1887

Abstract

A novel bacterium, designated NAS39, was isolated from the interfacial sediment of Taihu Lake in PR China and its taxonomic position was investigated by using a polyphasic approach. Cells of the isolate were Gram-stain-negative, aerobic, non-motile, catalase-positive, yellow and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences supported that strain NAS39 formed a cluster within the genus , and was most closely related to LB2P30 (98.4 %), followed by 0563 (97.4 %). The average nucleotide identity values between strain NAS39 and LB2P30 and 0563 were 82.5 and 75.3 %, respectively. The digital DNA–DNA hybridization values between strain NAS39 and LB2P30 and 0563 were 40.9 and 18.6 %, respectively. The genomic DNA G+C content was 34.1 mol%. The major respiratory quinone was menaquinone-6. The dominant cellular fatty acids were iso-C and summed feature 3 comprising C ω7/C ω6. The polar lipids comprised phosphatidyl ethanolamine, two amino lipids, three amino phospholipids and two unidentified lipids. Based on the phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain NAS39 (=MCCC 1K06094=KACC 22328) represents a novel species of the genus , for which the name sp. nov. is proposed.

Funding
This study was supported by the:
  • Innovative Funds Plan of Henan University of Technology (Award 2021ZKCJ15)
    • Principle Award Recipient: Jian-HangQu
  • National Natural Science Foundation of China (Award 42107139)
    • Principle Award Recipient: JiaZhou
  • Key Scientific Research Project of Colleges and Universities in Henan Province (Award 20A180009)
    • Principle Award Recipient: Jian-HangQu
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2022-06-13
2024-11-04
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References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II. Flavobacterium gen. nov. In Bergey’s Manual of Determinative Bacteriology Baltimore: Williams & Wilkins; 1923
    [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
    [Google Scholar]
  3. Dong K, Chen F, Du Y, Wang G. Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense. Int J Syst Evol Microbiol 2013; 63:886–892 [View Article] [PubMed]
    [Google Scholar]
  4. Kang JY, Chun J, Jahng KY. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63:1633–1638 [View Article] [PubMed]
    [Google Scholar]
  5. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai’i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63:3280–3286 [View Article] [PubMed]
    [Google Scholar]
  6. Bernardet J-F, 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 [View Article] [PubMed]
    [Google Scholar]
  7. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  8. Wu JH, You YX, Young CC, Kwon SW, Chen WM. Flavobacterium lotistagni sp. nov. and Flavobacterium celericrescens sp. nov., isolated from freshwater habitats. Int J Syst Evol Microbiol 2019; 71:004682 [View Article] [PubMed]
    [Google Scholar]
  9. Yang LL, Liu Q, Liu HC, Zhou YG, Xin YH. Flavobacterium laiguense sp. nov., a psychrophilic bacterium isolated from Laigu glacier on the Tibetan Plateau. Int J Syst Evol Microbiol 2019; 69:1821–1825 [View Article] [PubMed]
    [Google Scholar]
  10. Xin Y-H, Liang Z-H, Zhang D-C, Liu H-C, Zhang J-L et al. Flavobacterium tiangeerense sp. nov., a cold-living bacterium isolated from a glacier. Int J Syst Evol Microbiol 2009; 59:2773–2777 [View Article] [PubMed]
    [Google Scholar]
  11. Liu Q, Liu H, Zhang J, Zhou Y, Xin Y et al. Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice. Int J Syst Evol Microbiol 2013; 63:2819–2822 [View Article]
    [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 [View Article]
    [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 [View Article]
    [Google Scholar]
  14. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S et al. NCBI BLAST: a better web interface. Nucleic Acids Res 2008; 36:W5–9 [View Article] [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 [View Article] [PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [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 [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. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  20. Kumar S, Tamura K, Nei M. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput Appl Biosci 1994; 10:189–191 [View Article] [PubMed]
    [Google Scholar]
  21. Smibert RM, Krieg NR. Methods for general and molecular bacteriology. In Phenotypic Characterization Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  22. Qu J-H, Ma W-W, Li H-F, Wang X-F, Lu B-B et al. Altererythrobacter amylolyticus sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2019; 69:1231–1236 [View Article] [PubMed]
    [Google Scholar]
  23. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
    [Google Scholar]
  24. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article] [PubMed]
    [Google Scholar]
  25. Cowan ST, Feltham RKA, Barrow GI, Steel KJ. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press; 1993
    [Google Scholar]
  26. 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]
  27. 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; 50:321–329 [View Article] [PubMed]
    [Google Scholar]
  28. 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 [View Article] [PubMed]
    [Google Scholar]
  29. 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
    [Google Scholar]
  30. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1988; 19:161–207
    [Google Scholar]
  31. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 1990; 101:
    [Google Scholar]
  32. Neumann B, Pospiech A, Schairer HU. Rapid isolation of genomic DNA from Gram-negative bacteria. Trends Genet 1992; 8:332–333 [View Article] [PubMed]
    [Google Scholar]
  33. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
    [Google Scholar]
  34. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  35. 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]
  36. Qu JH, Yue YF, Zhou J, Qu LB, Wang LF. Dyadobacter flavalbus sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2020; 70:1064–1070 [View Article] [PubMed]
    [Google Scholar]
  37. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  38. Bernardet JF, Bowman J. The genus Flavobacterium. In The Prokaryotes: Handbook on the Biology of Bacteria vol 7 Springer; 2006 pp 481–531
    [Google Scholar]
  39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  40. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  41. 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 [View Article] [PubMed]
    [Google Scholar]
  42. 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 [View Article] [PubMed]
    [Google Scholar]
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