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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 63, Issue Pt_4

gen. nov., sp. nov., isolated from soil, and reclassification of Dastager 2009 as sp. nov., comb. nov. Free

Abstract

A Gram-stain-positive, non-motile rod, designated strain SGM3-12, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family . The nearest phylogenetic neighbour was MSL-13 (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12 and MSL-13 formed a distinct cluster within the family . Strain SGM3-12 contained MK-12(H) and MK-11(H) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C and iso-C as the major cellular fatty acids (>10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1δ with -Lys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12 represents a novel species within a new genus, for which the name gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12 = KACC 13362 = NBRC 107106). It is also proposed that be transferred to this genus as comb. nov. (the type strain is MSL-13 = DSM 19272 = JCM 16015 = KACC 21108 = KCTC 19267).

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Funding
This study was supported by the:
  • Research Program for Agricultural Science & Technology Development, National Academy of Agricultural Science, Rural Development Administration, Republic of Korea (Award PJ008666)
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2013-04-01
2025-05-16
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References

  1. An S.-Y., Yokota A. ( 2007 ). The status of the species Leifsonia rubra Reddy et al. 2003. Request for an opinion. . Int J Syst Evol Microbiol 57, 1163. [View Article] [PubMed]
    [Google Scholar]
  2. An S.-Y., Xiao T., Yokota A. ( 2008 ). Schumannella luteola gen. nov., sp. nov., a novel genus of the family Microbacteriaceae . . J Gen Appl Microbiol 54, 253–258. [View Article] [PubMed]
    [Google Scholar]
  3. An S.-Y., Xiao T., Yokota A. ( 2009 ). Leifsonia lichenia sp. nov., isolated from lichen in Japan. . J Gen Appl Microbiol 55, 339–343. [View Article] [PubMed]
    [Google Scholar]
  4. An S.-Y., Xiao T., Yokota A. ( 2010 ). Reclassification of Leifsonia aurea to the genus Rhodoglobus as Rhodoglobus aureus comb. nov., and emended description of Rhodoglobus vestalii Sheridan et al. 2003. . J Gen Appl Microbiol 56, 53–55. [View Article] [PubMed]
    [Google Scholar]
  5. Baik K. S., Park S. C., Kim H. J., Lee K. H., Seong C. N. ( 2010 ). Chryseoglobus frigidaquae gen. nov., sp. nov., a novel member of the family Microbacteriaceae . . Int J Syst Evol Microbiol 60, 1311–1316. [View Article] [PubMed]
    [Google Scholar]
  6. Behrendt U., Ulrich A., Schumann P., Naumann D., Suzuki K. ( 2002 ). Diversity of grass-associated Microbacteriaceae isolated from the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov.. Int J Syst Evol Microbiol 52, 1441–1454. [View Article] [PubMed]
    [Google Scholar]
  7. Behrendt U., Schumann P., Ulrich A. ( 2008 ). Agrococcus versicolor sp. nov., an actinobacterium associated with the phyllosphere of potato plants. . Int J Syst Evol Microbiol 58, 2833–2838. [View Article] [PubMed]
    [Google Scholar]
  8. Behrendt U., Schumann P., Hamada M., Suzuki K.-i., Spröer C., Ulrich A. ( 2011 ). Reclassification of Leifsonia ginsengi (Qiu et al. 2007) as Herbiconiux ginsengi gen. nov., comb. nov. and description of Herbiconiux solani sp. nov., an actinobacterium associated with the phyllosphere of Solanum tuberosum L.. Int J Syst Evol Microbiol 61, 1039–1047. [View Article] [PubMed]
    [Google Scholar]
  9. Bora N., Vancanneyt M., Gelsomino R., Swings J., Brennan N., Cogan T. M., Larpin S., Desmasures N., Lechner F. E. & other authors ( 2007 ). Agrococcus casei sp. nov., isolated from the surfaces of smear-ripened cheeses. . Int J Syst Evol Microbiol 57, 92–97. [View Article] [PubMed]
    [Google Scholar]
