1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 9

sp. nov. and sp. nov., two novel bacteria isolated from intertidal sediment No Access

Abstract

Two novel Gram-stain-negative, facultative anaerobic, chemoheterotrophic, non-motile and rod-shaped strains were isolated from intertidal sediment sampled at Xiaoshi Island, Weihai, PR China. Full sequence analysis of the 16S rRNA genes showed that the two strains were closely related to members of the genus and the phylogenetic similarities to their closest relative, , were 96.7 and 95.8 %, respectively. The DNA G+C contents of strains 2Y89 and D23 were 33.3 and 35.1 mol%, respectively. The respiratory quinone detected in both strains was MK-6. The major fatty acids detected in strain 2Y89 were iso-C and iso-CG, and in strain D23 they were iso-CG, iso-C and iso-C3–OH. The principal polar lipids of strain 2Y89 mainly included phosphatidylethanolamine, aminoglycolipids, unidentified aminolipids, unidentified glycolipids and unidentified lipids; strain D23 was the same as strain 2Y89 except that it did not contain aminoglycolipids. Based on the phenotypic, chemical taxonomic, genotypic and phylogenetic features established in this study, we suggest that the new strains represent two novel species of the genus , for which the names sp. nov. (type strain 2Y89=MCCC 1H00477=KCTC 92034) and sp. nov. (type strain D23=MCCC 1H00462=KCTC 92023) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome , phylogenetic , Winogradskyella alexanderae and Winogradskyella vincentii
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32070002)
    • Principle Award Recipient: Zong-JunDu
  • Science & Technology Fundamental Resources Investigation Program (Award No. 2022FY101100, 2019FY100700)
    • Principle Award Recipient: Zong-JunDu
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006039
2023-09-26
2024-05-08
Loading full text...

Full text loading...

