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Announcement
14 May 2020

Complete Genome Sequence of Halomonas meridiana Strain Eplume2, Isolated from a Hydrothermal Plume in the Northeast Pacific Ocean

ABSTRACT

Halomonas meridiana strain Eplume2 (ATCC BAA-804) is a Gram-negative bacterium isolated from hydrothermal plume seawater in the Northeast Pacific Ocean at a depth of 2,000 m. Here, we report the complete genome sequence of this strain, which has a total size of 4.12 Mbp and a 56.6% G+C content.

ANNOUNCEMENT

Halomonas is a genus of Gram-negative haloalkaliphilic proteobacteria. Some of its members are isolated from hypersaline environments, and most require high salinity for growth. This group of bacteria is resilient to various environmental stresses and is expected to become a reliable model organism for bioindustrial applications (1), including for the production of useful secondary metabolites (2, 3). Halomonas meridiana was first isolated from the hypersaline lakes of Vestfold Hills, Antarctica, in 1990 (4). Here, we report the complete genome of H. meridiana strain Eplume2 (ATCC BAA-804), isolated from hydrothermal plume seawater in the Northeast Pacific Ocean.
Halomonus meridiana strain Eplume2 (ATCC BAA-804) was isolated by Kaye et al. from hydrothermal plume water of the Juan de Fuca Ridge in the Northeast Pacific Ocean at a depth of 2,000 m (5). The strain was obtained from the original discoverer, J. Z. Kaye, in lyophilized form and is identical to the strain available at the ATCC (BAA-804; https://www.atcc.org/products/all/BAA-804.aspx). The dried sample was rehydrated in SW10 culture solution and spread onto an SW10 agar plate. A single colony of this strain was cultured overnight using SW10 medium at 37°C, and the total genomic DNA was extracted and purified using a Genomic-tip 20/G kit following the manufacturer’s protocol (Qiagen). The DNA library for long-read sequencing was prepared using a rapid barcoding kit (SQK-RBK004; Oxford Nanopore Technologies), and sequencing was performed on the GridION device with a FLO-MIN106 flow cell (Oxford Nanopore Technologies). Illumina sequencing was performed for error correction using a KAPA HyperPlus kit for library preparation, and the library was sequenced as 75-bp single-end reads with a NextSeq 500 sequencer with high-output mode and 75 cycles (Illumina). After Nanopore sequencing, a total of 108,276 reads (N50, 15.8 kbp) were obtained, and reads longer than 10,000 bp, corresponding to around 60× coverage, were used for assembly using Canu v.1.8 (6). The assembled sequence was manually circularized by deleting the overlapping end. Error correction was performed by mapping all 52 million raw Illumina reads with the Burrows-Wheeler Aligner (BWA) v.0.7.11 (7), and then polishing was performed for four rounds using Pilon v.1.23 (8). Assembly completeness was checked with Benchmarking Universal Single-Copy Orthologs (BUSCO) v.1 (9) on the gVolante server (10) and resulted in 100% completeness of all 40 core genes. The obtained complete genome sequence was functionally annotated using the DDBJ Fast Annotation and Submission Tool (DFAST) pipeline (11). The annotated genome has a total length of 4,118,995 bp with a 56.6% G+C content, harboring 3,941 coding sequences (CDSs), 60 tRNAs, and 18 rRNAs. All software was run using default parameters.
According to the annotation results, H. meridiana strain Eplume2 carries numerous genes involved in sulfur metabolism, including a homolog of the sulfite reductase cysI (HMEPL2_05320), a well-known enzyme responsible for the conversion of SO32− (sulfite) to H2S (hydrogen sulfide) (12). This is in agreement with the initial report describing this strain as positive for H2S production (5). The search for analogs of H2S-responsive genes in halophilic species could lead to the development of biosensors for H2S in hypersaline environments.

Data availability.

The complete genome sequence of H. meridiana strain Eplume2 has been deposited in DDBJ under the accession number AP022869 and in the Sequence Read Archive (SRA) under the BioProject number PRJNA613015.

ACKNOWLEDGMENTS

We thank J. Z. Kaye, the original discoverer of the strain, for donating his stocks and Yumi Murai and Nao Takeuchi for technical support and suggestions. The sequencing and assembly were conducted in the Genome Engineering Workshop course of the Systems Biology Program, Graduate School of Media and Governance, Keio University.
This work was supported, in part, by research funds from the Yamagata prefectural government and from Tsuruoka City, Japan.

REFERENCES

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Ito S, Kobayashi T, Ara K, Ozaki K, Kawai S, Hatada Y. 1998. Alkaline detergent enzymes from alkaliphiles: enzymatic properties, genetics and structures. Extremophiles 2:185–190.
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Margesin R, Schinner F. 2001. Potential of halotolerant and halophilic microorganisms for biotechnology. Extremophiles 5:73–83.
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James SR, Dobson SJ, Franzmann PD, McMeekin TA. 1990. Halomonas meridiana, a new species of extremely halotolerant bacteria isolated from Antarctic saline lakes. Syst Appl Microbiol 13:270–278.
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Kaye JZ, Márquez MC, Ventosa A, Baross JA. 2004. Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments. Int J Syst Evol Microbiol 54:499–511.
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Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736.
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Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963.
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Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212.
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Nishimura O, Hara Y, Kuraku S. 2017. gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics 33:3635–3637.
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Tanizawa Y, Fujisawa T, Nakamura Y. 2018. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34:1037–1039.
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Hallenbeck PC, Clark MA, Barrett EL. 1989. Characterization of anaerobic sulfite reduction by Salmonella typhimurium and purification of the anaerobically induced sulfite reductase. J Bacteriol 171:3008–3015.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 9Number 2014 May 2020
eLocator: 10.1128/mra.00330-20
Editor: J. Cameron Thrash, University of Southern California

History

Received: 30 March 2020
Accepted: 20 April 2020
Published online: 14 May 2020

Contributors

Authors

Yu Kurihara
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Faculty of Policy Management, Keio University, Fujisawa, Japan
Shingo Kawai
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
Ayano Sakai
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Josephine Galipon
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan

Editor

J. Cameron Thrash
Editor
University of Southern California

Notes

Address correspondence to Kazuharu Arakawa, [email protected].
Yu Kurihara, Shingo Kawai, and Ayano Sakai contributed equally to this work. Author order was determined by the number of words written by each of the authors in the draft manuscript.

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