1887

Abstract

A Gram-stain-negative, non-spore-forming, aerobic, motile, curved rod-shaped bacterium, designed strain R148 was isolated from a coralline algae sp. collected from Weizhou island, PR China. The optimal growth of R148 occurred at 25 °C, pH 8–9 in the presence of 0.5 % (w/v) NaCl on the basis of amended marine broth 2216. The genomic DNA G+C content was 59.5 mol%. The only detected respiratory quinone was Q-10. The major polar lipids were phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and three unidentified ninhydrin-positive lipids. The major cellular fatty acids were Cω7, Cω7, Ccyclo 9, 10 DMA and C. The results of 16S rRNA gene-based global alignment indicated that the closest neighbour of strain R148 was DSM 21314 (93.1 % similarity), the second is KCTC 42420 (92.2 %). The results of phylogenetic analysis indicated that R148 forms a distinct branch in the robust clade of R148 and DSM 21314, while the taxonomic position of this clade in the family is ambiguous among phylogenetic approaches. The low 16S rRNA gene similarity and distinct polar lipid and cellular fatty acid profile could readily distinguish R148 from closely related type strains. So R148 is suggested to represent a novel species in a novel genus, for which the name gen. nov., sp. nov. is proposed. The type strain is R148 (=MCCC 1K03781=KCTC 72137).

Funding
This study was supported by the:
  • Guanghua Wang , National Key R & D Program of China , (Award 2018YFD0900803)
  • Guanghua Wang , National Natural Science Foundation of China , (Award 41866004)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004173
2020-04-28
2020-06-04
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/5/3335.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004173&mimeType=html&fmt=ahah

References

  1. Pfennig N, Trüper HG. Higher taxa of the phototrophic bacteria. Int J Syst Bacteriol 1971; 21:17–18 [CrossRef]
    [Google Scholar]
  2. Wiese J, Thiel V, Gärtner A, Schmaljohann R, Imhoff JF. Kiloniella laminariae gen. nov., sp. nov., an alphaproteobacterium from the marine macroalga Laminaria saccharina . Int J Syst Evol Microbiol 2009; 59:350–356 [CrossRef]
    [Google Scholar]
  3. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [CrossRef]
    [Google Scholar]
  4. Degli Esposti M, Lozano L, Martínez-Romero E. Current phylogeny of Rhodospirillaceae: A multi-approach study. Mol Phylogenet Evol 2019; 139:106546 [CrossRef]
    [Google Scholar]
  5. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–175
    [Google Scholar]
  6. 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 [CrossRef]
    [Google Scholar]
  7. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [CrossRef]
    [Google Scholar]
  8. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef]
    [Google Scholar]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Swofford DL. PAUP: Phylogenetic analysis using parsimony, version 3.1.1 Champaign, IL: Illinois Natural History Survey; 1993
    [Google Scholar]
  11. 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]
  12. 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]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef]
    [Google Scholar]
  14. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [CrossRef]
    [Google Scholar]
  15. 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]
  16. 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 [CrossRef]
    [Google Scholar]
  17. Yoon S-H, Ha S-min, 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]
    [Google Scholar]
  18. SI N, Kim YO, Yoon SH, SM H, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285
    [Google Scholar]
  19. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [CrossRef]
    [Google Scholar]
  20. Bernardet JF, Nakagawa Y, Holmes B. 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
    [Google Scholar]
  21. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  22. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  23. Tindall BJ, Sikorski J, Smibert RM, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 330–393
    [Google Scholar]
  24. Kim J-H, Konkit M, Yoon J-H, Kim W. Limibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium in the family Rhodospirillaceae isolated from reclaimed land. Int J Syst Evol Microbiol 2015; 65:3155–3161 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  25. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994 pp 345–401
    [Google Scholar]
  26. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  27. Kamekura M. Lipids of extreme halophiles. In Vreeland RH, Hochstein LI. (editors) The Biology of Halophilic Bacteria Boca Raton: CRC Press; 1993 pp 135–161
    [Google Scholar]
  28. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [CrossRef]
    [Google Scholar]
  29. Choi DH, Hwang CY, Cho BC. Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater. Int J Syst Evol Microbiol 2009; 59:818–823 [CrossRef]
    [Google Scholar]
  30. Wang Y-X, Liu J-H, Zhang X-X, Chen Y-G, Wang Z-G et al. Fodinicurvata sediminis gen. nov., sp. nov. and Fodinicurvata fenggangensis sp. nov., poly-β-hydroxybutyrate-producing bacteria in the family Rhodospirillaceae . Int J Syst Evol Microbiol 2009; 59:2575–2581 [CrossRef]
    [Google Scholar]
  31. Wiese J, Thiel V, Gärtner A, Schmaljohann R, Imhoff JF et al. Kiloniella laminariae gen. nov., sp. nov., an alphaproteobacterium from the marine macroalga Laminaria saccharina . Int J Syst Evol Microbiol 2009; 59:350–356 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  32. Yang S-H, Seo H-S, Lee J-H, Kim S-J, Kwon KK. Kiloniella spongiae sp. nov., isolated from a marine sponge and emended description of the genus Kiloniella Wiese et al. 2009 and Kiloniella laminariae . Int J Syst Evol Microbiol 2015; 65:230–234 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004173
Loading
/content/journal/ijsem/10.1099/ijsem.0.004173
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