The taxonomic position of a novel bacterial strain, YC6269T, isolated from the rhizosphere of rice (Oryza sativa L.) managed under no-tillage practice in Jinju, South Korea, was studied using polyphasic approach. Cells of the strain were Gram-negative, rod-shaped and facultatively anaerobic. The novel strain grew at a temperature of 15–42 °C (optimum at 28 °C). Growth of the strain occurred between pH 5.5 and 11.0, with an optimum at pH 7.0–8.0. The G+C content of the total DNA was 67.4 mol%. The 16S rRNA gene sequence of the strain was most closely related to species of the genus Lysobacter, Lysobacter yangpyeongensis DSM 17635T (98.6 %), Lysobacter niabensis GH34-4T (97.2 %), Lysobacter enzymogenes DSM 2043T (96.9 %), Lysobacter daejeonensis DSM 17634T (96.3 %) and Lysobacter niastensis GH41-7T (96.2 %). The novel strain showed <96.0 % similarity with other species of the genus Lysobacter. Chemotaxonomic data (major quinone, Q-8; major polar lipids, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine, and major fatty acids, C15 : 0 iso, C16 : 0 iso, C17 : 0 iso and C17 : 1 iso ω9c) supported the affiliation of strain YC6269T to the genus Lysobacter. Phylogenetic analysis based on the 16S rRNA gene sequences, DNA–DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain YC6269T from recognized species of the genus Lysobacter. Strain YC6269T, therefore, represents a novel member of the genus Lysobacter, for which the name Lysobacter oryzae sp. nov. is proposed. The type strain is YC6269T (=KCTC 22249T=DSM 21044T).
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 Bioeng95, 27–34.[CrossRef][Google Scholar]
Atlas, R. M.(1993).Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
Ausubel, F. W., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K.(1995).Current Protocols in Molecular Biology. New York: Wiley.
Brown, A. E.(2007). Benson's Microbiological Applications. In Laboratory Manual in General Microbiology. New York: McGraw-Hill, Janice Roerig-Blong.
Cappuccino, J. G. & Sherman, N.(2002).Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings.
Chohnan, S., Nonaka, J., Teramoto, K., Taniguchi, K., Kameda, Y., Tamura, H., Kurusu, Y., Norioka, S., Masaki, T. & Sakiyama, F.(2002).Lysobacter strain with high lysyl endopeptidase production. FEMS Microbiol Lett213, 13–20.[CrossRef][Google Scholar]
Christensen, P. & Cook, F. D.(1978).Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol28, 367–393.[CrossRef][Google Scholar]
Chung, Y. R., Sung, K. C., Mo, H. K., Son, D. Y., Nam, J. S., Chun, J. & Bae, K. S.(1999).Kitasatospora cheerisanensis sp. nov., a new species of the genus Kitasatospora that produces an antifungal agent. Int J Syst Bacteriol49, 753–758.[CrossRef][Google Scholar]
Costilow, R. N.(1981). Biophysical factors in growth. In Manual of Methods for General Bacteriology, pp. 66–78. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Phillips. Washington, DC: American Society for Microbiology.
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 Bacteriol39, 224–229.[CrossRef][Google Scholar]
Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution39, 783–791.[CrossRef][Google Scholar]
Fitch, W. M.(1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool20, 406–416.[CrossRef][Google Scholar]
Folman, L. B., Postma, J. & Veen, J. A. V.(2001). Ecophysiological characterization of rhizosphere bacterial communities at different root locations and plant developmental stages of cucumber grown on rockwool. Microb Ecol42, 586–597.[CrossRef][Google Scholar]
Folman, L. B., De Klein, M. J. E. M., Postma, J. & van Veen, J. A.(2004). Production of antifungal compounds by Lysobacter enzymogenes isolate 3.1T8 under different conditions in relation to its efficacy as a biocontrol agent of Pythium aphanidermatum in cucumber. Biol Control31, 145–154.[CrossRef][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 Ser41, 95–98.
