Abstract
Acidovorax sp. strain NO1, isolated from gold mine soil, was shown to be a facultative anaerobic arsenite-oxidizing and nitrate-reducing bacterium. The reported draft genome predicts the presence of genes involved in arsenic metabolism, nitrate reduction, phosphate transport, and multiple metal resistances and indicates putative horizontal gene transfer events.
GENOME ANNOUNCEMENT
Acidovorax sp. strain NO1 was isolated from arsenic-contaminated soil of a gold mine in Daye, Hubei Province, China. It is highly arsenic resistant, with MICs of 20 mM and 200 mM for As(III) and As(V), respectively. Strain NO1 oxidized As(III) to As(V) aerobically and anaerobically with efficiencies of 121.7 μM h−1 OD−1 and 61.7 μM h−1 OD−1, respectively (where OD is optical density). It also reduced NO3− to NO2− under anaerobic conditions with an efficiency of 206.0 μM h−1 OD−1. Acidovorax sp. NO1 grew aerobically using 3-hydroxybenzoic acid as the sole carbon source. Strain NO1 was identified as a member of the genus Acidovorax using 16S rRNA sequence, fatty acid, and physiological/biochemical analyses.
Acidovorax is a bacterial genus whose main characteristics are that it is Gram-negative, has a motile rod with polar flagella, and is oxidase positive (13, 14). The sequenced genomes of Acidovorax members can be further separated into two groups, four environmental species, including those from soil and water habitats (NZ_ACQT00000000) (4, 6, 7), and three plant pathogens that cause fruit blotch or brown stripe (ADCB01000000) (3, 15), which makes the Acidovorax genus a good candidate for genome comparison to explore its different physiological and ecological roles.
The whole genomic sequence of Acidovorax sp. NO1, sequenced by a Roche 454 genome sequencer (GS) FLX instrument (9) and assembled by Roche GS Assembler version 2.0.01 software, contains 5,012,610 bp distributed in 167 contigs. The approximate genome coverage was 19 fold. CLC Sequence Viewer version 6.5.4 (CLC Bio) showed that Acidovorax sp. NO1 has an average GC content of 64.36%. The NCBI Prokaryotic Genomes Automatic Annotation Pipeline predicted 4,732 genes, with 46 tRNA genes, 1 rRNA gene, and 4,682 protein-coding genes (CDS), of which 3,816 were assigned to the clusters of orthologous groups (COG; http://www.ncbi.nlm.nih.gov/COG/). Genome comparison with reciprocal best BLAST demonstrated that Acidovorax sp. NO1 was most closely related to A. radicis strain N35 (3,050 CDS; E value, <1e−5; coverage, >50%; identity, >30%) (7), followed by A. delafieldii strain 2AN (2,845 CDS; NZ_ACQT00000000), Acidovorax sp. strain JS42 (2,532 CDS) (6), A. ebreus strain TPSY (2,531 CDS) (4), A. avenae ATCC 19860 (2,492 CDS; ADCB01000000), and A. citrulli strain AAC00-1 (2,481 CDS) (3).
Among all the sequenced Acidovorax strains, only strain NO1 has an aio operon responsible for arsenite oxidation (aioR-aioS-aioX-aioA-aioB-aioD-aioC) (5, 8, 9), found on contig 81 (AGTS01000077) with two adjacent arsenic resistance ars operons (arsH-arsC-acr3-arsC-arsR and arsR-arsC-arsD-arsA-CBS-arsB) (1, 8, 10) and a phosphate transport pst operon (pstS-pstC-pstA-pstB-phoU-phoR) (2, 8, 10). There is another ars operon (acr3-arsC-arsR) located on contig 75 (AGTS01000071). Both the arsR-arsC-arsD-arsA-CBS-arsB and acr3-arsC-arsR operons display putative horizontal gene transfer (HGT) origins. In addition to the pst cluster in the vicinity of the aio operon, strain NO1 has a pst cluster (pstS-pstC-pstA-pstB-phoU-phoB-phoR) on contig 147 (AGTS01000143) which is conserved in other Acidovorax strains that have only one pst cluster.
In contrast to other environmental Acidovorax strains that have a complete set of denitrification pathway genes (nar, nir, nor, and nos), strain NO1 contains nar, nor, and nos genes but lacks nir, which encodes nitrite reductase; in this way, it is the same as the arsenite-oxidizing strain MLHE-1 (11, 12).
Nucleotide sequence accession numbers.
The draft genome sequence of Acidovorax sp. NO1 has been deposited in DDBJ/EMBL/GenBank under accession number AGTS00000000. The version described in this paper is the first version, AGTS01000000.
ACKNOWLEDGMENTS
This work was supported by the National Natural Science Foundation of China (31170106).
Sequencing was performed at the University of Arizona Genetics Core.
REFERENCES
- 1. Achour AR, Bauda P, Billard P. 2007. Diversity of arsenite transporter genes from arsenic-resistant soil bacteria. Res. Microbiol. 158:128–137 [DOI] [PubMed] [Google Scholar]
- 2. Aguena M, Yagil E, Spira B. 2002. Transcriptional analysis of the pst operon of Escherichia coli. Mol. Genet. Genomics 268:518–524 [DOI] [PubMed] [Google Scholar]
- 3. Bahar O, Goffer T, Burdman S. 2009. Type IV pili are required for virulence, twitching motility, and biofilm formation of Acidovorax avenae subsp. citrulli. Mol. Plant Microbe Interact. 22:909–920 [DOI] [PubMed] [Google Scholar]
- 4. Byrne-Bailey KG, et al. 2010. Completed genome sequence of the anaerobic iron-oxidizing bacterium Acidovorax ebreus strain TPSY. J. Bacteriol. 192:1475–1476 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Cai L, Rensing C, Li X, Wang G. 2009. Novel gene clusters involved in arsenite oxidation and resistance in two arsenite oxidizers: Achromobacter sp. SY8 and Pseudomonas sp. TS44. Appl. Microbiol. Biotechnol. 83:715–725 [DOI] [PubMed] [Google Scholar]
- 6. Lee KS, Parales JV, Friemann R, Parales RE. 2005. Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42. J. Ind. Microbiol. Biotechnol. 32:465–473 [DOI] [PubMed] [Google Scholar]
- 7. Li D, et al. 2012. Phenotypic variation in Acidovorax radicis N35 influences plant growth promotion. FEMS Microbiol. Ecol. 79:751–762. [DOI] [PubMed] [Google Scholar]
- 8. Li X, et al. Genome sequence of a highly efficient arsenite-oxidizing bacterium, Achromobacter arsenitoxydans SY8. J. Bacteriol., in press [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Margulies M, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Muller D, et al. 2007. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet. 3:e53. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Oremland RS, et al. 2002. Anaerobic oxidation of arsenite in Mono Lake water and by a facultative, arsenite-oxidizing chemoautotroph, strain MLHE-1. Appl. Environ. Microbiol. 68:4795–4802 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Stolz JF, Basu P, Oremland RS. 2010. Microbial arsenic metabolism: new twists on an old poison. Microbe Mag. 5:53–59 [Google Scholar]
- 13. Willems A, et al. 1990. Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int. J. Syst. Evol. Microbiol. 40:384–398 [DOI] [PubMed] [Google Scholar]
- 14. Willems A, et al. 1992. Transfer of several phytopathogenic Pseudomonas species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov., Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci. Int. J. Syst. Evol. Microbiol. 42:107–119 [DOI] [PubMed] [Google Scholar]
- 15. Xie GL, et al. 2011. Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1. J. Bacteriol. 193:5013–5014 [DOI] [PMC free article] [PubMed] [Google Scholar]