1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 11

gen. nov., sp. nov., a member of the family isolated from coral Free

Abstract

A novel Gram-stain-negative, non-endospore-forming, non-motile, aerobic bacterium (strain R33) was isolated from coral and subjected to a polyphasic taxonomic study. The G+C content was 44.5 mol%. The only detected respiratory quinone was menaquinone 6 (MK-6). The major cellular fatty acids were iso-C and iso-C ω6. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Global alignment based on 16S rRNA gene sequences indicated that strain R33 shares the highest sequence identity of 93.2 % with A6B8 in the family . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R33 forms a distinct branch in a stable clade comprising strain R33 and members of the genera , , and . The phylogenomic analysis also supported this 16S rRNA gene-based phylogenetic result. Comparative genomic analysis indicated that strain R33 is rich in AraC-type DNA-binding domain-containing protein-coding genes, which means the regulation of carbon utilization is very complex. Low 16S rRNA gene identity, different polar lipids and/or cellular fatty acid profiles could readily distinguish strain R33 from any validly published type strains. Therefore, strain R33 is suggested to represent a new species in a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain is R33 (=MCCC 1K03853=KCTC 72443).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Porites lutea , Poritiphilus flavus and pure culture
Funding
This study was supported by the:
  • Natural Sciences Foundation of China (Award 41866004)
    • Principle Award Recipient: Guanghua Wang
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004452
2020-09-14
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/11/5620.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004452&mimeType=html&fmt=ahah

References

  1. Yu W, Wang W, Yu K, Wang Y, Huang X et al. Rapid decline of a relatively high latitude coral assemblage at Weizhou Island, Northern South China Sea. Biodivers Conserv 2019; 28:3925–3949 [View Article]
     [Google Scholar]
  2. Green DH, Edmunds PJ, Carpenter RC. Increasing relative abundance of Porites astreoides on Caribbean reefs mediated by an overall decline in coral cover. Mar Ecol Prog Ser 2008; 359:1–10 [View Article]
     [Google Scholar]
  3. Ainsworth TD, Gates RD. Corals' microbial sentinels. Science 2016; 352:1518–1519 [View Article]
     [Google Scholar]
  4. Hernandez-Agreda A, Leggat W, Bongaerts P, Ainsworth TD. The microbial signature provides insight into the mechanistic basis of coral success across reef habitats. mBio 2016; 7:e00560–16 [View Article][PubMed]
     [Google Scholar]
  5. Bernardet JF, Nakagawa Y. An introduction to the family Flavobacteriaceae. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH. (editors) The Prokaryotes, V7, 3rd ed. New York: Springer; 2006 pp 455–480
     [Google Scholar]
  6. Bernardet J-F, 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]
  7. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  8. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  9. 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]
  10. 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]
  11. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
     [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  13. 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]
  14. Swofford DL. PAUP: Phylogenetic analysis using parsimony, version 3.1.1 Champaign, IL: Illinois Natural History Survey; 1993
     [Google Scholar]
  15. 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]
  16. 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]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  18. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  19. 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 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article][PubMed]
     [Google Scholar]
  23. Wu S, Zhu Z, Fu L, Niu B, Li W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 2011; 12:444 [View Article][PubMed]
     [Google Scholar]
  24. 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 [View Article][PubMed]
     [Google Scholar]
  25. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 2020; 11:e02475–19 [View Article][PubMed]
     [Google Scholar]
  26. 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]
  27. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  28. 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]
  29. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  30. Hu J, Zhang W-Y, Zhang X-Q, Wu M et al. Muriicola marianensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2015; 65:407–411 [View Article][PubMed]
     [Google Scholar]
  31. Zhang J, Han J-R, Chen G-J, Du Z-J. Robiginitalea sediminis sp. nov., isolated from a sea cucumber culture pond. Antonie van Leeuwenhoek 2018; 111:905–911 [View Article][PubMed]
     [Google Scholar]
  32. Alain K, Intertaglia L, Catala P, Lebaron P. Eudoraea adriatica gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2008; 58:2275–2281 [View Article][PubMed]
     [Google Scholar]
  33. Asker D, Beppu T, Ueda K. Zeaxanthinibacter enoshimensis gen. nov., sp. nov., a novel zeaxanthin-producing marine bacterium of the family Flavobacteriaceae, isolated from seawater off Enoshima Island, Japan. Int J Syst Evol Microbiol 2007; 57:837–843 [View Article][PubMed]
     [Google Scholar]
  34. Kahng H-Y, Lee S-S, Kim JM, Jung JY, Lee MY et al. Muriicola jejuensis gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2010; 60:1644–1648 [View Article][PubMed]
     [Google Scholar]
  35. Cho J-C, Giovannoni SJ. Robiginitalea biformata gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae with a higher G+C content. Int J Syst Evol Microbiol 2004; 54:1101–1106 [View Article][PubMed]
     [Google Scholar]
  36. Manh HD, Matsuo Y, Katsuta A, Matsuda S, Shizuri Y et al. Robiginitalea myxolifaciens sp. nov., a novel myxol-producing bacterium isolated from marine sediment, and emended description of the genus Robiginitalea. Int J Syst Evol Microbiol 2008; 58:1660–1664 [View Article][PubMed]
     [Google Scholar]
  37. Siamphan C, Chang Y-H, Kim W. Eudoraea chungangensis sp. nov., isolated from an aquafarm waste water sludge. Antonie Van Leeuwenhoek 2015; 107:1009–1015 [View Article][PubMed]
     [Google Scholar]
  38. Lee Y, Jeong HI, Jeong SE, Jeon CO. Zeaxanthinibacter aestuarii sp. nov., isolated from estuary sediment and emended description of the genus Zeaxanthinibacter Asker et al. 2007. Int J Syst Evol Microbiol 2016; 66:3264–3269 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004452
Loading
Poritiphilus flavus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from coral Porites lutea
Int J Syst Evol Microbiol 70, 5620 (2020); https://doi.org/10.1099/ijsem.0.004452
/content/journal/ijsem/10.1099/ijsem.0.004452
/content/journal/ijsem/10.1099/ijsem.0.004452
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