1887

Abstract

A Gram-reaction-negative, peach-brown-pigmented, slightly curved-rod-shaped, aerobic, non-motile bacterium, designated GSA243-2, was isolated from fresh water samples collected from the Chishui River flowing through Maotai, Guizhou, south-west PR China. Phenotypic, chemotaxonomic and genomic traits were investigated. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus . The closest phylogenetic relative was ATCC BAA-1852 (98.35 %). The major fatty acids were C and Cω6 and/or Cω7. The major respiratory quinone was ubiquinone Q-8 and the major polar lipid was phosphatidylethanolamine. Genome sequencing revealed a genome size of 3.67 Mbp and a G+C content of 61.17 mol%. Pairwise-determined whole genome average nucleotide identity values and digital DNA–DNA hybridization values suggested that strain GSA243-2 represents a new species, for which we propose the name sp. nov. with the type strain GSA243-2 (=CGMCC 1.16288=KCTC 62564).

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/content/journal/ijsem/10.1099/ijsem.0.003700
2019-09-09
2019-09-18
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References

  1. Hiraishi A, Hoshino Y, Satoh T. Rhodoferax fermentans gen. nov., sp. nov., a phototrophic purple nonsulfur bacterium previously referred to as the? Rhodocyclus gelatinosus-like? group. Arch Microbiol 1991;155:330–336 [CrossRef]
    [Google Scholar]
  2. Madigan MT, Jung DO, Woese CR, Achenbach LA. Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat. Arch Microbiol 2000;173:269–277 [CrossRef][PubMed]
    [Google Scholar]
  3. Finneran KT, Johnsen CV, Lovley DR. Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III). Int J Syst Evol Microbiol 2003;53:669–673 [CrossRef][PubMed]
    [Google Scholar]
  4. Kaden R, Spröer C, Beyer D, Krolla-Sidenstein P. Rhodoferax saidenbachensis sp. nov., a psychrotolerant, very slowly growing bacterium within the family Comamonadaceae, proposal of appropriate taxonomic position of Albidiferax ferrireducens strain T118T in the genus Rhodoferax and emended description of the genus Rhodoferax. Int J Syst Evol Microbiol 2014;64:1186–1193 [CrossRef][PubMed]
    [Google Scholar]
  5. Farh ME, Kim YJ, Singh P, Jung SY, Kang JP et al. Rhodoferax koreense sp. nov, an obligately aerobic bacterium within the family Comamonadaceae, and emended description of the genus Rhodoferax. J Microbiol 2017;55:767–774 [CrossRef][PubMed]
    [Google Scholar]
  6. Tan X, Zhang RG, Meng TY, Liang HZ, Lv J. Taibaiella chishuiensis sp. nov., isolated from fresh water of the chishui river in maotai town, china. Int J Syst Evol Microbiol 2014;64:1795–1801
    [Google Scholar]
  7. Zhang RG, Tan X, Liang Y, Meng TY, Liang HZ et al. Description of Chishuiella changwenlii gen. nov., sp. nov., isolated from freshwater, and transfer of Wautersiella falsenii to the genus Empedobacter as Empedobacter falsenii comb. nov. Int J Syst Evol Microbiol 2014;64:2723–2728 [CrossRef][PubMed]
    [Google Scholar]
  8. Steven B, Briggs G, Mckay CP, Pollard WH, Greer CW et al. Characterization of the microbial diversity in a permafrost sample from the Canadian high Arctic using culture-dependent and culture-independent methods. FEMS Microbiol Ecol 2007;59:513–523 [CrossRef][PubMed]
    [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991; pp.115–175
    [Google Scholar]
  10. 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 [CrossRef][PubMed]
    [Google Scholar]
  11. 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 [CrossRef][PubMed]
    [Google Scholar]
  12. 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 [CrossRef][PubMed]
    [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  14. Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 1989;29:170–179 [CrossRef][PubMed]
    [Google Scholar]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  18. 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]
  19. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265–272 [CrossRef][PubMed]
    [Google Scholar]
  20. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24:713–714 [CrossRef][PubMed]
    [Google Scholar]
  21. 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 [CrossRef][PubMed]
    [Google Scholar]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. Lin SH, Liao YC. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One 2013;8:e60843 [CrossRef][PubMed]
    [Google Scholar]
  24. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015;43:D261–D269 [CrossRef][PubMed]
    [Google Scholar]
  25. Weon HY, Yoo SH, Hong SB, Kwon SW, Stackebrandt E et al. Polaromonas jejuensis sp. nov., isolated from soil in Korea. Int J Syst Evol Microbiol 2008;58:1525–1528 [CrossRef][PubMed]
    [Google Scholar]
  26. Murray R, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.21–41
    [Google Scholar]
  27. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  28. Bernardet JF, 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 [CrossRef][PubMed]
    [Google Scholar]
  29. Piao AL, Feng XM, Nogi Y, Han L, Li Y et al. Sphingomonas qilianensis sp. nov., isolated from surface soil in the permafrost region of qilian mountains, China. Curr Microbiol 2016;72:363–369 [CrossRef][PubMed]
    [Google Scholar]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Netwark, DE: MIDI Inc; 1990
    [Google Scholar]
  31. 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]
  32. da Costa MS, Albuquerque L, Nobre MF, Wait R. The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Methods Microbiol 2011;38:197–206
    [Google Scholar]
  33. da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Method Microbiol 2011;38:165–181
    [Google Scholar]
  34. Jeon CO, Park W, Ghiorse WC, Madsen EL. Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment. Int J Syst Evol Microbiol 2004;54:93–97 [CrossRef][PubMed]
    [Google Scholar]
  35. Ding L, Yokota A. Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. Int J Syst Evol Microbiol 2004;54:2223–2230 [CrossRef][PubMed]
    [Google Scholar]
  36. Coleman NV, Mattes TE, Gossett JM, Spain JC. Biodegradation of cis-dichloroethene as the sole carbon source by a beta-proteobacterium. Appl Environ Microbiol 2002;68:2726–2730 [CrossRef][PubMed]
    [Google Scholar]
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