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f sp. nov., isolated from activated sludge and sp. nov., isolated from freshwater sediment

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  • Authors: Muhammad Zubair Siddiqi1​ , Wan-Taek Im1​,2​
    • VIEW AFFILIATIONS
    • 1​ 1​Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea 2​ 2​Genomic Informatics Center, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do, 14 456-749, Republic of Korea
  • Wan-Taek Im [email protected]
  • First Published Online: 01 January 2016, International Journal of Systematic and Evolutionary Microbiology 66: 212-218, doi: 10.1099/ijsem.0.000699
  • Subject: NEW TAXA - Proteobacteria
  • Cover date:
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  • Two novel strains, designated KTCe-2 and 7C-9, isolated from an activated sludge and freshwater sediment, respectively in South Korea, were characterized by a polyphasic approach to clarify their taxonomic positions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus and are most closely related to ‘’ Dae 08 (98.5 % and 97.6 % similarity for strains KTCe-2 and 7C-9, respectively), KCTC 12130 (98.4 % and 97.2 %), and JCM 18257 (97.1 % and 96.8 %). The G+C content of the genomic DNA of strains KTCe-2 and 7C-9 was 68.6 % and 71.5 mol%, respectively. Strains KTCe-2 and 7C-9 possessed ubiquinone-8 as the sole respiratory quinone, and a fatty acid profile with iso-C and iso-C as the major fatty acids supported the affiliation of the two strains to the genus . Moreover, the physiological and biochemical results and low DNA–DNA relatedness values allowed the phenotypic and genotypic differentiation of strains KTCe-2 and 7C-9 from other species of the genus with validly published names. Therefore, the two isolates represent two novel species of the genus , for which the name sp. nov. (type strain KTCe-2 = JCM 18204 = KACC 16618) and sp. nov. (type strain 7C-9 = JCM 18205 = KACC 16617) are proposed.

  • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains KTCe-2 and 7C-9 are JQ349049 and JQ349048, respectively.

  • Three supplementary figures and a supplementary table are available with the online Supplementary Material.

