1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 1

sp. nov., a marine bacterium isolated from the brown alga Free

Abstract

A Gram-negative, aerobic, rod-shaped, non-flagellated and motile by gliding bacterium HL2-2, was isolated from the surface of the brown alga in China. The 16S rRNA gene sequence analysis showed that this strain was affiliated with the genus in the family and presented great similarity with the type strain KMM 6491 (97.9 % sequence similarity). The whole genome of strain HL2-2 comprised 3.6 Mbp with a G+C content of 31.9 mol%. The average nucleotide identity between strain HL2-2 and KMM 6491 was 83.7 %. Growth of the isolated strain was observed from 20–40 °C (optimum, 30 °C), at pH ranged from 5.5 to 8.0 (optimum, pH 6.0) and in the presence of 0–5 % (w/v) NaCl (optimum, 0–2 %). The major fatty acids (>10 % of the total) were C, iso-C and the predominant menaquinone was MK-6. The combined phylogenetic, physiological and chemotaxonomic analysis show that the strain HL2-2 represents a novel species belonging to the genus , for which the name sp. nov. is proposed, and which the type strain is HL2-2 (=CICC 24857=KCTC 72882).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): algae , taxonomy and Winogradskyella endarachnes
Funding
This study was supported by the:
  • Guangdong Basic and Applied Basic Research Foundation (Award 2020A1515011333)
    • Principle Award Recipient: HaibinLi
  • Shantou University Scientific Research Foundation for Talents (Award NTF19013)
    • Principle Award Recipient: TaoPeng
  • Innovation Team Project of Guangdong Normal University (Award 2018KCXTD012)
    • Principle Award Recipient: ZhongHu
  • Science and Technology Planning Project of Guangdong Province (Award 2019ny005)
    • Principle Award Recipient: HaibinLi
  • Science and Technology Planning Project of Guangdong Province (Award 2017A020217004)
    • Principle Award Recipient: MingqiZhong
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004577
2020-12-03
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/1/ijsem004577.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004577&mimeType=html&fmt=ahah

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][PubMed]
     [Google Scholar]
  3. Yoon BJ, Byun HD, Kim JY, Lee DH, Kahng HY 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]
  4. 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]
  5. Begum Z, Srinivas TNR, Manasa P, Sailaja B, Sunil B et al. Winogradskyella psychrotolerans sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from Arctic sediment. Int J Syst Evol Microbiol 2013; 63:1646–1652 [View Article][PubMed]
     [Google Scholar]
  6. Sun Y, Chen BY, Du Z-J. Winogradskyella aurantia sp. nov., isolated from a marine solar saltern. Antonie van Leeuwenhoek 2017; 110:1445–1452 [View Article][PubMed]
     [Google Scholar]
  7. Patrick FM. The use of membrane filtration and marine agar 2216E to enumerate marine heterotrophic bacteria. Aquaculture 1978; 13:369–372 [View Article]
     [Google Scholar]
  8. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
     [Google Scholar]
  9. Yoon SH, 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]
  10. 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]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  12. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article][PubMed]
     [Google Scholar]
  13. 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][PubMed]
     [Google Scholar]
  14. 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]
  15. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  16. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  17. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H, SM H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
     [Google Scholar]
  18. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  19. Emms DM, Kelly S. OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences. bioRxiv 2018; 466201:
     [Google Scholar]
  20. Katoh K, Misawa K, Kuma K-ichi, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4:e1900v1
     [Google Scholar]
  23. Yin Y, Mao X, Yang J, Chen X, Mao F et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2012; 40:W445–W451 [View Article][PubMed]
     [Google Scholar]
  24. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  25. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  26. Lapébie P, Lombard V, Drula E, Terrapon N, Henrissat B. Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat Commun 2019; 10:10 [View Article][PubMed]
     [Google Scholar]
  27. Halebian S, Harris B, Finegold SM, Rolfe RD. Rapid method that AIDS in distinguishing gram-positive from gram-negative anaerobic bacteria. J Clin Microbiol 1981; 13:444–448 [View Article][PubMed]
     [Google Scholar]
  28. Jung J, Bae SS, Chung D, Baek K. Tamlana carrageenivorans sp. nov., a carrageenan-degrading bacterium isolated from seawater. Int J Syst Evol Microbiol 2019; 69:1355–1360 [View Article][PubMed]
     [Google Scholar]
  29. 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; 52:1049–1070 [View Article][PubMed]
     [Google Scholar]
  30. Nakagawa Y, Yamasato K. Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J Gen Microbiol 1993; 139:1155–1161 [View Article][PubMed]
     [Google Scholar]
  31. Kates M. Radioisotopic techniques in lipidology. Techniques of Lipidology, 2nd rev ed. 1986 pp 106–241
     [Google Scholar]
  32. Shieh WY, Chen Y-W, Chaw S-M, Chiu H-H. Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. Int J Syst Evol Microbiol 2003; 53:479–484 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004577
Loading
Winogradskyella endarachnes sp. nov., a marine bacterium isolated from the brown alga Endarachne binghamiae
Int J Syst Evol Microbiol 71, 004577 (2020); https://doi.org/10.1099/ijsem.0.004577
/content/journal/ijsem/10.1099/ijsem.0.004577
/content/journal/ijsem/10.1099/ijsem.0.004577
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