  10. Breznak J. A., Costilow R. N. ( 1994 ). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, pp. 137–154. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  11. Dastager S. G., Lee J.-C., Ju Y.-J., Park D.-J., Kim C.-J. ( 2008 ). Leifsonia bigeumensis sp. nov., isolated from soil on Bigeum Island, Korea. . Int J Syst Evol Microbiol 58, 1935–1938. [View Article] [PubMed]
    [Google Scholar]
  12. Dastager S. G., Lee J.-C., Ju Y.-J., Park D.-J., Kim C.-J. ( 2009 ). Leifsonia kribbensis sp. nov., isolated from soil. . Int J Syst Evol Microbiol 59, 18–21. [View Article] [PubMed]
    [Google Scholar]
  13. Davis M. J., Gillaspie A. G., Vidaver A. K., Harris R. W. ( 1984 ). Clavibacter: a new genus containing some hytopathogenic coryneform bacteria, including Clavibacter xyli subsp. xyli sp. nov., subsp. nov. and Clavibacter xyli subsp. cynodontis subsp. nov., pathogens that cause ratoon stunting disease of sugarcane and bermudagrass stunting disease. . Int J Syst Bacteriol 34, 107–117. [View Article]
    [Google Scholar]
  14. Dhanjal S., Kaur I., Korpole S., Schumann P., Cameotra S. S., Pukall R., Klenk H.-P., Mayilraj S. ( 2011 ). Agrococcus carbonis sp. nov., isolated from soil of a coal mine. . Int J Syst Evol Microbiol 61, 1253–1258. [View Article] [PubMed]
    [Google Scholar]
  15. Evtushenko L. I., Dorofeeva L. V., Subbotin S. A., Cole J. R., Tiedje J. M. ( 2000 ). Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of ‘Corynebacterium aquaticum’ Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov.. Int J Syst Evol Microbiol 50, 371–380. [View Article] [PubMed]
    [Google Scholar]
  16. Evtushenko L. I., Dorofeeva L. V., Dobrovolskaya T. G., Streshinskaya G. M., Subbotin S. A., Tiedje J. M. ( 2001 ). Agreia bicolorata gen. nov., sp. nov., to accommodate actinobacteria isolated from narrow reed grass infected by the nematode Heteroanguina graminophila . . Int J Syst Evol Microbiol 51, 2073–2079. [View Article] [PubMed]
    [Google Scholar]
  17. Ganzert L., Bajerski F., Mangelsdorf K., Lipski A., Wagner D. ( 2011 ). Leifsonia psychrotolerans sp. nov., a psychrotolerant species of the family Microbacteriaceae from Livingston Island, Antarctica. . Int J Syst Evol Microbiol 61, 1938–1943. [View Article] [PubMed]
    [Google Scholar]
  18. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. (editors) ( 1994 ). Methods for General and Molecular Bacteriology. Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  19. Groth I., Schumann P., Weiss N., Martin K., Rainey F. A. ( 1996 ). Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. . Int J Syst Bacteriol 46, 234–239. [View Article] [PubMed]
    [Google Scholar]
  20. Hamada M., Iino T., Iwami T., Harayama S., Tamura T., Suzuki K. ( 2010 ). Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., two new members of the family Dermatophilaceae, and reclassification of Dermatophilus chelonae (Masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov.. J Gen Appl Microbiol 56, 427–436. [View Article] [PubMed]
    [Google Scholar]
  21. Han S. K., Nedashkovskaya O. I., Mikhailov V. V., Kim S. B., Bae K. S. ( 2003 ). Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. . Int J Syst Evol Microbiol 53, 2061–2066. [View Article] [PubMed]
    [Google Scholar]
  22. Katayama T., Kato T., Tanaka M., Douglas T. A., Brouchkov A., Fukuda M., Tomita F., Asano K. ( 2009 ). Glaciibacter superstes gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge. . Int J Syst Evol Microbiol 59, 482–486. [View Article] [PubMed]
    [Google Scholar]
  23. Kim B.-C., Park D.-S., Kim H., Oh H.-W., Lee K. H., Shin K.-S., Bae K. S. ( 2012 ). Herbiconiux moechotypicola sp. nov., a xylanolytic bacterium isolated from the gut of hairy long-horned toad beetles, Moechotypa diphysis (Pascoe). . Int J Syst Evol Microbiol 62, 90–95. [View Article] [PubMed]
    [Google Scholar]
  24. 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. [View Article] [PubMed]
    [Google Scholar]
  25. Lee S. D. ( 2007 ). Labedella gwakjiensis gen. nov., sp. nov., a novel actinomycete of the family Microbacteriaceae . . Int J Syst Evol Microbiol 57, 2498–2502. [View Article] [PubMed]
