ABSTRACT
Pseudomonas resinovorans strain MO-1, which possesses a high ability to oxidize Mn(II), has been isolated from oligotrophic pond sediment. The draft genome sequence consists of 6,252,942 bp and has a G+C content of 63.4%. Strain MO-1 has 5,694 coding sequences, including 13 putative Mn(II) oxidation genes.
GENOME ANNOUNCEMENT
Mn(II)-oxidizing bacteria (MnOB) produce biogenic Mn(III, IV) oxides (Bio-MnOx) in a wide variety of environments (1). The produced Bio-MnOx is abundant in natural environments and adsorbs metal ions and/or oxidizes metals (2), thereby contributing to the oxidation of organic matter (3, 4). Phylogenetically diverse MnOB species exist, many with differing Mn(II) oxidation abilities (5). However, the oxidation mechanisms are still not fully elucidated. Additionally, why MnOB oxidize Mn(II) at all remains unclear (6). The isolation and characterization of diverse MnOB are essential for solving these questions. We isolated and screened more than 50 strains of MnOB from various environments and identified the strain with the highest Mn(II) oxidation ability from a manganese- and iron-rich sediment in an oligotrophic pond (34°39.891′N, 132°71.226′E). We named this bacterium MO-1; it is a Pseudomonas resinovorans strain, yet surprisingly, it has not been confirmed as a MnOB. Here, we present the draft genome sequence and putative Mn(II) oxidation genes of strain MO-1.
Strain MO-1 genomic DNA was extracted using a commercial kit (NucleoSpin tissue kit; Macherey-Nagel), according to the manufacturer’s protocol. The extracted DNA was sequenced using a 101-bp paired-end sequencing method with an Illumina HiSeq 2500 platform at Hokkaido System Science Co., Ltd. (Sapporo, Japan), obtaining 22,074,708 reads, with approximately 350-fold genome coverage. After the adaptors were trimmed using the Trimmomatic program version 0.36 (7), the cleaned sequence reads were assembled using the Platanus program version 1.2.4 (8). We obtained 122 contigs by removing short contigs of less than 300 bp, resulting in a draft genome of 6,252,942 bp, with a G+C content of 63.4%. The longest contig has 314,004 bp, and the calculated N50 length is 110,654 bp. The draft genome was annotated using the Microbial Genome Annotation Pipeline (MiGAP) version 1.060 (http://www.migap.org/) and was estimated to have 5,694 coding sequences (CDSs), including 2 rRNA genes and 61 tRNA genes.
Two gene families encoding multicopper oxidase (MCO) and heme peroxidase oxidase domains play an important role in Mn(II) oxidation in several MnOB. Of our 5,694 CDSs, 1, 8, and 4 CDSs were identified as being related to Mn(II) oxidation; these were homologous to mnxG (locus tag PputGB1_2447 under GenBank accession no. CP000926), mcoA (locus tag PputGB1_2665 under GenBank accession no. CP000926) and mopA (locus tag PputGB1_3353 under GenBank accession no. CP000926) of Pseudomonas putida GB-1 (9, 10), respectively, using BLASTP analysis (E value ≤ e−50) (11). The highest similarities between our sequences and those P. putida sequences calculated by the Needleman-Wunsch global alignment algorithm (12) are 82.2, 67.3, and 56.7% for mnxG, mcoA, and mopA, respectively. Strain MO-1 possesses 13 putative Mn(II) oxidation genes, much more than the 3 annotated Mn(II) oxidation genes in P. putida GB-1.
Accession number(s).
The P. resinovorans strain MO-1 genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession no. BDMA00000000. The version described in this paper is the first version, BDMA01000000.
ACKNOWLEDGMENTS
This research was supported by the Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Scientific Research (A) no. JP23241029.
We thank Steven M. Thompson from the Edanz Group for editing a draft of the manuscript.
Footnotes
Citation Matsushita S, Nakano M, Aoi Y, Kindaichi T, Ozaki N, Ohashi A. 2018. Draft genome sequence of Mn(II)-oxidizing Pseudomonas resinovorans strain MO-1. Genome Announc 6:e00088-18. https://doi.org/10.1128/genomeA.00088-18.
REFERENCES
- 1.Tebo BM, Bargar JR, Clement BG, Dick GJ, Murray KJ, Parker D, Verity R, Webb SM. 2004. Biogenic manganese oxides: properties and mechanisms of formation. Annu Rev Earth Planet Sci 32:287–328. doi: 10.1146/annurev.earth.32.101802.120213. [DOI] [Google Scholar]
- 2.Tebo BM, Johnson HA, McCarthy JK, Templeton AS. 2005. Geomicrobiology of manganese(II) oxidation. Trends Microbiol 13:421–428. doi: 10.1016/j.tim.2005.07.009. [DOI] [PubMed] [Google Scholar]
- 3.Cao LTT, Kodera H, Abe K, Imachi H, Aoi Y, Kindaichi T, Ozaki N, Ohashi A. 2015. Biological oxidation of Mn(II) coupled with nitrification for removal and recovery of minor metals by downflow hanging sponge reactor. Water Res 68:545–553. doi: 10.1016/j.watres.2014.10.002. [DOI] [PubMed] [Google Scholar]
- 4.Matsushita S, Komizo D, Cao LTT, Aoi Y, Kindaichi T, Ozaki N, Imachi H, Ohashi A. 2018. Production of biogenic manganese oxides coupled with methane oxidation in a bioreactor for removing metals from wastewater. Water Res 130:224–233. doi: 10.1016/j.watres.2017.11.063. [DOI] [PubMed] [Google Scholar]
- 5.Spiro TG, Bargar JR, Sposito G, Tebo BM. 2010. Bacteriogenic manganese oxides. Acc Chem Res 43:2–9. doi: 10.1021/ar800232a. [DOI] [PubMed] [Google Scholar]
- 6.Geszvain K, Butterfield CN, Davis RE, Madison AS, Lee S-W, Parker DL, Soldatova AV, Spiro TG, Luther GW, Tebo BM. 2012. The molecular biogeochemistry of manganese(II) oxidation. Biochem Soc Trans 40:1244–1248. doi: 10.1042/BST20120229. [DOI] [PubMed] [Google Scholar]
- 7.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T. 2014. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24:1384–1395. doi: 10.1101/gr.170720.113. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Geszvain K, McCarthy JK, Tebo BM. 2013. Elimination of manganese(II, III) oxidation in Pseudomonas putida GB-1 by a double knockout of two putative multicopper oxidase genes. Appl Environ Microbiol 79:357–366. doi: 10.1128/AEM.01850-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Geszvain K, Smesrud L, Tebo BM. 2016. Identification of a third Mn(II) oxidase enzyme in Pseudomonas putida GB-1. Appl Environ Microbiol 82:3774–3782. doi: 10.1128/AEM.00046-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic Local Alignment Search Tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- 12.Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]