Search tips
Search criteria 


Logo of jbacterPermissionsJournals.ASM.orgJournalJB ArticleJournal InfoAuthorsReviewers
J Bacteriol. 2010 March; 192(5): 1475–1476.
Published online 2009 December 18. doi:  10.1128/JB.01449-09
PMCID: PMC2820844

Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY [down-pointing small open triangle]


Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for which there is a completed genome sequence. Preliminary protein annotation revealed an organism optimized for survival in a complex environmental system. Here, we briefly report the completed and annotated genome sequence of strain TPSY.

Microorganisms from diverse anoxic environments are capable of nitrate-dependent Fe(II) oxidation at circumneutral pH (4, 11, 17, 18, 20, 21). Despite their geochemical importance (22), little is known of the underlying biochemical and genetic mechanisms. Genome sequencing of several nitrate-dependent Fe(II) oxidizers will provide insight into this process. By comparing Fe(II) oxidation mechanisms in various organisms, we hope to identify both the conserved and disparate aspects of the metabolism. The genome of Acidovorax ebreus strain TPSY is the first of these to be sequenced.

Strain TPSY is a motile, Gram-negative facultative anaerobe isolated from groundwater collected from the U.S. Department of Energy Integrated Field Research Challenge site at Oak Ridge, TN. Growth experiments performed as previously described (21) revealed TPSY's incapacity for lithoautotrophic growth, which was supported by a lack of genes in the genome encoding any known CO2 fixation pathways. TPSY did grow mixotrophically with Fe(II) as the electron donor and a 0.1 mM acetate carbon source. 16S rRNA gene sequence analysis placed TPSY in the class Betaproteobacteria with 99.8% similarity to Acidovorax sp. strain JS42 in the family Comamonadaceae.

The completed genome consisted of a single circular chromosome of 3,796,573 bp with an average 66.8% G+C content. A total of 3,479 protein-encoding genes were predicted, and 34 (0.98%) had no similarity to public database sequences. Sequencing performed at the Department of Energy Joint Genome Institute (JGI) used Sanger sequencing and 454 pyrosequencing to a depth of 20× coverage. All JGI library construction and sequencing techniques can be found at Sequence assembly, quality assessment, and annotation were performed using the software Phred/Phrap/Consed ( (6-8), Dupfinisher (10), CRITICA (2), GLIMMER, and GENERATION (5) and the JGI Integrated Microbial Genomes site (12). The completed genome sequence contained 33,341 reads and had an average of ninefold coverage per base and an error rate of <1 in 100,000.

TPSY was named in part for its meandering motility, and its genome confirmed the twitching phenotype with the presence of pilT, pilU, and a complete set of flagellar and chemotaxis genes. The ability of TPSY to oxidize simple alcohols and acids with oxygen or nitrate respiration was confirmed by the genome. In addition, biosynthetic pathways for all amino acids except tyrosine and phenylalanine were present. No homologues of chorismate mutase (EC, an enzyme required for tyrosine and phenylalanine anabolism, were identified. The genome contained both intact Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in addition to a pentose phosphate pathway and a trichloroacetic acid cycle.

In support of its facultative anaerobicity, a complete set of genes for denitrification and three different terminal oxidases (cytochrome aa3, cbb3, and cytochrome d quinol oxidase) were present. The cbb3 and cytochrome d oxidases, with their high oxygen affinity, putatively enable survival in microaerobic environments (14).

TPSY had sequences encoding 30 transposases, 11 integrases, and 11 phage/prophage-related genes. A region of particular interest putatively conferred resistance to lead, arsenate, and mercury: pbrRATARTBC, arsRDAB, and merRPCADE. Evidence suggests horizontal transfer and insertion of this region, as it was flanked on the 5′ end by λ prophage-related genes and the 3′ end encoded a putative Tn21 transposase. Phenotypic studies by the method of Wang et al. (19) revealed MICs of 16 μM phenylmercuric acetate and 250 μM MgCl2. TPSY was also capable of growth in the presence of arsenate (10 mM) but did not use it as an electron acceptor.

Related to phage infection, one CRISPR (clustered, regularly interspaced, short palindromic repeats) region (3, 16) was predicted. The core proteins, the cas1 and cas2 genes, and a csn1 gene formed the CRISPR subtype Nmeni, which is associated with vertebrate pathogens and commensals (9). However, the lack of typical pathogenic type I or III secretion systems such as the hec cluster of Dickeya chrysanthemi (15) or the inv/spa system of Salmonella enterica serovar Typhimurium (13) indicated that TPSY would probably not exhibit a pathogenic lifestyle.

Nucleotide sequence accession number.

The genome sequence of Acidovorax ebreus strain TPSY (formerly Diaphorobacter sp. strain TPSY) reported in this paper has been deposited in the GenBank database under accession number NC_011992.


We thank Lynne Goodwin for her management of the sequencing project at the JGI.