© 2015 IUMS | Published by the Microbiology Society

  • Ahmed K., Chohnan S., Ohashi H., Hirata T., Masaki T., Sakiyama F.. ( 2003;). Purification, bacteriolytic activity, and specificity of β-lytic protease from Lysobacter sp. IB-9374. J Biosci Bioeng 95: 27––34 [CrossRef] [PubMed].
     [Google Scholar]
  • Atlas R. M.. ( 1993;). Handbook of Microbiological Media Boca Raton, FL; CRC Press:.
     [Google Scholar]
  • Bae H.-S., Im W.-T., Lee S.-T.. ( 2005;). Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor. Int J Syst Evol Microbiol 55: 1155––1161 [CrossRef] [PubMed].
     [Google Scholar]
  • Buck J. D.. ( 1982;). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44: 992––993 [PubMed].
     [Google Scholar]
  • Cappuccino J. G., Sherman N.. ( 2002;). Microbiology: a Laboratory Manual, 6th edn. California: Pearson Education, Inc;.
     [Google Scholar]
  • Choi J. H., Seok J. H., Cha J. H., Cha C. J.. ( 2014;). Lysobacter panacisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 64: 2193––2197 [CrossRef] [PubMed].
     [Google Scholar]
  • Christensen P., Cook F. D.. ( 1978;). Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28: 367––393 [CrossRef].
     [Google Scholar]
  • Ezaki T., Hashimoto Y., Yabuuchi E.. ( 1989;). 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 39: 224––229 [CrossRef].
     [Google Scholar]
  • Felsenstein J.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783––791 [CrossRef].
     [Google Scholar]
  • Fitch W. M.. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406––416 [CrossRef].
     [Google Scholar]
  • Fukuda W., Kimura T., Araki S., Miyoshi Y., Atomi H., Imanaka T.. ( 2013;). Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica. Int J Syst Evol Microbiol 63: 3313––3318 [CrossRef] [PubMed].
     [Google Scholar]
  • Hall T. A.. ( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95––98.
     [Google Scholar]
  • Hashizume H., Hattori S., Igarashi M., Akamatsu Y.. ( 2004;). Tripropeptin E, a new tripropeptin group antibiotic produced by Lysobacter sp. BMK333-48F3. J Antibiot (Tokyo) 57: 394––399 [CrossRef] [PubMed].
     [Google Scholar]
  • Hiraishi A., Ueda Y., Ishihara J., Mori T.. ( 1996;). Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42: 457––469 [CrossRef].
     [Google Scholar]
  • Im W.-T., Liu Q.-M., Yang J.-E., Kim M.-S., Kim S.-Y., Lee S.-T., Yi T.-H.. ( 2010;). Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field. J Microbiol 48: 262––266 [CrossRef] [PubMed].
     [Google Scholar]
  • Islam M. T., Hashidoko Y., Deora A., Ito T., Tahara S.. ( 2005;). Suppression of damping-off disease in host plants by the rhizoplane bacterium Lysobacter sp. strain SB-K88 is linked to plant colonization and antibiosis against soilborne Peronosporomycetes. Appl Environ Microbiol 71: 3786––3796 [CrossRef] [PubMed].
     [Google Scholar]
  • Kim O. S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716––721 [CrossRef] [PubMed].
     [Google Scholar]
  • Kimura M.. ( 1983;). The Neutral Theory of Molecular Evolution Cambridge:: [CrossRef] Cambridge University Press;.
     [Google Scholar]
  • Kouker G., Jaeger K.-E.. ( 1987;). Specific and sensitive plate assay for bacterial lipase. Appl Environ Microbiol 53: 211––213.
     [Google Scholar]
  • Mesbah M., Premachandran U., Whitman W. B.. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39: 159––167 [CrossRef].
     [Google Scholar]
  • Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H.. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2: 233––241 [CrossRef].
     [Google Scholar]
  • Moore D. D., Dowhan D.. ( 1995;). Preparation and analysis of DNA. . In Current Protocols in Molecular Biology, pp. 2––11. Edited by Ausubel F. W., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K.. New York: Wiley;.
     [Google Scholar]
  • Ngo H. T. T., Won K., Du J., Son H. M., Park Y., Kook M., Kim K. Y., Jin F. X., Yi T. H.. ( 2015;). Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil. Int J Syst Evol Microbiol 65: 587––592 [CrossRef] [PubMed].
     [Google Scholar]
  • Park J. H., Kim R., Aslam Z., Jeon C. O., Chung Y. R.. ( 2008;). Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter. Int J Syst Evol Microbiol 58: 387––392 [CrossRef] [PubMed].
     [Google Scholar]
  • Romanenko L. A., Uchino M., Tanaka N., Frolova G. M., Mikhailov V. V.. ( 2008;). Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge. Int J Syst Evol Microbiol 58: 370––374 [CrossRef] [PubMed].
     [Google Scholar]
  • Saitou N., Nei M.. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406––425 [PubMed].
     [Google Scholar]
  • Sasser M.. ( 1990;). Identification of bacteria through fatty acid analysis. . In Methods in Phytobacteriology, pp. 199––204. Edited by Klement Z., Rudolph K., Sands D. C.. Budapest: Akademiai Kaido;.
     [Google Scholar]
  • Singh H., Du J., Won K.-H., Yang J.-E., Akter S., Kim K.-Y., Yi T.-H.. ( 2015a;). Lysobacter novalis sp. nov., isolated from fallow farmland soil. Int J Syst Evol Microbiol 65: 3131––3136 [CrossRef] [PubMed].
     [Google Scholar]
  • Singh H., Won K., Du J., Yang J.-E., Akter S., Kim K.-Y., Yi T.-H.. ( 2015b;). Lysobacter agri sp. nov., a bacterium isolated from soil. Antonie van Leeuwenhoek 108: 553––561 [CrossRef] [PubMed].
     [Google Scholar]
  • Stackebrandt E., Goebel B. M.. ( 1994;). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846––849 [CrossRef].
     [Google Scholar]
  • Sullivan R. F., Holtman M. A., Zylstra G. J., White J.F., Jr, Kobayashi D. Y.. ( 2003;). Taxonomic positioning of two biological control agents for plant diseases as Lysobacter enzymogenes based on phylogenetic analysis of 16S rDNA, fatty acid composition and phenotypic characteristics. J Appl Microbiol 94: 1079––1086 [CrossRef] [PubMed].
     [Google Scholar]
  • Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731––2739 [CrossRef] [PubMed].
     [Google Scholar]
  • Ten L. N., Im W.-T., Kim M.-K., Kang M.-S., Lee S.-T.. ( 2004;). Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56: 375––382 [CrossRef] [PubMed].
     [Google Scholar]
  • Ten L. N., Jung H. M., Im W.-T., Yoo S.-A., Lee S.-T.. ( 2008;). Lysobacter daecheongensis sp. nov., isolated from sediment of stream near the Daechung dam in South Korea. J Microbiol 46: 519––524 [CrossRef] [PubMed].
     [Google Scholar]
  • Ten L. N., Jung H.-M., Im W.-T., Yoo S.-A., Oh H.-M., Lee S.-T.. ( 2009;). Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 59: 958––963 [CrossRef] [PubMed].
     [Google Scholar]
  • Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G.. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876––4882 [CrossRef] [PubMed].
     [Google Scholar]
  • Wang Y., Dai J., Zhang L., Luo X., Li Y., Chen G., Tang Y., Meng Y., Fang C.. ( 2009;). Lysobacter ximonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59: 786––789 [CrossRef] [PubMed].
     [Google Scholar]
  • Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. ( 1987;). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37: 463––464 [CrossRef].
     [Google Scholar]
  • Weon H.-Y., Kim B.-Y., Baek Y.-K., Yoo S.-H., Kwon S.-W., Stackebrandt E., Go S.-J.. ( 2006;). Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. Int J Syst Evol Microbiol 56: 947––951 [CrossRef] [PubMed].
     [Google Scholar]
  • Weon H.-Y., Kim B.-Y., Kim M.-K., Yoo S.-H., Kwon S.-W., Go S.-J., Stackebrandt E.. ( 2007;). Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 57: 548––551 [CrossRef] [PubMed].
     [Google Scholar]
  • Yang S.-Z., Feng G.-D., Zhu H.-H., Wang Y.-H.. ( 2015;). Lysobacter mobilis sp. nov., isolated from abandoned lead-zinc ore. Int J Syst Evol Microbiol 65: 833––837 [CrossRef] [PubMed].
     [Google Scholar]
  • Ye X.-M., Chu C.-W., Shi C., Zhu J.-C., He Q., He J.. ( 2015;). Lysobacter caeni sp. nov., isolated from the sludge of a pesticide manufacturing factory. Int J Syst Evol Microbiol 65: 845––850 [CrossRef] [PubMed].
     [Google Scholar]
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