have a website or do you wish to create a home page for the project in the GSC website? A home page does already exist: http://www.microbial-earth.org/ and is linked to the MEP website at GSC http://wiki.gensc.org/index.php?title=Microbial_Earth.

What other resources might you like from what the GSC can offer? A mailing list hosted by the GSC would also be quite useful.

What kind of timeline are you working to for building consensus, releasing a first version etc. A first version of standardized short reports for individual genome sequences (mainly type strains published in SIGS) is in operation since 2009. A refined standard for genomes of genera and families will be introduces with the upcoming publications of MEP phase II (mid of 2014).

How is this work currently funded? Funding for MEP is currently provided through DOE-JGI CSP grants for phase I [2012, about $ 1.5 Mio. for sequencing] (PI Nikos C. Kyrpides, co-PIs members of the steering committee) and phase II [2013, about $ 2 Mio. for sequencing] (PI Hans-Peter Klenk, co-PIs members of the steering committee), and institutional resources of steering committee members at JGI and DSMZ.

What resources will be required for completion? The project is mainly funded through annual proposals for DOE-JGI CSP funding for high quality microbial genome sequencing and annotation in collaboration of JGI, ATCC and DSMZ. Drafting of the third major proposal (for 2014) is currently in progress.

What are your current plans for publishing/promoting the project? A follow-up of the 2009 Genomic Encyclopedia of Bacteria and Archaea paper has been prepared in collaboration with a collection of leading colleagues in the field and is currently updated (?) for resubmission to a high impact journal to announce MEP to the wider public.

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