Abstract
Sphingobium chinhatense strain IP26T is a conducive hexachlorocyclohexane (HCH) degrader isolated from a heavily contaminated (450 mg HCH/g soil) HCH dumpsite. IP26T degrades α-, β-, γ-, and δ-HCH, which are highly persistent in the environment. Here we report the draft genome sequence (~5.8 Mbp) of this strain.
GENOME ANNOUNCEMENT
In order to study the evolution of hexachlorocyclohexane (HCH)-degrading phenotypes at intragenus level among sphingomonads, we have isolated several HCH-degrading and/or -tolerating genotypes, including Sphingobium chinhatense strain IP26T from the HCH dumpsite (1) located at Chinhat, Lucknow (26°54′ N and 81°09′ E), India. Gas-liquid chromatography-based HCH isomer degradation analysis (time dependent) revealed that IP26T is a faster degrader of HCH isomers than the prototype bacterium Sphingobium indicum strain B90AT (2).
A draft genome sequence of S. chinhatense IP26T was obtained by use of Illumina Genome Analyzer IIx and 454 GS FLX titanium platforms, which generated ~1.4 Gb (pair-end) and ~116 Mb (single-end) sequencing data with coverage of 131- and 20-fold, respectively. Raw data were assembled into contigs (n = 236, >500 bp) using the ABySS 1.3.3 assembler (3) set at a k-mer size of 61. The assembled genome had an N50 value of 142 kb and an average GC content of 64.1%. The draft genome was annotated using RAST version 4.0 (4) and NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 2.1 (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), which identified 5,703 protein-coding genes and 10 pseudogenes. Eleven rRNA and 66 tRNA genes were also predicted using PGAP annotations. A contig of size 5,392 bp possessing similar coding sequences (CDS) to plasmid pUT2 (5,398 bp) of S. japonicum UT26 (5) was also identified. Whole-genome-based average nucleotide identity (ANI) (6) comparisons revealed that Sphingobium indicum B90AT (97.98%), Sphingobium japonicum UT26S (97.79%), Sphingobium chlorophenolicum L-1 (90.55%), and Sphingomonas SKA58 (80.29%) are the closest phylogenetic neighbors of IP26T.
The potential to metabolize HCH isomers and a wide range of aromatic hydrocarbons is predicted from the genome. For instance, HCH-degrading lin genes associated with IS6100 elements were present in the genome assembly. IS6100 elements (n = 19) were identified using ISFinder (7). A full-length (1 kb) IS6100 element was observed with linA, linB, linC, and linR genes. In addition, a partial (~331 bp) IS6100 element was also observed with linF, linG, linH, linI, and linJ genes. The presence of 30 transposases and 24 phage integrases indicates that the genome is subjected to ongoing genetic rearrangement. Furthermore, phenol/toluene and chlorophenol degradation pathways were observed in IP26T. Unlike the genome of S. indicum B90AT (2), the draft genome assembly of IP26T was found to have a homogentisate degradation pathway. Genes encoding putative metal resistance/efflux proteins, including resistance proteins for lead, mercury, arsenic, copper, cobalt, cadmium, and zinc, were also identified.
Further analysis of this genome, coupled with the metagenomic data from the HCH dumpsite (8, 9), will be used to understand the possible mechanism of acquisition of lin genes and other catabolic genes in the sphingomonads, along with the highly diverse microbial community that has been reported from the HCH dumpsite (8, 9). In addition, sequencing and analysis of more HCH-degrading genotypes from the HCH dumpsite will augment the ongoing efforts to understand the pangenomic aspects of this widely distributed genus at the HCH dumpsite and will reveal the ambiguities that exist in the horizontal gene transfer (HGT) of lin genes and other catabolic genes involved in the biodegradation of aromatic compounds.
Nucleotide sequence accession numbers.
The draft genome sequence of S. chinhatense IP26T is available in GenBank database under accession number AUDA00000000. The version described in this paper is the first version, AUDA01000000.
ACKNOWLEDGMENTS
The work was supported by grants from the Department of Biotechnology (DBT), Government of India, under project BT/PR3301/BCE/8/875/11, University of Delhi/Department of Science and Technology Promotion of University Research and Scientific Excellence-DU-DST—PURSE, and the National Bureau of Agriculturally Important Microorganisms (NBAIM) AMASS/2006–07/NBAIM/CIR and All India Network Project Soil Biodiversity-Biofertilizer (ICAR). N.N., N.S., S.A., and P.S. gratefully acknowledge the Council for Scientific and Industrial Research (CSIR) and the University Grants Commission (UGC), New Delhi, for providing research fellowships.
Footnotes
Citation Niharika N, Sangwan N, Ahmad S, Singh P, Khurana JP, Lal R. 2013. Draft genome sequence of Sphingobium chinhatense strain IP26T, isolated from a hexachlorocyclohexane dumpsite. Genome Announc. 1(4):e00680-13. doi:10.1128/genomeA.00680-13.
REFERENCES
- 1. Dadhwal M, Jit S, Kumari H, Lal R. 2009. Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. Int. J. Syst. Evol. Microbiol. 59:3140–3144. 10.1099/ijs.0.005553-0 [DOI] [PubMed] [Google Scholar]
- 2. Anand S, Sangwan N, Lata P, Kaur J, Dua A, Singh AK, Verma M, Kaur J, Khurana JP, Khurana P, Mathur S, Lal R. 2012. Genome sequence of Sphingobium indicum B90A, a hexachlorocyclohexane-degrading bacterium. J. Bacteriol. 194:4471–4472. 10.1128/JB.00901-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol İ. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117–1123. 10.1101/gr.089532.108 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. 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. 10.1186/1471-2164-9-75 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Nagata Y, Natsui S, Endo R, Ohtsubo Y, Ichikawa N, Ankai A, Oguchi A, Fukui S, Fujita N, Tsuda M. 2011. Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium. Enzyme Microb. Technol. 49:499–508. 10.1016/j.enzmictec.2011.10.005 [DOI] [PubMed] [Google Scholar]
- 6. Konstantinidis KT, Tiedje JM. 2005. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 187:6258–6264. 10.1128/JB.187.18.6258-6264.2005 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. 2006. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34:D32–D36. 10.1093/nar/gkj014 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, Kaur J, Anand S, Malhotra J, Jindal S, Nigam A, Lal D, Dua A, Saxena A, Garg N, Verma M, Kaur J, Mukherjee U, Gilbert JA, Dowd SE, Raman R, Khurana P, Khurana JP, Lal R. 2012. Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels. PLoS One 7:e46219. 10.1371/journal.pone.0046219 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Sangwan N, Verma H, Kumar R, Negi V, Lax S, Khurana P, Khurana JP, Gilbert JA, Lal R. Reconstructing an ancestral genotype of two hexachlorocyclohexane degrading Sphingobium species using metagenomic sequence data. ISME J., in press [DOI] [PMC free article] [PubMed] [Google Scholar]