[Google Scholar]
Hamaki, T., Suzuki, M., Fudou, R., Jojima, Y., Kajiura, T., Tabuchi, A., Sen, K. & Shibai, H.(2005). Isolation of novel bacteria and actinomycetes using soil-extract agar medium. J Biosci Bioeng99, 485–492.[CrossRef][Google Scholar]
Hashizume, H., Hattor, 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][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 Microbiol71, 3786–3796.[CrossRef][Google Scholar]
Janssen, P. H., Yates, P. S., Grinton, B. E., Taylor, P. M. & Sait, M.(2002). Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol68, 2391–2396.[CrossRef][Google Scholar]
Joseph, S. J., Hugenholtz, P., Sangwan, P., Osborne, C. A. & Janssen, P. H.(2003). Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol69, 7210–7215.[CrossRef][Google Scholar]
Kato, A., Nakaya, S., Kokubo, N., Aiba, Y., Ohashi, Y. & Hirata, H.(1998). A new anti-MRSA antibiotic complex, WAP-8294A. J Antibiot (Tokyo)51, 929–935.[CrossRef][Google Scholar]
Kilic-Ekici, O. & Yuen, G. Y.(2003). Induced resistance as a mechanism of biological control by Lysobacter enzymogenes strain C3. Biol Control93, 1103–1110.
[Google Scholar]
Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
Kinyon, J. M. & Harris, D. L.(1979).Treponema innocens, a new species of intestinal bacteria, and emended description of the type strain of Treponema hyodysenteriae Harris et al. Int J Syst Bacteriol29, 102–109.
Lane, D. J.(1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
Lechevalier, M. P., De Bièvre, C. & Lechevalier, H. A.(1977). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol5, 249–260.[CrossRef][Google Scholar]
Lee, J. W., Im, W.-T., Kim, M. K. & Yang, D.-C.(2006a).Lysobacter koreensis sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol56, 231–235.[CrossRef][Google Scholar]
Lee, M. S., Do, J. O., Park, M. S., Jung, S., Lee, K. H., Bae, K. S., Park, S. J. & Kim, S. B.(2006b). Dominance of Lysobacter sp. in the rhizosphere of two coastal sand dune plant species, Calystegia soldanella and Elymus mollis. Antonie van Leeuwenhoek90, 19–27.[CrossRef][Google Scholar]
Lueders, T., Kindler, R., Miltner, A., Friedrich, M. W. & Kaestner, M.(2006). Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl Environ Microbiol72, 5342–5348.[CrossRef][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 Bacteriol39, 159–167.[CrossRef][Google Scholar]
Nakayama, T., Homma, Y., Hashidoko, Y., Mizutani, J. & Tahara, S.(1999). Possible role of xanthobaccins produced by Stenotrophomonas sp. strain SB-K88 in suppression of sugar beet damping-off disease. Appl Environ Microbiol65, 4334–4339.
[Google Scholar]
Ohman, D. E., Cryz, S. J. & Iglewski, B. H.(1980). Isolation and characterization of a Pseudomonas aeruginosa PAO mutant that produces altered elastase. J Bacteriol142, 836–842.
[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 Microbiol58, 387–392.[CrossRef][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 Microbiol58, 370–374.[CrossRef][Google Scholar]
Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4, 406–425.
[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 Bacteriol44, 846–849.[CrossRef][Google Scholar]
Tamura, K., Dudley, J., Nei, M. & Kumar, S.(2007).mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol24, 1596–1599.[CrossRef][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 Methods56, 375–382.[CrossRef][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 Res25, 4876–4882.[CrossRef][Google Scholar]
Tindall, B. J.(1990). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett66, 199–202.[CrossRef][Google Scholar]
Wallace, R. J., Jr, Brown, B. A., Blacklock, Z., Ulrich, R., Jost, K., Brown, J. M., McNeil, M. M., Onyi, G., Steingrube, V. A. & Gibson, J.(1995). New Nocardia taxon among isolates of Nocardia brasiliensis associated with invasive disease. J Clin Microbiol33, 1528–1533.
[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 Bacteriol37, 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 Microbiol56, 947–951.[CrossRef][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 Microbiol57, 548–551.[CrossRef][Google Scholar]
Yassin, A. F., Chen, W. M., Hupfer, H., Siering, C., Kroppenstedt, R. M., Arun, A. B., Lai, W. A., Shen, F. T., Rekha, P. D. & Young, C. C.(2007).Lysobacter defluvii sp. nov., isolated from municipal solid waste. Int J Syst Evol Microbiol57, 1131–1136.[CrossRef][Google Scholar]