1887

Abstract

In this study, we describe a Gram-stain-negative, rod-shaped, non-motile and aerobic bacterium, named strain MT3330, which was isolated from the deep-sea sediment of the Mariana Trench. Growth of MT3330 occurred at 15–40 °C (optimum, 25–30 °C), pH 5.0–10.0 (optimum, 7.0–8.0) and with 0–8.0 % (w/v) NaCl (optimum, 0–2.0 %). The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that MT3330 represented a member of the family and was most closely related to HN-Y44 (92.3 % sequence similarity). The results of genomic analysis indicated that MT3330 contains a circular chromosome of 4 365 036 bp with a DNA G+C content of 35.2 %. The predominant respiratory quinone of MT3330 was MK-6. The polar lipids of MT3330 included phosphatidylethanolamine, three unidentified amino lipids and four unidentified lipids. The major fatty acids of MT3330 included C, iso-CG, iso-C 3-OH, and iso-C 3-OH. On the basis of the results of the phylogenetic, physiological, biochemical and morphological analyses, it is suggested that strain MT3330 represents a novel genus and a novel species of the family , and the name gen. nov., sp. nov. is proposed. The type strain is MT3330 (=MCCC 1K06012=KCTC 82823).

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2022-07-18
2024-04-28
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References

  1. Jooste PJ, Britz TJ, De Haast J. A numerical taxonomic study of Flavobacterium-Cytophaga strains from dairy sources. J Appl Bacteriol 1985; 59:311–323 [View Article] [PubMed]
    [Google Scholar]
  2. Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. An Introduction to the Family Flavobacteriaceae. In The Prokaryotes, 3rd ed. New York, NY: Springer; 2006 pp 455–480 [View Article]
    [Google Scholar]
  3. Joung Y, Song J, Lee K, Oh H-M, Joh K et al. Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater. Int J Syst Evol Microbiol 2010; 60:2061–2065 [View Article] [PubMed]
    [Google Scholar]
  4. Jung YT, Yoon SY, Lee JS, Yoon JH. Taeania maliponensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater. Int J Syst Evol Microbiol 2016; 66:3552–3557 [View Article] [PubMed]
    [Google Scholar]
  5. Kirchman DL. The ecology of CytophagaFlavobacteria in aquatic environments. FEMS Microbiol Ecol 2002; 39:91–100 [View Article] [PubMed]
    [Google Scholar]
  6. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acids Techniques in Bacterial Systematics Chichester: John Wiley & Sons; 1991 pp 115–147
    [Google Scholar]
  7. 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 [View Article] [PubMed]
    [Google Scholar]
  8. 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]
  9. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
    [Google Scholar]
  10. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol 1992; 9:945–967
    [Google Scholar]
  11. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  12. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  13. 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]
  14. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  15. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  16. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785–786 [View Article] [PubMed]
    [Google Scholar]
  17. Zhuang LP, Lin BB, Qin F, Luo LZ. Zhouia spongiae sp. nov., isolated from a marine sponge. Int J Syst Evol Microbiol 2018; 68:2194–2198 [View Article] [PubMed]
    [Google Scholar]
  18. Liu Z-P, Wang B-J, Dai X, Liu X-Y, Liu S-J. Zhouia amylolytica gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from sediment of the South China Sea. Int J Syst Evol Microbiol 2006; 56:2825–2829 [View Article] [PubMed]
    [Google Scholar]
  19. Xu Y, Tian X-P, Liu Y-J, Li J, Kim C-J et al. Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 2013; 63:1045–1050 [View Article]
    [Google Scholar]
  20. Quan Z-X, Xiao Y-P, Roh SW, Nam Y-D, Chang H-W et al. Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the East Sea. Int J Syst Evol Microbiol 2008; 58:1388–1392 [View Article]
    [Google Scholar]
  21. Hameed A, Shahina M, Lin S-Y, Lai W-A, Liu Y-C et al. Robertkochia marina gen. nov., sp. nov., of the family Flavobacteriaceae, isolated from surface seawater, and emended descriptions of the genera Joostella and Galbibacter. Int J Syst Evol Microbiol 2014; 64:533–539 [View Article] [PubMed]
    [Google Scholar]
  22. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  23. 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 [View Article] [PubMed]
    [Google Scholar]
  24. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  25. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
    [Google Scholar]
  26. Zhuang L, Lin B, Xu L, Li G, Wu CJ et al. Erythrobacter spongiae sp. nov., isolated from marine sponge. Int J Syst Evol Microbiol 2019; 69:1111–1116 [View Article] [PubMed]
    [Google Scholar]
  27. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 1990; 20:1–6 [PubMed]
    [Google Scholar]
  28. Minnikin D-E, Odonnell A-G, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 1984; 2:233–241 [View Article] [PubMed]
    [Google Scholar]
  29. Zhuang L, Lin B, Xu L, Li G, Wu CJ et al. Erythrobacter spongiae sp. nov., isolated from marine sponge. Int J Syst Evol Microbiol 2019; 69:1111–1116
    [Google Scholar]
  30. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article]
    [Google Scholar]
  31. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  32. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to Identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
    [Google Scholar]
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