References

  1. Nedashkovskaya OI, Kim SB, Han SK, Snauwaert C, Vancanneyt M et al. Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2005; 55:49–55 [View Article] [PubMed]
     [Google Scholar]
  2. Ivanova EP, Christen R, Gorshkova NM, Zhukova NV, Kurilenko VV et al. Winogradskyella exilis sp. nov., isolated from the starfish Stellaster equestris, and emended description of the genus Winogradskyella. Int J Syst Evol Microbiol 2010; 60:1577–1580 [View Article]
     [Google Scholar]
  3. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:10 [View Article]
     [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  5. Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV. Winogradskyella ulvae sp. nov., an epiphyte of a Pacific seaweed, and emended descriptions of the genus Winogradskyella and Winogradskyella thalassocola, Winogradskyella echinorum, Winogradskyella exilis and Winogradskyella eximia. Int J Syst Evol Microbiol 2012; 62:1450–1456 [View Article] [PubMed]
     [Google Scholar]
  6. Yoon B-J, Byun H-D, Kim J-Y, Lee D-H, Kahng H-Y et al. Winogradskyella lutea sp. nov., isolated from seawater, and emended description of the genus Winogradskyella. Int J Syst Evol Microbiol 2011; 61:1539–1543 [View Article] [PubMed]
     [Google Scholar]
  7. Pinhassi J, Nedashkovskaya OI, Hagström A, Vancanneyt M. Winogradskyella rapida sp. nov., isolated from protein-enriched seawater. Int J Syst Evol Microbiol 2009; 59:2180–2184 [View Article] [PubMed]
     [Google Scholar]
  8. Kang H, Kim H, Joung Y, Joh K. Winogradskyella maritima sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:3840–3845 [View Article]
     [Google Scholar]
  9. Kang CH, Lee SY, Yoon JH. Winogradskyella litorisediminis sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2013; 63:1793–1799 [View Article] [PubMed]
     [Google Scholar]
  10. Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Winogradskyella arenosi sp. nov., a member of the family Flavobacteriaceae isolated from marine sediments from the Sea of Japan. Int J Syst Evol Microbiol 2009; 59:1443–1446 [View Article] [PubMed]
     [Google Scholar]
  11. Ivanova EP, Alexeeva YV, Flavier S, Wright JP, Zhukova NV et al. Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2004; 54:705–711 [View Article] [PubMed]
     [Google Scholar]
  12. Martin M, Barbeyron T, Martin R, Portetelle D, Michel G et al. The cultivable surface microbiota of the brown alga Ascophyllum nodosum is enriched in macroalgal-polysaccharide-degrading bacteria. Front Microbiol 2015; 6:1487 [View Article] [PubMed]
     [Google Scholar]
  13. Park SH, Kim JY, Kim YJ, Heo MS. Flavobacterium jejuensis sp. nov., isolated from marine brown alga Ecklonia cava. J Microbiol 2015; 53:756–761 [View Article] [PubMed]
     [Google Scholar]
  14. Cho ES, Cha IT, Choi HJ, Roh SW, Nam YD et al. Zunongwangia flava sp. nov., belonging to the family Flavobacteriaceae, isolated from Salicornia europaea. J Microbiol 2018; 56:868–873 [View Article] [PubMed]
     [Google Scholar]
  15. Schellenberg J, Busse H-J, Hardt M, Schubert P, Wilke T et al. Winogradskyella haliclonae sp. nov., isolated from a marine sponge of the genus Haliclona. Int J Syst Evol Microbiol 2017; 67:4902–4910 [View Article] [PubMed]
     [Google Scholar]
  16. Franco A, Busse H-J, Schubert P, Wilke T, Kämpfer P et al. Winogradskyella pocilloporae sp. nov. isolated from healthy tissue of the coral Pocillopora damicornis. Int J Syst Evol Microbiol 2018; 68:1689–1696 [View Article] [PubMed]
     [Google Scholar]
  17. Park S, Park JM, Won SM, Yoon JH. Winogradskyella crassostreae sp. nov., isolated from an oyster (Crassostrea gigas). Int J Syst Evol Microbiol 2015; 65:2890–2895 [View Article]
     [Google Scholar]
  18. Nedashkovskaya OI, Vancanneyt M, Kim SB, Zhukova NV. Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 2009; 59:1465–1468 [View Article] [PubMed]
     [Google Scholar]
  19. Valdenegro-Vega V, Naeem S, Carson J, Bowman JP, Tejedor del Real JL et al. Culturable microbiota of ranched southern bluefin tuna (Thunnusmaccoyii Castelnau). J Appl Microbiol 2013; 115:923–932 [View Article] [PubMed]
     [Google Scholar]
  20. Liu QQ, Wang Y, Li J, Du ZJ, Chen GJ. Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans. Int J Syst Evol Microbiol 2014; 64:2204–2209 [View Article] [PubMed]
     [Google Scholar]
  21. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  22. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  23. 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 [View Article] [PubMed]
     [Google Scholar]
  24. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  26. St. John K. Review paper: the shape of phylogenetic treespace. Syst Biol 2017; 66:e83–e94 [View Article] [PubMed]
     [Google Scholar]
  27. Felsenstein J. PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Seattle, USA: Department of Genome Sciences, University of Washington; 1993
  28. Li R, Yu C, Li Y, Lam T-W, Yiu S-M et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009; 25:1966–1967 [View Article] [PubMed]
     [Google Scholar]
  29. 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 [View Article] [PubMed]
     [Google Scholar]
  30. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  31. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  32. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
     [Google Scholar]
  33. Ju Z, Zhang R, Hou X-J, Han S-B, Li Y et al. Kordiimonas pumila sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2018; 68:1743–1748 [View Article] [PubMed]
     [Google Scholar]
  34. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article] [PubMed]
     [Google Scholar]
  35. Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 2016; 44:W232–5 [View Article] [PubMed]
     [Google Scholar]
  36. Feng X, Zou QH, Zhang XY, Ye MQ, Du ZJ. Oceanipulchritudo coccoides gen. nov., sp. nov., isolated from marine sediment within the family Puniceicoccaceae. Int J Syst Evol Microbiol 2020; 70:5654–5664 [View Article] [PubMed]
     [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 Pt 5:1861–1868 [View Article] [PubMed]
     [Google Scholar]
  38. Song J, Lim Y, Jang H-J, Joung Y, Kang I et al. Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta. J Microbiol 2019; 57:982–990 [View Article] [PubMed]
     [Google Scholar]
  39. Zhang J, Wang C, Han J-R, Chen G-J, Du Z-J. Alteromonas flava sp. nov. and Alteromonas facilis sp. nov., two novel copper tolerating bacteria isolated from a sea cucumber culture pond in China. Syst Appl Microbiol 2019; 42:217–222 [View Article] [PubMed]
     [Google Scholar]
  40. Smibert R, Krieg N, Gerhardt P, Murray R, Wood W. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  41. Kronvall G, Ringertz S. Antibiotic disk diffusion testing revisited. Single strain regression analysis. Review article. APMIS 1991; 99:295–306 [View Article] [PubMed]
     [Google Scholar]
  42. Dong XZ, Cai MY. Determination of biochemical characteristics. In Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001 pp 370–398
     [Google Scholar]
  43. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark: MIDI Inc; 1990
     [Google Scholar]
  44. Athalye M, Noble WC, Minnikin DE. Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 1985; 58:507–512 [View Article] [PubMed]
     [Google Scholar]
  45. Eder K. Gas chromatographic analysis of fatty acid methyl esters. J Chromatogr B 1995; 671:113–131 [View Article] [PubMed]
     [Google Scholar]
  46. Collins MD, Goodfellow M, Minnikin DE. Fatty acid, isoprenoid quinone and polar lipid composition in the classification of Curtobacterium and related taxa. J Gen Microbiol 1980; 118:29–37 [View Article] [PubMed]
     [Google Scholar]
  47. Bo J, Song X, Wang S, Du ZJ. Winogradskyella marina sp. nov., isolated from marine sediment. Arch Microbiol 2021; 203:5381–5386 [View Article]
     [Google Scholar]
  48. Vaskovsky VE, Kostetsky EY. Modified spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 1968; 9:396 [View Article] [PubMed]
     [Google Scholar]
  49. Tindall BJ, Sikorski J, Smibert RM, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology Wiley; 2007 pp 330–393 [View Article]
     [Google Scholar]
  50. Incha MR, Thompson MG, Blake-Hedges JM, Liu Y, Pearson AN et al. Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida. Metab Eng Commun 2020; 10:e00119 [View Article] [PubMed]
     [Google Scholar]
  51. Lee S-Y, Park S, Oh T-K, Yoon J-H. Winogradskyella aquimaris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:1814–1818 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006039
Loading
Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment
Int J Syst Evol Microbiol 73, 006039 (2023); https://doi.org/10.1099/ijsem.0.006039
/content/journal/ijsem/10.1099/ijsem.0.006039
/content/journal/ijsem/10.1099/ijsem.0.006039
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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