1887

Abstract

A taxonomic identification using a polyphasic approach was performed on strain NBS58-1, which was isolated from the interfacial sediment of Taihu Lake in China. Strain NBS58-1 was Gram-stain-negative, aerobic, non-spore-forming and catalase-positive. Phylogenetic analyses based on 16S rRNA gene and three housekeeping genes (, and ) sequences supported the position that strain NBS58-1 should be classified within the genus . The 16S rRNA gene sequence of strain NBS58-1 possessed the highest similarity to H-1 (96.60 %), followed by MDT1-10-3 (96.17 %). And the ANI value between strain NBS58-1 and MDT1-10-3 was 79.3 %. The respiratory quinone was menaquinone 7 (MK-7). The major cellular fatty acids comprised iso-C and summed feature 3. Phosphatidylethanolamine, two unidentified phospholipids and four unidentified lipids were the main polar lipids. The genomic DNA G+C content was 51.3 mol%. Based on phenotypic features and phylogenetic position, a novel species with the name sp. nov. is proposed. The type strain is NBS58-1=(KACC 21309=MCCC 1K04037). We also proposed as a latter heterotypic synonym of .

Funding
This study was supported by the:
  • Jian-Hang Qu , Key Scientific Research Project of Colleges and Universities in Henan Province , (Award 20A180009)
  • Jian-Hang Qu , National Natural Science Foundation of China , (Award 31370147)
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2020-10-13
2021-02-26
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References

  1. Abaydulla G, Luo X, Shi J, Peng F, Liu M et al. Rufibacter tibetensis gen. nov., sp. nov., a novel member of the family Cytophagaceae isolated from soil. Antonie van Leeuwenhoek 2012; 101:725–731 [CrossRef][PubMed]
    [Google Scholar]
  2. Takano H, Asker D, Beppu T, Ueda K. Genetic control for light-induced carotenoid production in non-phototrophic bacteria. J Ind Microbiol Biotechnol 2006; 33:88–93 [CrossRef][PubMed]
    [Google Scholar]
  3. Takano H. The regulatory mechanism underlying light-inducible production of carotenoids in nonphototrophic bacteria. Biosci Biotechnol Biochem 2016; 80:1264–1273 [CrossRef][PubMed]
    [Google Scholar]
  4. Zhang ZD, Gu MY, Zhu J, Li SH, Zhang LJ et al. Rufibacter roseus sp. nov., isolated from radiation-polluted soil. Int J Syst Evol Microbiol 2015; 65:1572–1577 [CrossRef][PubMed]
    [Google Scholar]
  5. Polkade AV, Ramana VV, Joshi A, Pardesi L, Shouche YS. Rufibacter immobilis sp. nov., isolated from a high-altitude saline lake. Int J Syst Evol Microbiol 2015; 65:1592–1597 [CrossRef][PubMed]
    [Google Scholar]
  6. Kýrová K, Sedláček I, Pantůček R, Králová S, Holochová P et al. Rufibacter ruber sp. nov., isolated from fragmentary rock. Int J Syst Evol Microbiol 2016; 66:4401–4405 [CrossRef][PubMed]
    [Google Scholar]
  7. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil. Int J Syst Evol Microbiol 2016; 66:315–318 [CrossRef][PubMed]
    [Google Scholar]
  8. Felföldi T, Mentes A, Schumann P, Kéki Z, Máthé I et al. Rufibacter quisquiliarum sp. nov., a new member of the phylum Bacteroidetes isolated from a bioreactor treating landfill leachate. Int J Syst Evol Microbiol 2016; 66:5150–5154 [CrossRef][PubMed]
    [Google Scholar]
  9. Qu JH, Zhang LJ, Fu YH, Li H-F. Rufibacter sediminis sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 2019; 69:662–666 [CrossRef][PubMed]
    [Google Scholar]
  10. Yoon SH, Ha SM, 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]
  11. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [CrossRef][PubMed]
    [Google Scholar]
  12. Chaudhary DK, Kim J. Flavobacterium naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:305–309 [CrossRef][PubMed]
    [Google Scholar]
  13. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [CrossRef][PubMed]
    [Google Scholar]
  14. Yoon SH, Ha SM, 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]
  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 [CrossRef][PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  17. 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][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 [CrossRef][PubMed]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  20. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  21. Modesto M, Michelini S, Stefanini I, Ferrara A, Tacconi S et al. Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2014; 64:2819–2827 [CrossRef][PubMed]
    [Google Scholar]
  22. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  23. Qu JH, Fu YH, Li XD, Li HF, Tian HL. Brevundimonas lutea sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2019; 69:1417–1422 [CrossRef][PubMed]
    [Google Scholar]
  24. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [CrossRef][PubMed]
    [Google Scholar]
  25. Qu JH, Ma WW, Li HF, Wang XF, Lu BB et al. Altererythrobacter amylolyticus sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2019; 69:1231–1236 [CrossRef][PubMed]
    [Google Scholar]
  26. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
    [Google Scholar]
  27. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [CrossRef][PubMed]
    [Google Scholar]
  28. Cowan ST, Feltham RKA, Barrow GI, Steel KJ. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge, New York: Cambridge University Press; 1993
    [Google Scholar]
  29. Tindall BJ, Sikorski J, Smibert RA, Krieg NR, Reddy CA et al. Phenotypic Characterization and the Principles of Comparative Systematics Washington, DC: American Society for Microbiology Press; 2017
    [Google Scholar]
  30. Shieh WY, Chen AL, Chiu HH. Vibrio aerogenes sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production. Int J Syst Evol Microbiol 2000; 50 Pt 1:321–329 [CrossRef][PubMed]
    [Google Scholar]
  31. Kang JW, Kim MS, Lee JH, Baik KS, Seong CN. Altererythrobacter rigui sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2016; 66:2491–2496 [CrossRef][PubMed]
    [Google Scholar]
  32. Boontosaeng T, Nimrat S, Vuthiphandchai V. Pigments production of bacteria isolated from dried seafood and capability to inhibit microbial pathogens. IOSR-JESTFT 2016; 10:30–34
    [Google Scholar]
  33. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial Systematics. Method Microbiol 1988; 19:161–207
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  35. Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet 1995; 11:217–218 [CrossRef][PubMed]
    [Google Scholar]
  36. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014; 30:2114–2120 [CrossRef][PubMed]
    [Google Scholar]
  37. 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 [CrossRef][PubMed]
    [Google Scholar]
  38. 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]
  39. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [CrossRef][PubMed]
    [Google Scholar]
  40. Zuo G, Hao B. CVTree3 web server for Whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321–331 [CrossRef][PubMed]
    [Google Scholar]
  41. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [CrossRef][PubMed]
    [Google Scholar]
  42. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [CrossRef][PubMed]
    [Google Scholar]
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