1887

Abstract

A Gram-stain-negative, motile, aerobic and heterotrophic bacterium, designated as GYS_M3H, was isolated from marine coastal sediment sampled at Xiamen Island. Cells were rod-shaped with one polar flagellum and weakly positive for oxidase and catalase. Growth of the strain occurred at pH 6–9 (optimum, pH 7–8), at 15–37 °C (optimum, 28 °C) and with NaCl concentrations of 1.0–6.0 % (optimum, 2.0 %). It had highest 16S rRNA similarity (97.7 %) to GI5, followed by the members of the genus (lower than 91.2 %). The results of phylogenetic analysis indicated that it belonged to the genus within the family . In addition, the average nucleotide identity and digital DNA–DNA hybridization values between strain GYS_M3H and GI5 were 71.4 and 19.7 %, respectively, indicating that strain GYS_M3H belonged to a novel species. Its genome consisted of 5 318 758 bp, with a genomic DNA G+C content of 50.0 mol%. The respiratory quinone was Q-8 and the dominant fatty acids were identified as iso-C (25.4 %), C ω6c/C ω7 (14.4 %) and iso-C (7.2 %). The main polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Therefore, based on phenotypic, chemotaxonomic and phylogenetic results, strain GYS_M3H represents a novel species within the genus , for which the name sp. nov. is proposed, with the type strain GYS_M3H (=MCCC 1A13808=KCTC 72247).

Keyword(s): Ketobacter and taxonomy
Funding
This study was supported by the:
  • Zongze Shao , National Infrastructure of Microbial Resources of China , (Award NIMR-2020-9)
  • Zongze Shao , COMRA program , (Award DY135-B2-01)
  • Zongze Shao , NSFC Hydrosphere Project , (Award 91851203)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004365
2020-08-07
2020-10-20
Loading full text...

Full text loading...

References

  1. Golyshin PN, Harayama S, Timmis KN, Yakimov MM. Family II. Alcanivoraceae fam. nov.. Bergey's Manual of Systematic Bacteriology 2 New York: Springer; 2007 p p.295
    [Google Scholar]
  2. Silveira CB, Thompson F et al. The family Alcanivoraceae . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes: Gammaproteobacteria 9, 4th ed. New York: Springer; 2014 p 59
    [Google Scholar]
  3. Kim S-H, Kim J-G, Jung M-Y, Kim S-J, Gwak J-H et al. Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater. Int J Syst Evol Microbiol 2018; 68:2258–2264 [CrossRef][PubMed]
    [Google Scholar]
  4. Li J, Huang Z, Lai Q, Liu X, Wang G et al. Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:4930–4935 [CrossRef][PubMed]
    [Google Scholar]
  5. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [CrossRef][PubMed]
    [Google Scholar]
  8. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [CrossRef][PubMed]
    [Google Scholar]
  9. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  10. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  11. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  12. Lagesen K, Hallin P, Rødland E, Stærfeldt H, Ussery D. Rt: RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 2007; 35:3100–3108
    [Google Scholar]
  13. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P et al. Report of the AD hoc Committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef]
    [Google Scholar]
  15. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [CrossRef][PubMed]
    [Google Scholar]
  16. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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][PubMed]
    [Google Scholar]
  17. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [CrossRef][PubMed]
    [Google Scholar]
  18. 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][PubMed]
    [Google Scholar]
  19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  21. Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics 1987; 116:153–159[PubMed]
    [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  23. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  24. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, In: MIDI Technical Note 101. MIDI Inc, Newark, DE; 1990
    [Google Scholar]
  25. Kyoung Kwon K, Hye Oh J, Yang S-H, Seo H-S, Lee J-H. Alcanivorax gelatiniphagus sp. nov., a marine bacterium isolated from tidal flat sediments enriched with crude oil. Int J Syst Evol Microbiol 2015; 65:2204–2208 [CrossRef][PubMed]
    [Google Scholar]
  26. 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]
  27. Ross HNM, Collins MD, Tindall BJ, Grant WD. A rapid procedure for the detection of archaebacterial lipids in halophilic bacteria. Microbiology 1981; 123:75–80 [CrossRef]
    [Google Scholar]
  28. Collins M. Isoprenoid quinone analyses in bacterial classification and identification. Society for Applied Bacteriology Technical Series 1985; 20:267–287
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004365
Loading
/content/journal/ijsem/10.1099/ijsem.0.004365
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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