ABSTRACT

We report here the draft genome sequence of a strain of Tenacibaculum discolor (Bacteroidetes) that was isolated from the river-ocean interface at Trunk River in Falmouth, Massachusetts. The isolation and genomic sequencing were performed during the 2016 and 2018 Microbial Diversity summer programs at the Marine Biological Laboratory in Woods Hole, Massachusetts.

ANNOUNCEMENT

Tenacibaculum discolor strain IMLK18 was isolated from a seawater sample collected from the river-ocean interface between the Trunk River outlet and Vineyard Sound (Atlantic Ocean) in Falmouth, Massachusetts, in July 2016. A dilution of the seawater sample was cultured on sea water complete (SWC) agar at 25°C for 1 week. One colony exhibited iridescence in hues of green and orange; this was streaked for purity via three successive clonal picks. Surface translocation by gliding motility was observed. Strain IMLK18 is composed of rods of 1 μm in length. The 16S rRNA gene sequence of strain IMLK18 was analyzed after colony PCR amplification and Sanger DNA sequencing; it was 94% similar to that of T. discolor strain LL04 11.1.1. The LL04 11.1.1 strain of T. discolor was obtained from the kidney of a specimen of sole (Solea senegalensis, from Galicia, Spain) that displayed characteristics of marine fish disease flexibacteriosis, e.g., rotten mouth and fin and skin lesions (1).
The original isolate was stored at −80°C in SWC and 15% glycerol, and from this, a culture was grown on SWC agar and used to grow an overnight culture at 30°C in SWC broth. Genomic DNA was extracted from the pelleted cells from the liquid culture using the Maxwell RSC PureFood genetically modified organism (GMO) and authentication kit (Promega) and quantified using the double-stranded DNA (dsDNA) QuantiFluor ONE kit (Promega) using the Quantas system (Promega). Libraries were generated using the Nextera DNA flex library kit. Genome sequencing was conducted using the Illumina HiSeq 2500 platform (2 × 250-nucleotide [nt] paired-end reads). FastQC was utilized to assess the quality of the sequence reads. Genome assembly of 2,948,886 paired reads was performed using SPAdes 3.12.0 (2). The genome consists of 109 contigs yielding a total length of 3,388,982 bp, an N50 contig size of 431,359 bp, and coverage of 441×. The average G+C content was 31.60%. The average nucleotide identity (ANI) (3) value of 98.23% to the genome of T. discolor strain DSM 18842 is above the criterion (95%) for assignment to the same species, which indicates that strain IMLK18 is a new strain of T. discolor. Genome annotation was completed using Prodigal 2.6.1 (4) and resulted in 3,285 coding sequences (5). Gene annotation reveals the presence of genes involved in gliding motility and the type IX secretion system, including gldA and sprF that were previously shown to result in iridescent defects when disrupted in the bacterium Flavobacterium sp. strain IR1 (6, 7). Further research will provide insights into mechanisms of biological iridescence, as well fish pathogenicity by marine Bacteroidetes species. The genome sequence of T. discolor strain IMLK18 will improve our understanding and facilitate future comparative studies of the genus Tenacibaculum.

Data availability.

The GenBank accession number for this genome sequence is RCVH00000000, and the SRA accession number for the Illumina sequencing run is SRS4170023.

ACKNOWLEDGMENTS

This isolation and culturing of T. discolor IMLK18 were conducted during the 2016 Microbial Diversity summer course at the Marine Biological Laboratory (Woods Hole, MA), and genomic sequencing was conducted during the 2018 Microbial Diversity summer course. We thank Patrick Degnan, Whitney England, Rachel Whitaker, George O’Toole, Callie Rogers, Jose de la Torre, Gabriela Kovacikova, Titus Brown, and Kyle Costa for their assistance and advice. The Promega Corporation donated the molecular reagents used in this project.
H.L.K. was supported by funding from Stetson University and the Marine Biological Laboratory (Whitman Center Fellowship). Participation in and research activities during the summer program were supported by the Simons Foundation (grant 309981 to the Marine Biological Laboratory), the Helmsley Charitable Trust, the Waksman Foundation, Howard Hughes Medical Institute, the National Aeronautics and Space Administration (grant NNA13AA92A), the National Science Foundation (grant DEB-1822263), and the U.S. Department of Energy (grant DE-SC0016127). These funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publication.

REFERENCES

1.
Piñeiro-Vidal M, Riaza A, Santos Y. 2008. Tenacibaculum discolor sp. nov. and Tenacibaculum gallaicum sp. nov., isolated from sole (Solea senegalensis) and turbot (Psetta maxima) culture systems. Int J Syst Evol Microbiol 58:21–25.
2.
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.
3.
Rodriguez-R LM, Konstantinidis KT. 2014. Bypassing cultivation to identify bacterial species culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species. Microbe 9:111–117.
4.
Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
5.
Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57.
6.
McBride MJ, Zhu Y. 2013. Gliding motility and Por secretion system genes are widespread among members of the phylum bacteroidetes. J Bacteriol 195:270–278.
7.
Johansen VE, Catón L, Hamidjaja R, Oosterink E, Wilts BD, Rasmussen TS, Sherlock MM, Ingham CJ, Vignolini S. 2018. Genetic manipulation of structural color in bacterial colonies. Proc Natl Acad Sci USA 115:2652–2657.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 8Number 531 January 2019
eLocator: 10.1128/mra.01683-18
Editor: David Rasko, University of Maryland School of Medicine

History

Received: 18 December 2018
Accepted: 8 January 2019
Published online: 31 January 2019

Contributors

Authors

Department of Biology, Stetson University, Deland, Florida, USA
Irina V. Mikheyeva
Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
Rebecca L. Mickol
American Society for Engineering Education, Washington, DC, USA
Department of Microbiology and Molecular Genetics, College of Biological Science, University of California, Davis, Davis, California, USA
Division of Geological and Planetary Sciences, The California Institute of Technology, Pasadena, California, USA
Division of Biology & Biological Engineering, The California Institute of Technology, Pasadena, California, USA
Jared R. Leadbetter
Division of Biology & Biological Engineering, The California Institute of Technology, Pasadena, California, USA
Divisions of Engineering & Applied Science, The California Institute of Technology, Pasadena, California, USA

Editor

David Rasko
Editor
University of Maryland School of Medicine

Notes

Address correspondence to H. Lynn Kee, [email protected].

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