1887

Abstract

A novel Gram-stain-negative, non-flagellated, non-motile, rod-shaped (0.4–0.6×1.8–2.5 µm), aerobic bacterial strain, designated JLT21, was isolated from seawater of a shallow-sea hydrothermal system. Growth occurred with 0–4.0 % (w/v) NaCl (optimum, 2.0 % NaCl), at 8–45 °C (optimum, 25 °C) and at pH 3.0–10.0 (optimum, pH 7.0). Analysis of 16S rRNA gene sequences revealed that strain JLT21 showed the highest 16S rRNA gene sequence similarity to KEM-8 (97.2 %), IMCC1914 (96.9 %) and GW1-1 (96.9 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JLT21 clustered with GW1-1. The predominant respiratory quinone of strain JLT21 was menaquinone-6 (MK-6). Polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids and four unidentified lipids. The major fatty acids of strain JLT21 were iso-C (21.7 %), C 6/7 (11.5 %) and iso-C 3-OH (10.9 %). The DNA G+C content of strain JLT21 was 32.6 %. On the basis of polyphasic analysis, strain JLT21 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain of is JLT21 (=CGMCC 1.15787=JCM 31511). The study helps us better understand the bacterial species in the shallow-sea hydrothermal system and their adaptations to the hydrothermal environment.

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2020-10-19
2020-12-01
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References

  1. Kwon KK, Lee HS, Jung H-B, Kang J-H, Kim SJ. Yeosuana aromativorans gen. nov., sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae, isolated from estuarine sediment of the South Sea, Korea. Int J Syst Evol Microbiol 2006; 56:727–732 [CrossRef][PubMed]
    [Google Scholar]
  2. 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 [CrossRef][PubMed]
    [Google Scholar]
  3. Tang K, Liu K, Jiao N, Zhang Y, Chen CTA. Functional metagenomic investigations of microbial communities in a shallow-sea hydrothermal system. PLoS One 2013; 8:e72958 [CrossRef][PubMed]
    [Google Scholar]
  4. Dong XZ, Cai MY. Determination of biochemical properties. Manual for the Systematic Identification of General Bacteria Beijing: Scientific Press; 2001 pp 353–412
    [Google Scholar]
  5. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 1994 pp 611–654
    [Google Scholar]
  6. Rüger HJ, Krambeck HJ. Evaluation of the Biolog substrate metabolism system for classification of marine bacteria. Syst Appl Microbiol 1994; 17:281–288 [CrossRef]
    [Google Scholar]
  7. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [CrossRef][PubMed]
    [Google Scholar]
  8. Andrews S. FastQC: a quality control tool for high throughput sequence data. Reference Source 2014
    [Google Scholar]
  9. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437:376–380 [CrossRef][PubMed]
    [Google Scholar]
  10. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [CrossRef][PubMed]
    [Google Scholar]
  11. Luo R, Liu B, Xie Y, Li Z, Huang W, Wang J et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [CrossRef][PubMed]
    [Google Scholar]
  12. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  14. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed]
    [Google Scholar]
  16. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [CrossRef][PubMed]
    [Google Scholar]
  17. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Rao BS et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003; 4:41–14 [CrossRef]
    [Google Scholar]
  18. Embley TM. The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol 1991; 13:171–174 [CrossRef][PubMed]
    [Google Scholar]
  19. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [CrossRef][PubMed]
    [Google Scholar]
  20. 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][PubMed]
    [Google Scholar]
  21. 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]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  26. Fitch WM, Margoliash E. Construction of phylogenetic trees. Science 1967; 155:279–284 [CrossRef][PubMed]
    [Google Scholar]
  27. 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]
  28. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
  30. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [CrossRef]
    [Google Scholar]
  31. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  32. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [CrossRef]
    [Google Scholar]
  33. Kroppenstedt RM, Minnikin DE, Minnikin DE. Fatty acid and menaquinone analysis of actinomycetes and related organisms.. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series 20 New York: Academic Press; 1985 pp 173–199
    [Google Scholar]
  34. Collins MD, Goodfellow M, Minnikin DE. Fatty acid, isoprenoid quinone and polar lipid composition in the classification of Curtobacterium and related taxa. J Gen Microbiol 1980; 118:29–37 [CrossRef][PubMed]
    [Google Scholar]
  35. Kates M. Techniques of Lipidology 106-107, 2nd ed. Amsterdam: Elsevier; 1986 pp 241–246
    [Google Scholar]
  36. Jung YT, Lee JS, Yoon JH. Gaetbulibacter aquiaggeris sp. nov., a member of the Flavobacteriaceae isolated from seawater. Int J Syst Evol Microbiol 2016; 66:1131–1137 [CrossRef][PubMed]
    [Google Scholar]
  37. Zhang Y, Tang K, Shi X, Zhang XH. Flaviramulus ichthyoenteri sp. nov., an N-acylhomoserine lactone-degrading bacterium isolated from the intestine of a flounder (Paralichthys olivaceus), and emended descriptions of the genus Flaviramulus and Flaviramulus basaltis. Int J Syst Evol Microbiol 2013; 63:4477–4483 [CrossRef][PubMed]
    [Google Scholar]
  38. Nedashkovskaya OI, Kim SB, Han SK, Rhee MS, Lysenko AM, Rohde M et al. Algibacter lectus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from green algae. Int J Syst Evol Microbiol 2004; 54:1257–1261 [CrossRef][PubMed]
    [Google Scholar]
  39. Jung YT, Kim JH, Oh T-K, Yoon J-H. Mariniflexile aquimaris sp. nov., isolated from seawater, and emended description of the genus Mariniflexile Nedashkovskaya et al. 2006. Int J Syst Evol Microbiol 2012; 62:539–544 [CrossRef][PubMed]
    [Google Scholar]
  40. Jung YT, Yoon JH. Mariniflexile jejuense sp. nov., isolated from the junction between seawater and a freshwater spring, and emended description of the genus Mariniflexile. Int J Syst Evol Microbiol 2013; 63:1329–1334 [CrossRef][PubMed]
    [Google Scholar]
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