Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

William B Whitman; Tanja Woyke; Hans-Peter Klenk; Yuguang Zhou; Timothy G Lilburn; Brian J Beck; Paul De Vos; Peter Vandamme; Jonathan A Eisen; George Garrity; Philip Hugenholtz; Nikos C Kyrpides

doi:10.1186/s40793-015-0017-x

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

Stand Genomic Sci. 2015 May 17:10:26. doi: 10.1186/s40793-015-0017-x. eCollection 2015.

Authors

Affiliations

¹ Department of Microbiology, University of Georgia, Athens, GA, Greece.
² DOE Joint Genome Institute, Walnut Creek, CA, USA.
³ School of Biology, Newcastle University, Newcastle upon Tyne, UK.
⁴ China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
⁵ American Type Culture Collection, Manassas, VA, USA ; Current addresses: Novozymes North America Inc., Durham 27709, NC, USA.
⁶ American Type Culture Collection, Manassas, VA, USA ; Current addresses: Microbiologics, St. Cloud, MN, USA.
⁷ BCCM/LMG Bacteria Collection and Laboratory of Microbiology, Ghent University, Ghent, Belgium.
⁸ University of California, Davis, CA, USA.
⁹ Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA, and NamesforLife, LLC, East Lansing, MI, USA.
¹⁰ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, QLD, Australia.

Abstract

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity.

Keywords: Genome sequencing; Prokaryotes; Type stains.