1887

Abstract

A taxonomic study was carried out on strain SH27, which was isolated from seawater collected around Xiaoshi Island, PR China. Cells of strain SH27 were Gram-stain-negative, non-motile, rod-shaped, orange-pigmented and grew at 15–37 °C (optimum, 28 °C), at pH 6.0–8.0 (pH 7.0) and in 1.0–7.0 % (w/v) NaCl (2.0–3.0 %). The isolate was positive for catalase, but negative for nitrate reduction, oxidase, indole production and urease. Carotenoid pigment was produced. Phylogenetic analysis based on the 16S rRNA gene placed strain SH27 in the genus with the closest relative being KCTC 12391, exhibiting 96.7 % 16S rRNA gene pairwise similarity. The results of genomic comparisons, including average nucleotide identity and digital DNA–DNA hybridization, showed 72.9 and 19.2 % identity to KCTC 12391, respectively. The major cellular fatty acids were iso-C, iso-C G and iso-C 3-OH. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Menaquinone-6 was the only respiratory quinone. The G+C content of the genomic DNA was 32.9 mol%. On the basis of the phenotypic and phylogenetic data, strain SH27 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain SH27 (MCCC 1H00358=CCTCC AB 2018323=KCTC 62962).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003949
2020-01-02
2020-01-24
Loading full text...

Full text loading...

