Abstract
Here, we report the whole-genome sequence of Aquamicrobium sp. strain SK-2, a bacterium which can use 2,2′,4,4′,5,5′-hexachlorobiphenyl as the sole carbon source for its growth. An approximately 9.23-Mb genome sequence of SK-2 will greatly facilitate research efforts regarding the study of the polychlorinated biphenyl (PCB) degradation mechanism.
GENOME ANNOUNCEMENT
Biphenyl and polychlorinated biphenyl (PCB) (a synthetic biphenyl) are persistent organic pollutants in the environment and are causing serious environmental problems around the world (1). In Japan, the manufacture, import, and use of PCBs were prohibited in 1974. However, environmental pollution with PCB is still ubiquitous in Japan. Aquamicrobium sp. strain SK-2 (accession no. AB612121) was originally isolated from sewage sludge in South Korea, and it can utilize PCB congeners containing one to six chlorine substituents, such as 2,2′,4,4′,5,5′-hexachlorobiphenyl (2). Strain SK-2 can also degrade biphenyl and PCB in the presence of high concentrations of NaCl and nitrate. In addition, the PCB degradation rate of strain SK-2 is higher than that of previously reported PCB congener-degrading bacteria (3, 4). Therefore, the isolated strain SK-2 might be a good candidate for the bioremediation of PCB-contaminated soil, especially in high-saline soils. Therefore, the whole-genome sequence of Aquamicrobium sp. SK-2 is reported here, and it can be useful for further investigating the roles of genes that are involved in biphenyl and PCB degradation.
We report the whole-genome sequence of Aquamicrobium sp. SK-2, the first whole-genome sequence of the genus Aquamicrobium and the first whole-genome sequence of the hexachlorobiphenyl-utilizing bacterium. Strain SK-2 was sequenced using a multiplex (8 samples on one lane) Illumina HiSeq 2000/2500 platform, yielding 29.8 million reads at 325× coverage. For the SK-2 datasets, we assembled the reads into a set of 180 contigs using Velvet (version 1.2.08) (5). The final circular genome of SK-2 has 9,230,439 bp, with an overall G+C content of 66%. Sequence annotation and open reading frame (ORF) prediction were performed using the Rapid Annotations using Subsystems Technology (RAST) version 2.0 pipeline (6). The rRNAs and tRNAs were identified using the search_for_RNAs script developed by Niels Larsen (6) and tRNAscan-SE (7), respectively. By these analyses, 96 tRNAs and 4 rRNA operons, comprising 5S, 16S, and 23S rRNA genes, were detected in the genome of SK-2.
Strain SK-2 has a genome (9.23 Mb) similar to those of other PCB degraders, such as Burkholderia xenovorans LB400 (9.73 Mb) (8), Rhodococcus jostii RHA1 (9.70 Mb) (9), and Rhodococcus sp. strain R04 (9.13 Mb) (10). The SK-2 whole-genome sequence may assist in the improvement of PCB bioremediation technology.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers BBWE01000001 to BBWE01000180 (BioProject no. PRJDB93210).
ACKNOWLEDGMENTS
We thank M. Venkateswar Reddy of the Muroran Institute of Technology for helpful suggestion and critical reading of the manuscript.
This work was partially supported by a grant-in-aid for scientific research (no. 26340067) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
Footnotes
Citation Chang Y-C, Sawada K, Kim E-S, Jung K, Kikuchi S. 2015. Whole-genome sequence of Aquamicrobium sp. strain SK-2, a polychlorinated biphenyl-utilizing bacterium isolated from sewage sludge. Genome Announc 3(3):e00439-15. doi:10.1128/genomeA.00439-15.
REFERENCES
- 1.Pieper DH. 2005. Aerobic degradation of polychlorinated biphenyls. Appl Microbiol Biotechnol 67:170–191. doi: 10.1007/s00253-004-1810-4. [DOI] [PubMed] [Google Scholar]
- 2.Chang YC, Takada K, Choi D, Toyama T, Sawada K, Kikuchi S. 2013. Isolation of biphenyl and polychlorinated biphenyl-degrading bacteria and their degradation pathway. Appl Biochem Biotechnol 170:381–398. doi: 10.1007/s12010-013-0191-5. [DOI] [PubMed] [Google Scholar]
- 3.Hatamian-Zarmi A, Shojaosadati SA, Vasheghani-Farahani E, Hosseinkhani S, Emamzadeh A. 2009. Extensive biodegradation of highly chlorinated biphenyl and Aroclor 1242 by Pseudomonas aeruginosa TMU56 isolated from contaminated soils. Int Biodeter Biodegr 63:788–794. doi: 10.1016/j.ibiod.2009.06.009. [DOI] [Google Scholar]
- 4.Adebusoye SA, Picardal FW, Ilori MO, Amund OO. 2008. Evidence of aerobic utilization of di-ortho-substituted trichlorobiphenyls as growth substrates by Pseudomonas sp. SA-6 and Ralstonia sp. SA-4. Environ Microbiol 10:1165–1174. doi: 10.1111/j.1462-2920.2007.01533.x. [DOI] [PubMed] [Google Scholar]
- 5.Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi: 10.1101/gr.074492.107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS Web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–W689. doi: 10.1093/nar/gki366. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA 103:15280–15287. doi: 10.1073/pnas.0606924103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. 2006. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A 103:15582–15587. doi: 10.1073/pnas.0607048103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Yang X, Xue R, Shen C, Li S, Gao C, Wang Q, Zhao X. 2011. Genome sequence of Rhodococcus sp. strain R04, a polychlorinated-biphenyl biodegrader. J Bacteriol 193:5032–5033. doi: 10.1128/JB.05635-11. [DOI] [PMC free article] [PubMed] [Google Scholar]