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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 7

sp. nov. and sp. nov., isolated from a mariculture fishpond Free

Abstract

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13C and H41) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13C and H41 shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus . YJ13C only shared 93.8 % 16S rRNA gene sequence similarity with H41. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13C and H41 clustered closely with species of the genus . The calculated pairwise orthologous average nucleotide identity with (OrthoANIu) values between strains YJ13C and H41 and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13C and H41 was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13C and H41 and their major cellular fatty acids contained iso-C, C ω7 and C ω9. The polar lipids profiles of YJ13C and H41 consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13C and H41 represent two distinct novel species of the genus , for which the names sp. nov. (type strain YJ13C=GDMCC 1.2178=KCTC 82450) and sp. nov. (type strain H41=GDMCC 1.2179=KCTC 82451) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Algoriphagus , mariculture fishpond and polyphasic taxonomy
Funding
This study was supported by the:
  • gdas’ special project of science and technology development (Award 2020GDASYL-20200103016; 2020GDASYL-20200402001)
    • Principle Award Recipient: MeiyingXu
  • guangdong mepp fund (Award NO. GDOE(2019)A34)
    • Principle Award Recipient: MeiyingXu
  • guangdong provincial programs for science and technology development (Award 2020B0202080005; 2019B110205004)
    • Principle Award Recipient: MeiyingXu
  • guangdong technological innovation strategy of special funds (Award Key Areas of Research and Development Program (2018B020205003))
    • Principle Award Recipient: MeiyingXu
© 2021 The Authors
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2021-07-22
2024-12-08
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References

  1. Bowman JP, Nichols CM, Gibson JAE. Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 2003; 53:1343–1355 [View Article] [PubMed]
     [Google Scholar]
  2. Nedashkovskaya OI, Vancanneyt M, Van Trappen S, Vandemeulebroecke K, Lysenko AM et al. Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004. Int J Syst Evol Microbiol 2004; 54:1757–1764 [View Article] [PubMed]
     [Google Scholar]
  3. Nedashkovskaya OI, Kim SB, Kwon KK, Shin DS, Luo X et al. Proposal of Algoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskaya et al. 2004. Int J Syst Evol Microbiol 2007; 57:1988–1994 [View Article] [PubMed]
     [Google Scholar]
  4. Rau JE, Blotevogel KH, Fischer U. Algoriphagus aquaeductus sp. nov., isolated from a freshwater pipe. Int J Syst Evol Microbiol 2012; 62:675–682 [View Article] [PubMed]
     [Google Scholar]
  5. Wang XM, Wang XT, Wang XQ, Mu DS, Du ZJ. Algoriphagus lacus sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2020; 70:193–198 [View Article]
     [Google Scholar]
  6. Han J-R, Geng Q-L, Wang F-Q, Du Z-J, Chen G-J. Algoriphagus marinus sp. nov., isolated from marine sediment and emended description of the genus Algoriphagus. Int J Syst Evol Microbiol 2017; 67:2412–2417 [View Article]
     [Google Scholar]
  7. Ye MQ, Wang XT, Zhang J, Chen GJ, Du ZJ. Algoriphagus formosus sp. nov., isolated from coastal sediment. Antonie Van Leeuwenhoek 2018; 111:913–920 [View Article]
     [Google Scholar]
  8. Young C-C, Lin S-Y, Arun AB, Shen F-T, Chen W-M et al. Algoriphagus olei sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2009; 59:2909–2915 [View Article] [PubMed]
     [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acid Sequencing Techniques in Bacterial Systematics New York, USA: Wiley; 1991 pp 115–175
     [Google Scholar]
  10. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing Ezbiocloud: A taxonomically united database of 16s rrna and whole genome assemblies. Int J Syst Evol Microbiol 2016; 67:1613–1617
     [Google Scholar]
  11. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  12. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  13. 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]
  14. 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]
  15. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Systematic Zoology 1969; 18:1 [View Article]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  19. 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 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. 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; 110:1–6
     [Google Scholar]
  22. 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]
     [Google Scholar]
  23. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article]
     [Google Scholar]
  24. Minoru K, Yoko S, Miho F, Kanae M, Mao T. New approach for understanding genome variations in KEGG. Nucleic Acids Res 2019; 47:590–595
     [Google Scholar]
  25. Contreras-Moreira B, Vinuesa P. Get_homologues, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
     [Google Scholar]
  26. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article] [PubMed]
     [Google Scholar]
  27. Zhu XF. Modern experimental technique of microbiology Hangzhou, China: Zhejiang University Press; 2011
     [Google Scholar]
  28. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic gram-negative rods. J Gen Microbiol 1982; 128:1959–1968
     [Google Scholar]
  29. Zhong Z-P, Liu Y, Wang F, Zhou Y-G, Liu H-C et al. Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:422–429 [View Article] [PubMed]
     [Google Scholar]
  30. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. International Journal of Systematic Bacteriology 1988; 38:358–361 [View Article]
     [Google Scholar]
  31. Sasser M. Identification of bacteria through fatty acid analysis. Klement Z, Rudolph K, Sands D. eds In Methods in Phytobacteriology Budapest, Hungary: Akademiai Kaido; 1990 pp 199–204
     [Google Scholar]
  32. 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. Journal of Microbiological Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  33. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiology Letters 1990; 66:199–202 [View Article]
     [Google Scholar]
  34. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  35. 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. International Journal of Systematic and Evolutionary Microbiology 1987; 37:463–464 [View Article]
     [Google Scholar]
  36. Yi H, Chun J. Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2004; 54:157–162 [View Article] [PubMed]
     [Google Scholar]
  37. Park S, Kang S-J, Oh K-H, Oh T-K, Yoon J-H. Algoriphagus lutimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2010; 60:200–204 [View Article]
     [Google Scholar]
  38. Jung YT, Lee JS, Yoon JH. Algoriphagus aestuarii sp. nov., a member of the Cyclobacteriaceae isolated from a tidal-flat sediment of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2015; 65:3439–3446 [View Article] [PubMed]
     [Google Scholar]
  39. Sun QL, Sun L. Description of Algoriphagus iocasae sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2017; 67:243–249 [View Article] [PubMed]
     [Google Scholar]
  40. Jia X, Jia B, Kim KH, Jeon CO. Algoriphagus aestuariicola sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2017; 67:914–919 [View Article] [PubMed]
     [Google Scholar]
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Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond
Int J Syst Evol Microbiol 71, 004914 (2021); https://doi.org/10.1099/ijsem.0.004914
/content/journal/ijsem/10.1099/ijsem.0.004914
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