References

  1. Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG et al. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J 2013;7:1026–1037 [CrossRef]
    [Google Scholar]
  2. Gómez-Pereira PR, Schüler M, Fuchs BM, Bennke C, Teeling H et al. Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ Microbiol 2012;14:52–66 [CrossRef]
    [Google Scholar]
  3. Sun C, Fu GY, Zhang CY, Hu J, Xu L et al. Isolation and complete genome sequence of Algibacter alginolytica sp. nov., a novel seaweed-degrading Bacteroidetes bacterium with diverse putative polysaccharide utilization loci. Appl Environ Microbiol 2016;82:2975–2987 [CrossRef]
    [Google Scholar]
  4. Williams TJ, Wilkins D, Long E, Evans F, DeMaere MZ et al. The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. Environ Microbiol 2013;15:1302–1317 [CrossRef]
    [Google Scholar]
  5. Bunse C, Pinhassi J. Marine bacterioplankton seasonal succession dynamics. Trends Microbiol 2017;25:494–505 [CrossRef]
    [Google Scholar]
  6. Bernardet JF, Nakagawa Y.An introduction to the family Flavobacteriaceae In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E. (editors) In The Prokaryotes7, 3rd edn. . New York: Springer; 2006; pp455–480
    [Google Scholar]
  7. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef]
    [Google Scholar]
  8. Yoon JH, Kang SJ, Lee CH, Oh TK. Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water. Int J Syst Evol Microbiol 2005;55:2323–2328 [CrossRef]
    [Google Scholar]
  9. Choi S, Kang JW, Kim MS, Yoon J-H, Seong CN. Dokdonia aurantiaca sp. nov., isolated from seaweed Zostera marina. Int J Syst Evol Microbiol 2018;68:1697–1701 [CrossRef]
    [Google Scholar]
  10. Khan ST, Nakagawa Y, Harayama S. Krokinobacter gen. nov., with three novel species, in the family Flavobacteriaceae. Int J Syst Evol Microbiol 2006;56:323–328 [CrossRef]
    [Google Scholar]
  11. Yoon JH, Kang SJ, Park S, Oh TK. Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005. Int J Syst Evol Microbiol 2012;62:1896–1901 [CrossRef]
    [Google Scholar]
  12. Choi S, Kang JW, Yoon JH, Seong CN. Dokdonia flava sp. nov., isolated from the seaweed Zostera marina. Int J Syst Evol Microbiol 2018;68:899–904 [CrossRef]
    [Google Scholar]
  13. Choi S, Kang JW, Lee JH, Seong CN. Dokdonia lutea sp. nov., isolated from Sargassum fulvellum seaweed. Int J Syst Evol Microbiol 2017;67:4482–4486 [CrossRef]
    [Google Scholar]
  14. Zhang Z, Gao X, Wang L, Zhang XH. Dokdonia pacifica sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2015;65:2222–2226 [CrossRef]
    [Google Scholar]
  15. Mu DS, Liang QY, Wang XM, Lu DC, Shi MJ et al. Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. Microbiome 2018;6:230 [CrossRef]
    [Google Scholar]
  16. Liu QQ, Li XL, Rooney AP, Du ZJ, Chen GJ et al. Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae. Int J Syst Evol Microbiol 2014;64:3473–3477 [CrossRef]
    [Google Scholar]
  17. Li R, Li Y, Kristiansen K, Wang J. Soap: short oligonucleotide alignment program. Bioinformatics 2008;24:713–714 [CrossRef]
    [Google Scholar]
  18. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265–272 [CrossRef]
    [Google Scholar]
  19. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 2008;12:137–141 [CrossRef]
    [Google Scholar]
  20. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. Kegg as a reference resource for gene and protein annotation. Nucleic Acids Res 2016;44:D457–D462 [CrossRef]
    [Google Scholar]
  21. Kanehisa M, Sato Y, Morishima K, BlastKOALA MK. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016;428:726–731 [CrossRef]
    [Google Scholar]
  22. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014;42:D206–D214 [CrossRef]
    [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef]
    [Google Scholar]
  24. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Soc Study Evol 1985;39:1–15
    [Google Scholar]
  26. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef]
    [Google Scholar]
  27. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. Dna-Dna hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef]
    [Google Scholar]
  28. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014;196:2210–2215 [CrossRef]
    [Google Scholar]
  29. Wayne LG. International Committee on systematic bacteriology: announcement of the report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988;268:433–434 [CrossRef]
    [Google Scholar]
  30. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013;14:913 [CrossRef]
    [Google Scholar]
  31. Fuhrman JA, Schwalbach MS, Stingl U. Proteorhodopsins: an array of physiological roles?. Nat Rev Microbiol 2008;6:488–494 [CrossRef]
    [Google Scholar]
  32. Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown LS et al. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014;114:126–163 [CrossRef]
    [Google Scholar]
  33. Inoue K, Kato Y, Kandori H. Light-Driven ion-translocating rhodopsins in marine bacteria. Trends Microbiol 2015;23:91–98 [CrossRef]
    [Google Scholar]
  34. Kwon SK, Kim BK, Song JY, Kwak MJ, Lee CH et al. Genomic makeup of the marine Flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins. Genome Biol Evol 2013;5:187–199 [CrossRef]
    [Google Scholar]
  35. Lois LM, Campos N, Putra SR, Danielsen K, Rohmer M et al. Cloning and characterization of a gene from Escherichia coli encoding a transketolase-like enzyme that catalyzes the synthesis of D-1-deoxyxylulose 5-phosphate, a common precursor for isoprenoid, thiamin, and pyridoxol biosynthesis. Proc Natl Acad Sci U S A 1998;95:2105–2110 [CrossRef]
    [Google Scholar]
  36. Wang N-N, Liu Z-Y, Jiang L-X, Li Y-X, Du Z-J. Roseovarius salinarum sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2018;68:1986–1991 [CrossRef]
    [Google Scholar]
  37. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000;50:1861–1868 [CrossRef]
    [Google Scholar]
  38. Zhou LY, Wang NN, Mu DS, Liu Y, Du ZJ. Coraliomargarita sinensis sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2019;69:701–707 [CrossRef]
    [Google Scholar]
  39. Cowan ST, Steel KJ, Characters B. Characterization, 2nd ed. Cambridge, UK: Cambridge University Press; 1974
    [Google Scholar]
  40. CLSI Performance Standards for Antimicrobial Susceptibility Testing, Twenty-Second Informational Supplement CLSI document M100-S22. Wayne, PA: Clinical and Laboratory Standards Institute; 2012
    [Google Scholar]
  41. Asker D, Beppu T, Ueda K. Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan. Int J Syst Evol Microbiol 2007;57:1435–1441 [CrossRef]
    [Google Scholar]
  42. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  43. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241 [CrossRef]
    [Google Scholar]
  44. Fang DB, Han JR, Liu Y, Du ZJ. Seonamhaeicola marinus sp. nov., isolated from marine algae. Int J Syst Evol Microbiol 2017;67:4857–4861 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003949
Loading
/content/journal/ijsem/10.1099/ijsem.0.003949
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error