Abstract
Here we report the draft genome sequence of strain Q-1, an iodide (I−)-oxidizing heterotrophic bacterium in the class Alphaproteobacteria isolated from natural gas brine water. The genome sequence contained a multicopper oxidase gene probably responsible for iodide oxidation. A photosynthetic gene cluster was found but genes for carbon-fixation were absent.
GENOME ANNOUNCEMENT
Iodide-oxidizing bacteria are able to oxidize iodide (I−) to molecular iodine (I2) and have been isolated from natural gas brine water containing very high concentrations (60 µM to 1.2 mM) of iodide (1). They are aerobic heterotrophic bacteria in the class Alphaproteobacteria and can also be enriched from natural seawater supplemented with iodide, due to much higher I2 tolerance than the other heterotrophic bacteria in seawater (2). Recently, such bacteria have been found to be involved in microbial clogging of well pipes in iodine-producing facilities (3, 4). Strain Q-1 was isolated from brine water in Miyazaki, Japan, and was phylogenetically related to the halophilic photosynthetic bacterium Rhodothalassium salexigens, with a 16S rRNA gene sequence similarity of 90% (1). This strain showed a strong iodide-oxidizing enzyme activity, which was later found to be one of multicopper oxidases (5). Here we report the draft genome sequence of strain Q-1.
Strain Q-1 was grown in Marine Broth 2216 (Becton Dickinson, Sparks, MD) and DNA was extracted using a DNeasy Blood & Tissue kit (Qiagen, Hilden, Germany). A DNA library with a median insert size of 200 bp was constructed. The library was sequenced on a genome analyzer II (Illumina, San Diego, CA), with a read length of 75 bp, trimmed to 40 bp prior to assembly. This produced a total of 11,698,620 paired-end read sequences with 468 Mb of total read data. Genome assembly was performed using SPAdes version 3.0.0 (6), yielding a collection of 109 contigs at least 200 bp long, with an N50 size of 102,443 bp. This assembly had 3,085,726 bp, with a genome coverage of 152× and a G+C content of 56.1%. Genome annotation was performed using Prokka 1.8 (7), yielding a total of 2,788 protein-coding genes (CDSs), 46 tRNA genes, and one copy of the 16S-23S-5S rRNA gene.
The genome contains one multicopper oxidase gene (ioxA), which was previously found to be involved in iodide oxidation by this strain (5). The genome also contains one continuous 45,135-bp-long photosynthetic gene cluster. The organization of the genes in the cluster is pufCMLAB-bchZYXC-crtFEDC-open reading frame (ORF)-crtBI-ORF-bchODI-ORFs-bchP-pucC-bchG-ppsR-ppaA-bchFNBHLM-lhaA-puhABC-ORF-acsF-puhE-hemA-tspO. There are no autotrophic CO2 fixation pathway genes such as those for ribulose-1,5-bisphosphate carboxylase/oxygenase and components of the reductive tricarboxylic acid (TCA) cycle in the draft genome sequence. A key gene encoding phosphofructokinase for glycolysis is absent, but a complete set of genes for the TCA cycle, pentose phosphate pathway, and Entner-Doudoroff pathway are predicted. The genome contains nitrate reductase genes (nar) but not nitrite reductase (nir) and nitrogenase (nif) genes. A complete set of genes for the type II secretion system (gsp) as well as for the flagellar system (fli, flg, and mot) was identified. Various proteins that may be involved in aerobic metabolism were identified, including NADH dehydrogenase, succinate dehydrogenase, cytochrome-c oxidase, catalase-peroxidase, and superoxide dismutase. These results suggest that strain Q-1 is one of the aerobic anoxygenic phototrophic bacteria.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. BAYV00000000. The version described in this paper is the first version, BAYV01000000.
ACKNOWLEDGMENTS
This work was partially supported by grants from JSPS KAKENHI (20780049), MEXT-Supported Program for the Strategic Research Foundation at Private Universities, 2013–2017 (S1311017), and the Institute of Fermentation, Osaka, Japan.
Footnotes
Citation Ehara A, Suzuki H, Kanesaki Y, Yoshikawa H, Amachi S. 2014. Draft genome sequence of strain Q-1, an iodide-oxidizing alphaproteobacterium isolated from natural gas brine water. Genome Announc. 2(4):e00659-14. doi:10.1128/genomeA.00659-14.
REFERENCES
- 1. Amachi S, Muramatsu Y, Akiyama Y, Miyazaki K, Yoshiki S, Hanada S, Kamagata Y, Ban-nai T, Shinoyama H, Fujii T. 2005. Isolation of iodide-oxidizing bacteria from iodide-rich natural gas brines and seawaters. Microb. Ecol. 49:547–557. 10.1007/s00248-004-0056-0 [DOI] [PubMed] [Google Scholar]
- 2. Arakawa Y, Akiyama Y, Furukawa H, Suda W, Amachi S. 2012. Growth stimulation of iodide-oxidizing α-Proteobacteria in iodide-rich environments. Microb. Ecol. 63:522–531. 10.1007/s00248-011-9986-5 [DOI] [PubMed] [Google Scholar]
- 3. Sugai Y, Sasaki K, Wakizono R, Higuchi Y, Muraoka N. 2013. Considerations on the possibility of microbial clogging of re-injection wells of the wastewater generated in a water-dissolved natural gas field. Int. Biodeterior. Biodegradation 81:35–43. 10.1016/j.ibiod.2012.10.003 [DOI] [Google Scholar]
- 4. Wakai S, Ito K, Iino T, Tomoe Y, Mori K, Harayama S. 27 May 2014. Corrosion of iron by iodide-oxidizing bacteria isolated from brine in an iodine production facility. Microb. Ecol. 10.1007/s00248-014-0438-x [DOI] [PubMed] [Google Scholar]
- 5. Suzuki M, Eda Y, Ohsawa S, Kanesaki Y, Yoshikawa H, Tanaka K, Muramatsu Y, Yoshikawa J, Sato I, Fujii T, Amachi S. 2012. Iodide oxidation by a novel multicopper oxidase from the alphaproteobacterium strain Q-1. Appl. Environ. Microbiol. 78:3941–3949. 10.1128/AEM.00084-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19:455–477. 10.1089/cmb.2012.0021 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Seemann T. 18 March 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 10.1093/bioinformatics/btu153 [DOI] [PubMed] [Google Scholar]