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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 6

sp. nov., an ammonifying bacterium isolated from a freshwater lake No Access

Abstract

A Gram-stain-negative, aerobic, non-spore-forming, nonmotile, rod-shaped, and yellow-pigmented bacterium, designated strain JXAS1, was isolated from a freshwater sample collected from Poyang Lake in China. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the isolate belonged to the genus , being closest to DSM 6368 (98.61 %). The genome size of strain JXAS1 was 4.66 Mb with DNA G+C content 35.7 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain JXAS1 and its closest relatives were below the threshold values of 95 and 70 %, respectively. The strain contained menaquinone 6 (MK-6) as the predominant menaquinone and the major polar lipids were phosphatidylethanolamine, one unidentified glycolipid, and one unidentified polar lipid. The major fatty acids (>5 %) were iso-C, summed feature 3 (C 7 and/or C 6), C, iso-C 3OH, iso-C 3OH, and summed feature 9 (iso-C 9 and/or 10-methyl C). Based on phylogenetic, genotypic, and phenotypic evidence, the isolated strain represents a new species in the genus , and the name is proposed. The type strain is JXAS1 (=GDMCC 1.1378=KCTC 62719).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidota , Flavobacteriaceae , Flavobacterium poyangense and new taxa
Funding
This study was supported by the:
  • Key Research and Development Program of Jiangxi Province (Award 20212BCD42014)
    • Principle Award Recipient: LinYuan
  • Key Research and Development Program of Jiangxi Province (Award 20223BBF61015)
    • Principle Award Recipient: TaoDeng
  • Pilot Demonstration Project of Ceilings in Funding for Provincial Science and Technology Program of Jiangxi Academy of Sciences (Award 2023YSBG22008)
    • Principle Award Recipient: YaLi
  • National Natural Science Foundation of China (Award 41867065)
    • Principle Award Recipient: YaLi
© 2024 The Authors
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References

  1. Holmes B, Snell JJS, Lapage SP. Revised description, from clinical strains, of Flavobacterium breve (Lustig) Bergey et al. 1923 and proposal of the neotype strain. Int J Syst Bacteriol 1978; 28:201–208 [View Article]
     [Google Scholar]
  2. Bernardet JF, 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 hydatisnom. nov. (basonym, Cytophagaaquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
     [Google Scholar]
  3. 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]
  4. Dong K, Xu B, Zhu F, Wang G. Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli. Int J Syst Evol Microbiol 2013; 63:3237–3242 [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. Chaudhary DK, Kim D-U, Kim D, Kim J. Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil. Sci Rep 2019; 9:4134 [View Article] [PubMed]
     [Google Scholar]
  7. Ahn JH, Kim TW, Kim T-S, Joung Y, Kim SB. Flavobacterium fluminis sp. nov. to accommodate an aerobic, halotolerant and gliding flavobacterium isolated from freshwater. Int J Syst Evol Microbiol 2017; 67:3117–3121 [View Article] [PubMed]
     [Google Scholar]
  8. Liu H, Lu P, Zhu G. Flavobacterium cloacae sp. nov., isolated from waste water. Int J Syst Evol Microbiol 2017; 67:659–663 [View Article] [PubMed]
     [Google Scholar]
  9. Fu Y, Tang X, Lai Q, Zhang C, Zhong H et al. Flavobacterium beibuense sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61:205–209 [View Article] [PubMed]
     [Google Scholar]
  10. Xin YH, Liang ZH, Zhang DC, Liu HC, Zhang JL 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. Zhao JC, Cheng J, Zhang Q, Gao ZW, Zhang MY et al. Flavobacterium artemisiae sp. nov., isolated from the rhizosphere of Artemisia annua L. and emended descriptions of Flavobacterium compostarboris and Flavobacterium procerum. Int J Syst Evol Microbiol 2018; 68:1509–1513 [View Article] [PubMed]
     [Google Scholar]
  12. Zamora L, Vela AI, Sánchez-Porro C, Palacios MA, Moore ERB et al. Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss). Int J Syst Evol Microbiol 2014; 64:392–399 [View Article] [PubMed]
     [Google Scholar]
  13. Kołacińska K, Koncki R. A novel optoelectronic detector and improved flow analysis procedure for ammonia determination with Nessler’s reagent. Anal Sci Int J Japan Soc Anal Chem 2014; 30:1019–1022 [View Article] [PubMed]
     [Google Scholar]
  14. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [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. 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]
  19. Kim M, Oh H-S, Park S-C, 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] [PubMed]
     [Google Scholar]
  20. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 [View Article]
     [Google Scholar]
  21. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–D280 [View Article] [PubMed]
     [Google Scholar]
  22. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2014; 43:261–269 [View Article] [PubMed]
     [Google Scholar]
  23. Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 2002; 18:77–82 [View Article] [PubMed]
     [Google Scholar]
  24. Amos B, Rolf A. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2001; 28:45–48 [View Article] [PubMed]
     [Google Scholar]
  25. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program: table 1. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article] [PubMed]
     [Google Scholar]
  30. Yang JY, Peng W, Li CY, Dong S, Song X-Y et al. Characterization of a new M13 metallopeptidase from deep-sea Shewanella sp. E525-6 and mechanistic insight into its catalysis. Front Microbiol 2016; 6:1498 [View Article] [PubMed]
     [Google Scholar]
  31. 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 [View Article] [PubMed]
     [Google Scholar]
  32. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci 2005; 102:2567–2572 [View Article] [PubMed]
     [Google Scholar]
  33. Bernardet JF, 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]
     [Google Scholar]
  34. Da XY, Jiang F, Chang XL, Ren LZ, Qiu X et al. Pedobacter ardleyensis sp nov, isolated from soil of the Ardley Island, South Shetland Islands in Antarctica. Int J Syst Evol Microbiol 2015; 65:3841–3846 [View Article]
     [Google Scholar]
  35. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note 101 Newark DE: MIDI Inc; 1990
     [Google Scholar]
  36. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  37. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66:2205–2211 [View Article] [PubMed]
     [Google Scholar]
  38. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  39. McCammon SA, Innes BH, Bowman JP, Franzmann PD, Dobson SJ et al. Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic lake. Int J Syst Bacteriol 1998; 48:1405–1412 [View Article] [PubMed]
     [Google Scholar]
  40. Bernardet JF, 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]
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Flavobacterium poyangense sp. nov., an ammonifying bacterium isolated from a freshwater lake
Int J Syst Evol Microbiol 74, 006416 (2024); https://doi.org/10.1099/ijsem.0.006416
/content/journal/ijsem/10.1099/ijsem.0.006416
/content/journal/ijsem/10.1099/ijsem.0.006416
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