    [Google Scholar]
  26. Lee S. D. ( 2008 ). Agrococcus jejuensis sp. nov., isolated from dried seaweed. . Int J Syst Evol Microbiol 58, 2297–2300. [View Article] [PubMed]
    [Google Scholar]
  27. Lee D. W., Lee J. M., Seo J. P., Schumann P., Kim S. J., Lee S. D. ( 2008 ). Phycicola gilvus gen. nov., sp. nov., an actinobacterium isolated from living seaweed. . Int J Syst Evol Microbiol 58, 1318–1323. [View Article] [PubMed]
    [Google Scholar]
  28. Leifson E. ( 1962 ). The bacterial flora of distilled and stored water. III. New species of the genera Corynebacterium, Flavobacterium, Spirillum and Pseudomonas . . Int J Syst Evol Microbiol 12, 161–170. [View Article]
    [Google Scholar]
  29. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. & other authors ( 2004 ). arb: a software environment for sequence data. . Nucleic Acids Res 32, 1363–1371. [View Article] [PubMed]
    [Google Scholar]
  30. Madhaiyan M., Poonguzhali S., Lee J.-S., Senthilkumar M., Lee K. C., Sundaram S. ( 2010 ). Leifsonia soli sp. nov., a yellow-pigmented actinobacterium isolated from teak rhizosphere soil. . Int J Syst Evol Microbiol 60, 1322–1327. [View Article] [PubMed]
    [Google Scholar]
  31. Männistö M. K., Schumann P., Rainey F. A., Kämpfer P., Tsitko I., Tiirola M. A., Salkinoja-Salonen M. S. ( 2000 ). Subtercola boreus gen. nov., sp. nov. and Subtercola frigoramans sp. nov., two new psychrophilic actinobacteria isolated from boreal groundwater. . Int J Syst Evol Microbiol 50, 1731–1739.[PubMed]
    [Google Scholar]
  32. Matsumoto A., Yamada M., Omura S., Takahashi Y. ( 2008 ). Microterricola viridarii gen. nov., sp. nov., a new member of the family Microbacteriaceae . . Int J Syst Evol Microbiol 58, 1019–1023. [View Article] [PubMed]
    [Google Scholar]
  33. Mayilraj S., Suresh K., Schumann P., Kroppenstedt R. M., Saini H. S. ( 2006 ). Agrococcus lahaulensis sp. nov., isolated from a cold desert of the Indian Himalayas. . Int J Syst Evol Microbiol 56, 1807–1810. [View Article] [PubMed]
    [Google Scholar]
  34. 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. [View Article]
    [Google Scholar]
  35. 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. [View Article]
    [Google Scholar]
  36. Park Y.-H., Suzuki K.-i., Yim D.-G., Lee K.-C., Kim E., Yoon J.-s., Kim S., Kho Y.-H., Goodfellow M., Komagata K. ( 1993 ). Suprageneric classification of peptidoglycan group B actinomycetes by nucleotide sequencing of 5S ribosomal RNA. . Antonie van Leeuwenhoek 64, 307–313. [View Article] [PubMed]
    [Google Scholar]
  37. Pindi P. K., Kishore K. H., Reddy G. S. N., Shivaji S. ( 2009 ). Description of Leifsonia kafniensis sp. nov. and Leifsonia antarctica sp. nov.. Int J Syst Evol Microbiol 59, 1348–1352. [View Article] [PubMed]
    [Google Scholar]
  38. Pruesse E., Quast C., Knittel K., Fuchs B. M., Ludwig W., Peplies J., Glöckner F. O. ( 2007 ). silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with arb . . Nucleic Acids Res 35, 7188–7196. [View Article] [PubMed]
    [Google Scholar]
  39. Qiu F., Huang Y., Sun L., Zhang X., Liu Z., Song W. ( 2007 ). Leifsonia ginsengi sp. nov., isolated from ginseng root. . Int J Syst Evol Microbiol 57, 405–408. [View Article] [PubMed]
    [Google Scholar]
  40. Reddy G. S. N., Prakash J. S. S., Srinivas R., Matsumoto G. I., Shivaji S. ( 2003 ). Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov., psychrophiles from a pond in Antarctica. . Int J Syst Evol Microbiol 53, 977–984. [View Article] [PubMed]
    [Google Scholar]
  41. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  42. Schumann P., Behrendt U., Ulrich A., Suzuki K. ( 2003 ). Reclassification of Subtercola pratensis Behrendt et al. 2002 as Agreia pratensis comb. nov. . Int J Syst Evol Microbiol 53, 2041–2044. [View Article] [PubMed]
    [Google Scholar]
  43. Seldin L., Dubnau D. ( 1985 ). Deoxyribonucleic acid homology among Bacillus polymyxa, Bacillus macerans, Bacillus azotofixans, and other nitrogen-fixing Bacillus strains. . Int J Syst Bacteriol 35, 151–154. [View Article]
