Complete Genome Sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T
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Michael Pester, Evelyne Brambilla, Didier Alazard, Thomas Rattei, Thomas Weinmaier, James Han, Susan Lucas, Alla Lapidus, Jan-Fang Cheng, Lynne Goodwin, Sam Pitluck, Lin Peters, Galina Ovchinnikova, Hazuki Teshima, John C. Detter, Cliff S. Han, Roxanne Tapia, Miriam L. Land, Loren Hauser, Nikos C. Kyrpides, Natalia N. Ivanova, Ioanna Pagani, Marcel Huntmann, Chia-Lin Wei, Karen W. Davenport, Hajnalka Daligault, Patrick S. G. Chain, Amy Chen, Konstantinos Mavromatis, Victor Markowitz, Ernest Szeto, Natalia Mikhailova, Amrita Pati, Michael Wagner, Tanja Woyke, Bernard Ollivier, Hans-Peter Klenk, Stefan Spring and Alexander Loy J. Bacteriol. 2012, 194(22):6300. DOI: 10.1128/JB.01392-12.
GENOME ANNOUNCEMENT
Complete Genome Sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T Michael Pester,a Evelyne Brambilla,b Didier Alazard,c Thomas Rattei,d Thomas Weinmaier,d James Han,e Susan Lucas,f Alla Lapidus,e Jan-Fang Cheng,e Lynne Goodwin,f Sam Pitluck,e Lin Peters,e Galina Ovchinnikova,e Hazuki Teshima,f John C. Detter,e,f Cliff S. Han,e,f Roxanne Tapia,e,f Miriam L. Land,e,g Loren Hauser,e,g Nikos C. Kyrpides,e Natalia N. Ivanova,e Ioanna Pagani,e Marcel Huntmann,e Chia-Lin Wei,f Karen W. Davenport,f Hajnalka Daligault,f Patrick S. G. Chain,e Amy Chen,e Konstantinos Mavromatis,e Victor Markowitz,f Ernest Szeto,e Natalia Mikhailova,e Amrita Pati,e Michael Wagner,a Tanja Woyke,e Bernard Ollivier,c Hans-Peter Klenk,b Stefan Spring,b and Alexander Loya
Desulfosporosinus species are sulfate-reducing bacteria belonging to the Firmicutes. Their genomes will give insights into the genetic repertoire and evolution of sulfate reducers typically thriving in terrestrial environments and able to degrade toluene (Desulfosporosinus youngiae), to reduce Fe(III) (Desulfosporosinus meridiei, Desulfosporosinus orientis), and to grow under acidic conditions (Desulfosporosinus acidiphilus).
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he sequenced Desulfosporosinus type strains (2, 3, 14, 20) represent four out of eight described species belonging to the genus Desulfosporosinus and cover its phylogenetic and physiological breadth. Besides their ability to reduce sulfate for energy conservation, some Desulfosporosinus species can also grow by using nitrate, Fe(III), or As(V) as terminal electron acceptors or by fermentative processes. They can utilize a wide spectrum of energy sources, ranging from aromatic compounds to short-chained fatty acids. A characteristic feature of many Desulfosporosinus species, distinguishing them from their closest sulfate-reducing relatives of the genus Desulfotomaculum, is their ability to grow chemolithoautotrophically on hydrogen (3, 14, 15, 19, 21–23). Members of the genus Desulfosporosinus are found in low-sulfate freshwater and soil environments but also in sulfate-rich heavymetal-contaminated environments, such as acid mine/rock drainage sites. In addition, Desulfosporosinus species are often observed in low-pH habitats (1, 3, 5–7, 12, 13, 17, 18), with the sequenced Desulfosporosinus acidiphilus strain being the first validly described sulfate-reducing acidophile (3). Genomic DNA was isolated using the Jetflex genomic DNA purification kit (GENOMED, Löhne, Germany) and subjected to sequencing using a combination of 454 Titanium (16) and Illumina (4) technologies. Sequences were assembled with Newbler (version 2.3-PreRelease-6/30/2009) and Velvet (version 1.0.13) (24) for 454 and Illumina data, respectively. Consensus sequences were obtained using computationally shredded Illumina and 454 reads together with 454 paired-end data using parallel Phrap (version SPS-4.24; High Performance Software, LLC). Identification of sequencing errors and improvement of consensus quality were done with Polisher (A. Lapidus, unpublished data) using Illumina data. GapResolution (C. Han, unpublished data), Dupfinisher (11), or sequencing cloned bridging PCR fragments with subcloning were used to correct misassemblies. Gaps between contigs were closed by editing in Consed (8–10), by PCR, and by Bubble
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PCR (J.-F. Cheng, unpublished data) primer walks. Automated genome annotation was performed at the Oak Ridge National Laboratory and is available at http://genome.ornl.gov/. The circular chromosomes of Desulfosporosinus orientis, Desulfosporosinus youngiae, Desulfosporosinus meridiei, and D. acidiphilus have sizes of 5,863,081 bp, 5,660,978 bp, 4,873,567 bp, and 4,926,837 bp, respectively. The genome of D. acidiphilus additionally harbors two plasmids of 60,447 bp and 3,897 bp. The genomes, in the order listed above, have G⫹C contents of 43%, 44%, 42%, and 42%, respectively, preliminary gene counts of 5,638, 5,456, 4,664, and 4,799 genes, respectively, and 8, 9, 10, and 8 rRNA operons, respectively. D. meridiei and D. acidiphilus contain one additional 16S rRNA gene each. The four strains harbor all genes coding for the core enzyme trio of dissimilatory sulfate reduction, ATP sulfurylase, adenosine 5=-phosphosulfate reductase, and dissimilatory (bi)sulfite reductase. The sequenced genomes will enable an encompassing view on the genetic repertoire and metabolic potential within the genus Desulfosporosinus and allow phylogenomic comparisons to the sulfite-reducing sister genus Desulfitobacterium and other sulfate/ sulfite-reducing genera within the Firmicutes (e.g., Desulfotomaculum and Desulforudis). Nucleotide sequence accession numbers. The genomes of D. orientis, D. youngiae, D. meridiei, and D. acidiphilus were deposited in GenBank under the accession numbers CP003108, CM001441, CP003629, and CP003639, respectively.
Received 1 August 2012 Accepted 29 August 2012 Address correspondence to Michael Pester,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.01392-12
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Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austriaa; Leibniz-Institut DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen), Braunschweig, Germanyb; Aix-Marseille University, Mediterranean Institute of Oceanography (MIO), UMR/ IRD 235, UMR/CNRS 7294 Equipe MEB, ESIL, Case 925, Marseille, Francec; Department of Computational Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austriad; U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USAe; Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science, Los Alamos, New Mexico, USAf; and Oak Ridge National Laboratory, Bioscience Division, Oak Ridge, Tennessee, USAg
Genome Announcement
ACKNOWLEDGMENTS The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. This research was further financially supported by the Austrian Science Fund (P23117-B17 to M. Pester; P20185-B17 to A. Loy).
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