skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Journal Article · · Standards in Genomic Sciences
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [7];  [8];  [9];  [10];  [2]
  1. Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Newcastle Univ., Newcastle upon Tyne (United Kingdom). School of Biology
  4. Chinese Academy of Sciences (CAS), Beijing (China). China General Microbiological Culture Collection Center (CGMCC), Inst. of Microbiology
  5. American Type Culture Collection, Manassas, VA (United States); Novozymes North America Inc., Durham, NC (United States)
  6. American Type Culture Collection, Manassas, VA (United States); Microbiologics, St. Cloud, MN (United States)
  7. Ghent Univ., Ghent (Belgium). BCCM/LMG Bacteria Collection and Lab. of Microbiology
  8. Univ. of California, Davis, CA (United States)
  9. Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics
  10. Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences
+ Show Author Affiliations

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. Here in this paper, 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

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1407293
Journal Information:
Standards in Genomic Sciences, Vol. 10, Issue 1; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 48 works
Citation information provided by
Web of Science

References (18)

Global distribution of microbial abundance and biomass in subseafloor sediment journal August 2012
Prokaryotes: The unseen majority journal June 1998
Towards a prokaryotic genomic taxonomy journal April 2005
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics journal October 1987
Assessment and Evaluation of Soil Ecosystem Services journal January 2013
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project journal December 2013
Genome sequence-based species delimitation with confidence intervals and improved distance functions journal January 2013
Mapping the Tree of Life: Progress and Prospects journal November 2009
Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream journal July 2009
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains journal August 2014
Insights into the phylogeny and coding potential of microbial dark matter journal July 2013
Towards a prokaryotic genomic taxonomy journal April 2005
Towards a Genome-Based Taxonomy for Prokaryotes journal September 2005
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities journal January 2007
En route to a genome-based classification of Archaea and Bacteria? journal June 2010
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea journal December 2009
A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera journal October 2008
Genetic transfer and bacterial taxonomy. journal January 1970

Cited By (2)

Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov. journal December 2017
Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T journal December 2017

Similar Records

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
Journal Article · Sun Jun 15 00:00:00 EDT 2014 · Standards in Genomic Sciences · OSTI ID:1407293
+6 more
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
Journal Article · Tue Aug 05 00:00:00 EDT 2014 · PLoS Biology (Online) · OSTI ID:1407293
+61 more
Expansion of the Genomic Encyclopedia of Bacteria and Archaea
Conference · Thu Jun 02 00:00:00 EDT 2011 · OSTI ID:1407293
+12 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Genome sequencing
Type stains
Prokaryotes