    [Google Scholar]
  44. Sheridan P. P., Loveland-Curtze J., Miteva V. I., Brenchley J. E. ( 2003 ). Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake. . Int J Syst Evol Microbiol 53, 985–994. [View Article] [PubMed]
    [Google Scholar]
  45. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  46. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. ( 1997 ). Proposal for a new hierarchic classification system, Actinobacteria classis nov. . Int J Syst Bacteriol 47, 479–491. [View Article]
    [Google Scholar]
  47. Suzuki K. I., Suzuki M., Sasaki J., Park Y. H., Komagata K. K. ( 1999 ). Leifsonia gen. nov., a genus for 2, 4-diaminobutyric acid-containing actinomycetes to accommodate ‘Corynebacterium aquaticum’ Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al. 1984. . J Gen Appl Microbiol 45, 253–262. [View Article] [PubMed]
    [Google Scholar]
  48. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 1596–1599. [View Article] [PubMed]
    [Google Scholar]
  49. Teather R. M., Wood P. J. ( 1982 ). Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. . Appl Environ Microbiol 43, 777–780.[PubMed]
    [Google Scholar]
  50. Tiago I., Pires C., Mendes V., Morais P. V., da Costa M., Veríssimo A. ( 2005 ). Microcella putealis gen. nov., sp. nov., a gram-positive alkaliphilic bacterium isolated from a nonsaline alkaline groundwater. . Syst Appl Microbiol 28, 479–487. [View Article] [PubMed]
    [Google Scholar]
  51. Tiago I., Morais P. V., da Costa M. S., Veríssimo A. ( 2006 ). Microcella alkaliphila sp. nov., a novel member of the family Microbacteriaceae isolated from a non-saline alkaline groundwater, and emended description of the genus Microcella . . Int J Syst Evol Microbiol 56, 2313–2316. [View Article] [PubMed]
    [Google Scholar]
  52. Uchida K., Aida K. ( 1984 ). An improved method for the glycolate test for simple identification of acyl type of bacterial cell walls. . J Gen Appl Microbiol 30, 131–134. [View Article]
    [Google Scholar]
  53. Weon H.-Y., Kim B.-Y., Yoo S.-H., Lee S.-Y., Kwon S.-W., Go S.-J., Stackebrandt E. ( 2006 ). Niastella koreensis gen. nov., sp. nov. andNiastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. . Int J Syst Evol Microbiol 56, 1777–1782. [View Article] [PubMed]
    [Google Scholar]
  54. Wieser M., Schumann P., Martin K., Altenburger P., Burghardt J., Lubitz W., Busse H.-J. ( 1999 ). Agrococcus citreus sp. nov., isolated from a medieval wall painting of the chapel of Castle Herberstein (Austria). . Int J Syst Bacteriol 49, 1165–1170. [View Article] [PubMed]
    [Google Scholar]
  55. Yoon J.-H., Kang S.-J., Schumann P., Oh T.-K. ( 2006 ). Yonghaparkia alkaliphila gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an alkaline soil. . Int J Syst Evol Microbiol 56, 2415–2420. [View Article] [PubMed]
    [Google Scholar]
  56. Zhang D.-C., Liu H.C., Xin Y.-H., Yu Y., Zhou P.-J., Zhou Y.-G. ( 2008 ). Salinibacterium xinjiangense sp. nov., a psychrophilic bacterium isolated from the China No. 1 glacier. . Int J Syst Evol Microbiol 58, 2739–2742. [View Article] [PubMed]
    [Google Scholar]
  57. Zhang J.-Y., Liu X.-Y., Liu S.-J. ( 2010 ). Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil. . Int J Syst Evol Microbiol 60, 1897–1903. [View Article] [PubMed]
    [Google Scholar]
  58. Zhi X.-Y., Li W.-J., Stackebrandt E. ( 2009 ). An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. . Int J Syst Evol Microbiol 59, 589–608. [View Article] [PubMed]
    [Google Scholar]
  59. Zlamala C., Schumann P., Kämpfer P., Rosselló-Mora R., Lubitz W., Busse H.-J. ( 2002 ). Agrococcus baldri sp. nov., isolated from the air in the ‘Virgilkapelle’ in Vienna. . Int J Syst Evol Microbiol 52, 1211–1216. [View Article] [PubMed]
    [Google Scholar]
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Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov.
Int J Syst Evol Microbiol 63, 1403 (2013); https://doi.org/10.1099/ijs.0.042945-0
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