1887

Abstract

A Gram-stain-negative, aerobic, non-motile and coccoid-, ovoid- or rod-shaped bacterial strain, designated KEM-5, was isolated from water sampled at an estuary environment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain KEM-5 fell within the clade comprising the type strains of species. Strain KEM-5 exhibited 16S rRNA gene sequence similarities of 97.01–97.66 % to the type strains of , and and of 94.18–96.95 % to the type strains of the other species. The genomicaverage nucleotide identity values of strain KEM-5 with a non-type strain (LAMA 915) of and SW-135 were 76.04 and 74.98 %, respectively. Mean DNA–DNA relatedness values between strain KEM-5 and the type strains of , and were 10–18 %. Strain KEM-5 contained Q-10 as the predominant ubiquinone and C 7, summed feature 3 (Cω7 and/or Cω6), C and Cω6 as the major fatty acids. The major polar lipids of strain KEM-5 were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The DNA G+C content of strain KEM-5 was 62.4 mol%. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain KEM-5 is separated from recognized species. On the basis of the data presented here, strain KEM-5 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KEM-5 (=KACC 19865=KCTC 62896=NBRC 113546).

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2019-09-01
2019-09-22
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References

  1. Lee KB, Liu CT, Anzai Y, Kim H, Aono T et al. The hierarchical system of the 'Alphaproteobacteria': description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 2005;55:1907–1919 [CrossRef][PubMed]
    [Google Scholar]
  2. Shiba T, Simidu U. Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a. Int J Syst Bacteriol 1982;32:211–217 [CrossRef]
    [Google Scholar]
  3. 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 [CrossRef][PubMed]
    [Google Scholar]
  4. Yurkov V, Stackebrandt E, Holmes A, Fuerst JA, Hugenholtz P et al. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 1994;44:427–434 [CrossRef][PubMed]
    [Google Scholar]
  5. Denner EB, Vybiral D, Koblízek M, Kämpfer P, Busse HJ et al. Erythrobacter citreus sp. nov., a yellow-pigmented bacterium that lacks bacteriochlorophyll a, isolated from the western Mediterranean Sea. Int J Syst Evol Microbiol 2002;52:1655–1661 [CrossRef][PubMed]
    [Google Scholar]
  6. Yoon JH, Kim H, Kim IG, Kang KH, Park YH. Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. Int J Syst Evol Microbiol 2003;53:1169–1174 [CrossRef][PubMed]
    [Google Scholar]
  7. Yoon JH, Kang KH, Oh TK, Park YH. Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2004;54:1981–1985 [CrossRef][PubMed]
    [Google Scholar]
  8. Yoon JH, Oh TK, Park YH. Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005;55:71–75 [CrossRef][PubMed]
    [Google Scholar]
  9. Ivanova EP, Bowman JP, Lysenko AM, Zhukova NV, Gorshkova NM et al. Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates. Syst Appl Microbiol 2005;28:123–130 [CrossRef][PubMed]
    [Google Scholar]
  10. Xu M, Xin Y, Yu Y, Zhang J, Zhou Y et al. Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea. Int J Syst Evol Microbiol 2010;60:2215–2220 [CrossRef][PubMed]
    [Google Scholar]
  11. Jung YT, Park S, Lee JS, Yoon JH. Erythrobacter lutimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014;64:4184–4190 [CrossRef][PubMed]
    [Google Scholar]
  12. Lei X, Zhang H, Chen Y, Li Y, Chen Z et al. Erythrobacter luteus sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2015;65:2472–2478 [CrossRef][PubMed]
    [Google Scholar]
  13. Zhuang L, Liu Y, Wang L, Wang W, Shao Z. Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 2015;65:3714–3719 [CrossRef][PubMed]
    [Google Scholar]
  14. Park S, Jung YT, Choi SJ, Yoon JH. Erythrobacter aquimixticola sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017;67:2964–2969 [CrossRef][PubMed]
    [Google Scholar]
  15. Xing T, Liu Y, Wang N, Xu B, Liu K et al. Erythrobacter arachoides sp. nov., isolated from ice core. Int J Syst Evol Microbiol 2017;67:4235–4239 [CrossRef][PubMed]
    [Google Scholar]
  16. Park S, Jung YT, Park JM, Yoon JH. Algoriphagus aquaemixtae sp. nov., isolated from water in an estuary environment. Int J Syst Evol Microbiol 2017;67:4168–4174 [CrossRef][PubMed]
    [Google Scholar]
  17. Yoon J-H, Kim H, Kim S-B, Kim H-J, Kim WY et al. Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. Int J Syst Bacteriol 1996;46:502–505 [CrossRef]
    [Google Scholar]
  18. Yoon J-H, Lee ST, Kim S-B, Kim WY, Goodfellow M et al. Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains. Int J Syst Bacteriol 1997;47:111–114 [CrossRef]
    [Google Scholar]
  19. Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 2012;7:e42304 [CrossRef][PubMed]
    [Google Scholar]
  20. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017;110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  21. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989;39:224–229 [CrossRef]
    [Google Scholar]
  22. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207
    [Google Scholar]
  23. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  24. 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]
  25. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Modern Microbial Methods. Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994; pp.121–161
    [Google Scholar]
  26. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984;25:125–128 [CrossRef]
    [Google Scholar]
  27. Park S, Won SM, Kim H, Park DS, Yoon JH. Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014;64:2969–2974 [CrossRef][PubMed]
    [Google Scholar]
  28. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Mocrobiol 1987;19:1–67
    [Google Scholar]
  29. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001;51:1997–2006 [CrossRef][PubMed]
    [Google Scholar]
  30. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 1993
    [Google Scholar]
  31. Baumann P, Baumann L. The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG et al. (editors) The Prokaryotes Berlin: Springer; 1981; pp.1302–1331
    [Google Scholar]
  32. Cohen-Bazire G, Sistrom WR, Stanier RY. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J Cell Comp Physiol 1957;49:25–68 [CrossRef][PubMed]
    [Google Scholar]
  33. Staley JT. Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 1968;95:1921–1942[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 [CrossRef]
    [Google Scholar]
  35. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846–849 [CrossRef]
    [Google Scholar]
  36. 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 [CrossRef][PubMed]
    [Google Scholar]
  37. Wu HX, Lai PY, Lee OO, Zhou XJ, Miao L et al. Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea. Int J Syst Evol Microbiol 2012;62:1348–1353 [CrossRef][PubMed]
    [Google Scholar]
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