1887

Abstract

A Gram-stain-negative, rod-shaped bacterium, designated Ery1, was isolated from deep-sea seawater collected from the Mariana Trench and subjected to a polyphasic investigation for taxonomy. Strain Ery1 was able to grow in medium containing 0–10 % NaCl (w/v; optimum, 0–1.0 %), pH 5.0–9.5 (optimum, pH 6.0–7.0) and at temperatures between 10–45 °C (optimum, 30–40 °C). The comparison of 16S rRNA gene sequences revealed that strain Ery1 showed highest similarity to A ltererythrobacter xinjiangensis S3-63 (97.7 %) and A ltererythrobacter rigui WW3 (97.6 %), and exhibited less than 97.5 % sequence similarity to other type strains of the species with validly published names. Phylogenetic analyses indicated that strain Ery1 fell within the cluster comprising the Altererythrobacter species and formed a coherent clade with A ltererythrobacter xinjiangensis and A ltererythrobacter soli . The OrthoANIu and in silico DNA–DNA hybridization values between strain Ery1 and the reference strains were 73.8–75.9 % and 19.2–20.1 %, respectively. Strain Ery1 contained Q-10 as the major respiratory quinone and Q-11 in a minor amount. The major fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C18 : 1ω7c 11-methyl and C14 : 0 2-OH. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidyglycerol, phatidylethanolamine, phosphatidylcholine and three unidentified glycolipids. Differential phenotypic properties, chemotaxonomic differences, phylogenetic distinctiveness, together with the genomic data demonstrated that strain Ery1 represents a novel species of the genus Altererythrobacter , for which named as Altererythrobacter aerophilus sp. nov. with the type strain Ery1 (=KCTC 62387=CGMCC 1.16499=MCCC 1A10037).

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2019-04-03
2021-06-23
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References

  1. Kwon KK, Woo JH, Yang SH, Kang JH, Kang SG et al. Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov. Int J Syst Evol Microbiol 2007; 57:2207–2211 [View Article][PubMed]
    [Google Scholar]
  2. 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]
  3. Xue H, Piao CG, Guo MW, Wang LF, Fang W et al. Description of Altererythrobacter aerius sp. nov., isolated from air, and emended description of the genus Altererythrobacter . Int J Syst Evol Microbiol 2016; 66:4543–4548 [View Article][PubMed]
    [Google Scholar]
  4. Zhao Q, Li HR, Han QQ, He AL, Nie CY, Hr L, Al H et al. Altererythrobacter soli sp. nov., isolated from desert sand. Int J Syst Evol Microbiol 2017; 67:454–459 [View Article][PubMed]
    [Google Scholar]
  5. Xue X, Zhang K, Cai F, Dai J, Wang Y et al. Altererythrobacter xinjiangensis sp. nov., isolated from desert sand, and emended description of the genus Altererythrobacter . Int J Syst Evol Microbiol 2012; 62:28–32 [View Article][PubMed]
    [Google Scholar]
  6. Dahal RH, Kim J. Altererythrobacter fulvus sp. nov., a novel alkalitolerant alphaproteobacterium isolated from forest soil. Int J Syst Evol Microbiol 2018; 68:1502–1508 [View Article][PubMed]
    [Google Scholar]
  7. Liao H, Li Y, Zhang M, Lin X, Lai Q et al. Altererythrobacter mangrovi sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2017; 67:4851–4856 [View Article][PubMed]
    [Google Scholar]
  8. Zhang W, Yuan X, Feng Q, Zhang R, Zhao X et al. Altererythrobacter buctense sp. nov., isolated from mudstone core. Antonie van Leeuwenhoek 2016; 109:793–799 [View Article][PubMed]
    [Google Scholar]
  9. Jung YT, Park S, Lee JS, Yoon JH. Altererythrobacter aestiaquae sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:3943–3949 [View Article][PubMed]
    [Google Scholar]
  10. Park SC, Baik KS, Choe HN, Lim CH, Kim HJ et al. Altererythrobacter namhicola sp. nov. and Altererythrobacter aestuarii sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2011; 61:709–715 [View Article][PubMed]
    [Google Scholar]
  11. Wu YH, Xu L, Meng FX, Zhang DS, Wang CS et al. Altererythrobacter atlanticus sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:116–121 [View Article][PubMed]
    [Google Scholar]
  12. Matsumoto M, Iwama D, Arakaki A, Tanaka A, Tanaka T et al. Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from a marine sediment. Int J Syst Evol Microbiol 2011; 61:2956–2961 [View Article][PubMed]
    [Google Scholar]
  13. Jung YT, Park S, Lee JS, Yoon JH. Altererythrobacter aquiaggeris sp. nov., isolated from water of an estuary bank. Int J Syst Evol Microbiol 2017; 67:3410–3416 [View Article][PubMed]
    [Google Scholar]
  14. Fan ZY, Xiao YP, Hui W, Tian GR, Lee JS et al. Altererythrobacter dongtanensis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2011; 61:2035–2039 [View Article][PubMed]
    [Google Scholar]
  15. Jeong SH, Jin HM, Lee HJ, Jeon CO. Altererythrobacter gangjinensis sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2013; 63:971–976 [View Article][PubMed]
    [Google Scholar]
  16. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7[PubMed]
    [Google Scholar]
  17. Guo LL, Wu YH, Xu XW, Huang CJ, Xu YY et al. Actibacterium pelagium sp. nov., a novel alphaproteobacterium, and emended description of the genus Actibacterium . Int J Syst Evol Microbiol 2017; 67:5080–5086 [View Article][PubMed]
    [Google Scholar]
  18. 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 [View Article][PubMed]
    [Google Scholar]
  19. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  20. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article][PubMed]
    [Google Scholar]
  21. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35:7188–7196 [View Article][PubMed]
    [Google Scholar]
  22. 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]
  23. 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]
  24. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  26. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
  29. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  32. Yan ZF, Lin P, Won KH, Yang JE, Li CT, Ct L et al. Altererythrobacter deserti sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2017; 67:3806–3811 [View Article][PubMed]
    [Google Scholar]
  33. 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]
  34. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad Hoc Committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  35. Cai MY, Dong XZ. Determinative Manual for Routine Bacteriology BeiJing: Scientific Press; 2001
    [Google Scholar]
  36. Farmer III JJ, Janda JM, Brenner FW, Cameron DN, Birkhead KM et al. Genus I. Vibrio Pacini 1854, 411AL. In Garrity GM, Brenner DJ, Krieg NR, Staley JT. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. vol. 2, The Proteobacteria, Part B, The Gammaproteobacteria New York: Springer; 2005 pp. 494–546
    [Google Scholar]
  37. Leifson E. Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 1963; 85:1183–1184[PubMed]
    [Google Scholar]
  38. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: USA: ASM Press; 2007 pp. 330–393
    [Google Scholar]
  39. Fang C, Wu YH, Xamxidin M, Wang CS, Xu XW. Maribacter cobaltidurans sp. nov., a heavy-metal-tolerant bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2017; 67:5261–5267 [View Article][PubMed]
    [Google Scholar]
  40. 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]
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