This research was supported by Office of Science (BER), U.S. Department of Energy, grant DE-FG02-07ER64390 to J.D.C. at UCB and by the Nebraska Tobacco Settlement Biomedical Research Development Fund to K.A.W. at the University of Nebraska, Lincoln.

The sequencing work on behalf of J.D.C. was performed through the Community Sequencing Project 2008 for the JGI under the auspices of the U.S. Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California Lawrence Berkeley National Laboratory under contract DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344, and Los Alamos National Laboratory under contract DE AC02-06NA25396.


[down-pointing small open triangle]Published ahead of print on 18 December 2009.


1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410. [PubMed]
2. Badger, J. H., and G. J. Olsen. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16:512-524. [PubMed]
3. Barrangou, R., C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S. Moineau, D. A. Romero, and P. Horvath. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712. [PubMed]
4. Chaudhuri, S. K., J. G. Lack, and J. D. Coates. 2001. Biogenic magnetite formation through anaerobic biooxidation of Fe(II). Appl. Environ. Microbiol. 67:2844-2848. [PMC free article] [PubMed]
5. Delcher, A. L., D. Harmon, S. Kasif, O. White, and S. L. Salzberg. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636-4641. [PMC free article] [PubMed]
6. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186-194. [PubMed]
7. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8:175-185. [PubMed]
8. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202. [PubMed]
9. Haft, D. H., J. Selengut, E. F. Mongodin, and K. E. Nelson. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1:e60. [PubMed]
10. Han, C. S., and P. Chain. 2006. Finishing repeat regions automatically with Dupfinisher, p. 141-146. In H. R. Arabnia and H. Valafar (ed.), Proc. 2006 Int. Conf. Bioinformatics Comput. Biol. CSREA Press, Las Vegas, NV.
11. Lack, J. G., S. K. Chaudhuri, R. Chakraborty, L. A. Achenbach, and J. D. Coates. 2002. Anaerobic biooxidation of Fe(II) by Dechlorosoma suillum. Microb. Ecol. 43:424-431. [PubMed]
12. Markowitz, V. M., E. Szeto, K. Palaniappan, Y. Grechkin, K. Chu, I. M. Chen, I. Dubchak, I. Anderson, A. Lykidis, K. Mavromatis, N. N. Ivanova, and N. C. Kyrpides. 2008. The Integrated Microbial Genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 36:D528-D533. [PMC free article] [PubMed]
13. Nies, D. H. 1995. The cobalt, zinc, and cadmium efflux system CzcABC from Alcaligenes eutrophus functions as a cation-proton antiporter in Escherichia coli. J. Bacteriol. 177:2707-2712. [PMC free article] [PubMed]
14. Preisig, O., D. Anthamatten, and H. Hennecke. 1993. Genes for a microaerobically induced oxidase complex in Bradyrhizobium japonicum are essential for a nitrogen-fixing endosymbiosis. Proc. Natl. Acad. Sci. U. S. A. 90:3309-3313. [PubMed]
15. Rojas, C. M., J. H. Ham, W. L. Deng, J. J. Doyle, and A. Collmer. 2002. HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings. Proc. Natl. Acad. Sci. U. S. A. 99:13142-13147. [PubMed]
16. Sorek, R., V. Kunin, and P. Hugenholtz. 2008. CRISPR—a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6:181-186. [PubMed]
17. Straub, K. L., M. Benz, B. Schink, and F. Widdel. 1996. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl. Environ. Microbiol. 62:1458-1460. [PMC free article] [PubMed]
18. Straub, K. L., and B. E. E. Buchholz-Cleven. 1998. Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments. Appl. Environ. Microbiol. 64:4846-4856. [PMC free article] [PubMed]
19. Wang, Y., M. Moore, H. S. Levinson, S. Silver, C. Walsh, and I. Mahler. 1989. Nucleotide sequence of a chromosomal mercury resistance determinant from a Bacillus sp. with broad-spectrum mercury resistance. J. Bacteriol. 171:83-92. [PMC free article] [PubMed]
20. Weber, K. A., D. B. Hedrick, A. D. Peacock, J. C. Thrash, D. C. White, L. A. Achenbach, and J. D. Coates. 2009. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002. Appl. Microbiol. Biotechnol. 83:555-565. [PubMed]
21. Weber, K. A., J. Pollock, K. A. Cole, S. M. O'Connor, L. A. Achenbach, and J. D. Coates. 2006. Anaerobic nitrate-dependent iron(II) bio-oxidation by a novel lithoautotrophic betaproteobacterium, strain 2002. Appl. Environ. Microbiol. 72:686-694. [PMC free article] [PubMed]
22. Weber, K. A., M. M. Urrutia, P. F. Churchill, R. K. Kukkadapu, and E. E. Roden. 2006. Anaerobic redox cycling of iron by freshwater sediment microorganisms. Environ. Microbiol. 8:100-113. [PubMed]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)