1887

Abstract

A novel Gram-stain-negative, non-endospore-forming, motile, and aerobic bacterial strain, M105, was isolated from coral , and was subjected to a polyphasic taxonomic study. Global alignment based on 16S rRNA gene sequences indicated that M105 shares the highest sequence identity of 94.5 % with GYP-15. The average nucleotide identity (ANI) and average amino acid identity (AAI) between M105 and GYP-15 was 69.8 and 71.6 %, respectively. On the basis of the results of phenotypic, chemotaxonomic, phylogenetic, phylogenomic, and comparative genomic analyses, it is concluded that M105 should represent a novel species in the genus , for which the name sp. nov. is proposed. The type strain is M105 (=MCCC 1K03773= KCTC 72442). Furthermore, the family was classified into two families on the basis of phylogenetic, phylogenomic, polar lipid profile and motility variations. The novel family fam. nov. is proposed to accommodate the genera and .

Funding
This study was supported by the:
  • Natural Science Foundation of China (Award 41866004)
    • Principle Award Recipient: Guanghua Wang
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2020-10-09
2024-04-20
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References

  1. Wang G, Tang M, Wu H, Dai S, Li T et al. Aliikangiella marina gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122, and proposal of Kangiellaceae fam. nov. in the order Oceanospirillales. Int J Syst Evol Microbiol 2015; 65:4488–4494 [View Article][PubMed]
    [Google Scholar]
  2. Yoon J-H, Oh T-K, Park Y-H. Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2004; 54:1829–1835 [View Article][PubMed]
    [Google Scholar]
  3. Yoon J-H, Kang S-J, Lee S-Y, Lee J-S, Oh T-K. Kangiella geojedonensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:511–514 [View Article][PubMed]
    [Google Scholar]
  4. Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Kangiella japonica sp. nov., isolated from a marine environment. Int J Syst Evol Microbiol 2010; 60:2583–2586 [View Article][PubMed]
    [Google Scholar]
  5. Ahn J, Park J-W, McConnell JA, Ahn Y-B, Häggblom MM. Kangiella spongicola sp. nov., a halophilic marine bacterium isolated from the sponge Chondrilla nucula. Int J Syst Evol Microbiol 2011; 61:961–964 [View Article][PubMed]
    [Google Scholar]
  6. Jean WD, Huang S-P, Chen J-S, Shieh WY. Kangiella taiwanensis sp. nov. and Kangiella marina sp. nov., marine bacteria isolated from shallow coastal water. Int J Syst Evol Microbiol 2012; 62:2229–2234 [View Article][PubMed]
    [Google Scholar]
  7. Lee S-Y, Park S, Oh T-K, Yoon J-H. Kangiella sediminilitoris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2013; 63:1001–1006 [View Article][PubMed]
    [Google Scholar]
  8. Kim J-H, Ward AC, Kim W. Kangiella chungangensis sp. nov. isolated from a marine sand. Antonie Van Leeuwenhoek 2015; 107:1291–1298 [View Article][PubMed]
    [Google Scholar]
  9. Xu F-di, Li X-G, Xiao X, Xu J. Kangiella profundi sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2015; 65:2315–2319 [View Article][PubMed]
    [Google Scholar]
  10. Choe H, Kim S, Oh J, Nasir A, Kim BK et al. Complete genome of Kangiella geojedonensis KCTC 23420T, putative evidence for recent genome reduction in marine environments. Mar Genomics 2015; 24:215–217 [View Article][PubMed]
    [Google Scholar]
  11. Wang J, Lu Y, Nawaz MZ, Xu J. Comparative genomics reveals evidence of genome reduction and high extracellular protein degradation potential in Kangiella. Front Microbiol 2018; 9:1224 [View Article][PubMed]
    [Google Scholar]
  12. Fagervold SK, Urios L, Intertaglia L, Batailler N, Lebaron P et al. Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2013; 63:2700–2705 [View Article][PubMed]
    [Google Scholar]
  13. Luo Y, Lai Q, Yuan J, Huang Z. Pleionea sediminis sp. nov., isolated from coastal sediment and emendation of the description of the genus Pleionea. Int J Syst Evol Microbiol 2019; 69:3524–3528 [View Article][PubMed]
    [Google Scholar]
  14. Xu S, Yu K, Su H, Chen B, Huang W et al. Proposal of Parashewanella gen. nov. to accommodate Parashewanella curva sp. nov. and Parashewanella spongiae comb. nov. in the Shewanellaceae. Int J Syst Evol Microbiol 2019; 69:1259–1264 [View Article][PubMed]
    [Google Scholar]
  15. 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]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. Swofford DL. PAUP: Phylogenetic analysis using parsimony, version 3.1.1. Champaign, IL: Illinois Natural History Survey; 1993
    [Google Scholar]
  20. 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]
  21. 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]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Lim HJ, Lee E-H, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379–387 [View Article][PubMed]
    [Google Scholar]
  25. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. 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]
  28. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article][PubMed]
    [Google Scholar]
  29. Lin S-H, Liao Y-C. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One 2013; 8:e60843 [View Article][PubMed]
    [Google Scholar]
  30. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article][PubMed]
    [Google Scholar]
  31. 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]
  32. 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]
  33. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article][PubMed]
    [Google Scholar]
  34. 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]
  35. 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]
  36. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article][PubMed]
    [Google Scholar]
  37. 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]
  38. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:44324450 [View Article][PubMed]
    [Google Scholar]
  39. 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]
  40. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  41. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  42. Tindall BJ, Sikorski J, Smibert RM, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 330–393
    [Google Scholar]
  43. 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]
  44. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  45. 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]
  46. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  47. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article][PubMed]
    [Google Scholar]
  48. Teramoto M, Yagyu K-I, Nishijima M. Perspicuibacter marinus gen. nov., sp. nov., a semi-transparent bacterium isolated from surface seawater, and description of Arenicellaceae fam. nov. and Arenicellales ord. nov. Int J Syst Evol Microbiol 2015; 65:353–358 [View Article][PubMed]
    [Google Scholar]
  49. Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment. Int J Syst Evol Microbiol 2010; 60:1832–1836 [View Article][PubMed]
    [Google Scholar]
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