1887

Abstract

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9 formed a monophyletic branch affiliated to the family , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with DSM 17368, followed by similarities of 90.4, 90.1 and 88.8 % with MCCC 1F01079, DSM 103558 and MCCC 1K02288, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9 and DSM 17368 shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9 contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C (37.5 %), iso-C 3-OH (12.4 %), and summed feature 3 (Cω7 /C1ω6, 11.6 %). Combining the genotypic and phenotypic data, A20-9 could be distinguished from the members of other genera within the family and represents a novel genus, for which the name gen. nov., sp. nov. is proposed. The type strain is A20-9 (=MCCC 1A17358 =KCTC 72878).

Funding
This study was supported by the:
  • National Infrastructure of Natural Resources for Science and Technology Program of China (Award NIMR-2020-9)
    • Principle Award Recipient: ZongzeShao
  • Secretaria de Desenvolvimento Econômico, Ciência, Tecnologia e Inovação (BR) (Award 16PZP001SF16)
    • Principle Award Recipient: ZongzeShao
  • COMRA program (Award No. DY135-B2-01)
    • Principle Award Recipient: ZongzeShao
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2021-04-13
2021-05-15
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References

  1. Cottrell MT, Kirchman DL. Natural assemblages of marine Proteobacteria and members of the CytophagaFlavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol 2000; 66:1692–1697 [CrossRef][PubMed]
    [Google Scholar]
  2. Roager L, Sonnenschein EC. Bacterial candidates for colonization and degradation of marine plastic debris. Environ Sci Technol 2019; 53:11636–11643 [CrossRef][PubMed]
    [Google Scholar]
  3. Lau KWK, Ng CYM, Ren J, Lau SCL, Qian P-Y et al. Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum 'Bacteroidetes'. Int J Syst Evol Microbiol 2005; 55:1051–1057 [CrossRef][PubMed]
    [Google Scholar]
  4. Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Schleiferia thermophila gen. nov., sp. nov., a slightly thermophilic bacterium of the phylum 'Bacteroidetes' and the proposal of Schleiferiaceae fam. nov. Int J Syst Evol Microbiol 2011; 61:2450–2455 [CrossRef][PubMed]
    [Google Scholar]
  5. Iino T, Kawai S, Yuki M, Dekio I, Ohkuma M et al. Thermaurantimonas aggregans gen. nov., sp. nov., a moderately thermophilic heterotrophic aggregating bacterium isolated from microbial mats at a terrestrial hot spring. Int J Syst Evol Microbiol 2020; 70:1117–1121 [CrossRef][PubMed]
    [Google Scholar]
  6. Bowman JP. Out from the shadows – resolution of the taxonomy of the family Cryomorphaceae . Front Microbiol 2020; 11:795 [CrossRef][PubMed]
    [Google Scholar]
  7. Zhou Y, Su J, Lai Q, Li X, Yang X et al. Phaeocystidibacter luteus gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from the marine alga Phaeocystis globosa, and emended description of Owenweeksia hongkongensis . Int J Syst Evol Microbiol 2013; 63:1143–1148 [CrossRef][PubMed]
    [Google Scholar]
  8. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019; 36:1925–1927 [CrossRef][PubMed]
    [Google Scholar]
  9. Dyksterhouse SE, Gray JP, Herwig RP, Lara JC, Staley JT. Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int J Syst Bacteriol 1995; 45:116–123 [CrossRef][PubMed]
    [Google Scholar]
  10. Liu Q-Q, Wang Y, Li J, Du Z-J, Chen G-J. Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans . Int J Syst Evol Microbiol 2014; 64:2204–2209 [CrossRef][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003; 4:41 [CrossRef][PubMed]
    [Google Scholar]
  16. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [CrossRef][PubMed]
    [Google Scholar]
  17. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [CrossRef][PubMed]
    [Google Scholar]
  18. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  19. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  20. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. Isme J 2017; 11:2399–2406 [CrossRef][PubMed]
    [Google Scholar]
  21. Liu Y, Lai Q, Du J, Shao Z. Bacillus zhangzhouensis sp. nov. and Bacillus australimaris sp. nov. Int J Syst Evol Microbiol 2016; 66:1193–1199 [CrossRef][PubMed]
    [Google Scholar]
  22. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50 Pt 5:1861–1868 [CrossRef][PubMed]
    [Google Scholar]
  23. Cowan ST, Steel KJ, Mccoy E. Manual for the identification of medical bacteria. Proc R Soc Med 1966; 59:468–472
    [Google Scholar]
  24. Hameed A, Shahina M, Lin S-Y, Sridhar KR, Young L-S et al. Siansivirga zeaxanthinifaciens gen. nov., sp. nov., a novel zeaxanthin-producing member of the family Flavobacteriaceae isolated from coastal seawater of Taiwan. FEMS Microbiol Lett 2012; 333:37–45 [CrossRef][PubMed]
    [Google Scholar]
  25. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark,DE: MIDI Inc; 1990
    [Google Scholar]
  26. 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 [CrossRef]
    [Google Scholar]
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