Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b

doi:10.1128/JB.00303-11

J Bacteriol. 2011 June; 193(11): 2880–2881.

PMCID: PMC3133134

Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b

Tatiana A. Vishnivetskaya,^1,²^* Susan Lucas,⁴ Alex Copeland,⁴ Alla Lapidus,⁴ Tijana Glavina del Rio,⁴ E. Dalin,⁴ Hope Tice,⁴ David C. Bruce,⁵ Lynne A. Goodwin,⁵ Sam Pitluck,⁴ E. Saunders,⁴ Tom Brettin,⁴ Chris Detter,⁴ Cliff Han,⁵ Frank Larimer,² Miriam L. Land,² Loren J. Hauser,^2,³ Nikos C. Kyrpides,⁴ Galina Ovchinnikova,⁴ Sophia Kathariou,⁶ Robert F. Ramaley,⁷ Debora F. Rodrigues,⁸ Christie Hendrix,⁹ Paul Richardson,⁴ and James M. Tiedje¹⁰

¹Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37932

²Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831

³BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831

⁴DOE Joint Genome Institute, Walnut Creek, California 94598

⁵Los Alamos National Laboratory, Los Alamos, New Mexico 87545

⁶Department of Food Sciences, North Carolina State University, Raleigh, North Carolina 27695

⁷Nebraska Medical Center, Omaha, Nebraska 68198

⁸Department of Civil and Environmental Engineering, University of Houston, Houston, Texas 77204

⁹Yellowstone National Park, Yellowstone NP, Wyoming 82190

¹⁰Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824

^*Corresponding author. Mailing address: The University of Tennessee, Center for Environmental Biotechnology, 676 Dabney-Buehler Hall, Knoxville, TN 37996-1605. Phone: (865) 574-7338. Fax: (865) 576-8646. E-mail: vishnivetsta/at/ornl.gov or ; Email: tvishniv/at/utk.edu.

Received March 3, 2011; Accepted March 25, 2011.

This article has been cited by other articles in PMC.

Abstract

Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physicochemical gradient. This genome was sequenced to be a comparative resource for the study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy's (DOE's) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).

TEXT

Exiguobacterium sp. AT1b (= ATCC BAA-1283) is a thermophilic, facultative anaerobic bacterium isolated from a slightly alkaline, highly carbonate hot spring water sample from Angel Terrace, which is part of Mammoth Terrace, Yellowstone National Park. The non-spore-forming, low-GC, Gram-positive, catalase-positive, nuclease-active Exiguobacterium AT1b strain clusters phylogenetically with other hot spring and marine isolates within Bacillales family XII incertae sedis, Firmicutes. Its 16S rRNA gene has 94% identity and DNA-DNA hybridization of <70% with Exiguobacterium 255-15 (7, 8), indicating that it is a different species from its psychroactive relative. Strain AT1b cells occur singly, in pairs, or infrequently in chains and are able to grow from 15 to 50°C; at 37°C they are ovoid rods about 2 μm in length, and they are longer at 50°C (10). Colonies appear round, shiny, irregular, elevated, and orange colored on tryptic soy agar (TSA); the pigment does not diffuse into the medium.

The genome of Exiguobacterium sp. AT1b was sequenced by the DOE JGI using a combination of 6.1-kb and 37.5-kb DNA libraries. General aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov/. Draft assemblies were based on 21,659 total reads. Both libraries provided 7.3× coverage of the genome. In addition to Sanger sequencing, 454 pyrosequencing was done to a depth of 20× coverage. The Phred/Phrap/Consed software package was used for sequence assembly and quality assessment (1–3) in the following finishing process. The genome was annotated at Oak Ridge National Laboratory (ORNL) using the automated annotation pipeline, which is driven by the gene prediction algorithm Prodigal (4), followed by a round of manual curation using the JGI GenePRIMP pipeline (5).

Exiguobacterium sp. AT1b contains a single replication unit consisting of 2,999,895 bp, which encodes 3,043 (96.9%) putative proteins. Genes are evenly distributed between the forward (49.9%) and reverse (50.1%) chromosome strands; the average coding sequence length is 891 bp, and 89.6% of the coding bases are in sequences encoding putative proteins. The GC content is constant across the genome with an average value of 48.5%. AT-rich fragments encode uncharacterized proteins, sulfurtransferase, and sulfur modification protein. Nine rRNA operons are present in the positive (4 copies) and negative (5 copies) strands. The average CG content of the rRNA operons is 56.1%, which is higher than the average genome value. Three transposases of the IS605 orfB family with 90.3 to 96.5% identity between them are predicted in the genome. DNase production is supported by the presence of restriction endonucleases, ribonucleases, and exonucleases. Exiguobacterium sp. AT1b contains genes for cellulose and hemicellulose degradation, as indicated by the presence of glycosyltransferases and glycoside hydrolases, which may be adapted to function at higher temperatures.

Having the strains and genome sequences of thermophilic Exiguobacterium sp. AT1b and its psychroactive relative, Exiguobacterium sibiricum 255-15, which was isolated from Siberian permafrost and has a growth range from −6° to 40°C (6, 9), enables investigation of the genetic basis of microbial adaptation to different temperatures and is of interest in the fields of agriculture, industrial microbiology, and astrobiology.

Nucleotide sequence accession numbers.

The final annotated genome sequence was deposited in GenBank under the accession number CP001615, the IMG database under identifier (ID) 643692023, the Genomes OnLine Database (GOLD) under ID Gc01000, and the GreenGenes database under ID 284647.

Acknowledgments

We thank the National Park Service for coordinating and allowing sampling under permit YELL-1502. Work at the Joint Genome Institute is performed under the auspices of the U.S. Department of Energy's Office of Science, Biological and Environmental Research Program and by the University of California Lawrence Berkeley National Laboratory under contract DE-AC02-05CH11231, by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344, and by Los Alamos National Laboratory under contract DE-AC02-85 06NA25396. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.

Footnotes

Published ahead of print on 1 April 2011.

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