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Volume 65, Issue Pt_3

sp. nov., from soil of a Japanese rice field Free

Abstract

An obligately anaerobic bacterial strain designated KC3 was isolated from a rice straw-degrading culture, for which soil of a Japanese rice field was used as the inoculum. Cells of strain KC3 were determined to be non-cellulolytic, Gram-stain-positive, non-motile, ellipsoidal, spore-forming rods, 0.8–1×4–25 µm. Endospores were formed at a terminal position in elongated cells (12–25 µm, mean 15 µm). The temperature range for growth was 20–50 °C, with an optimum at 37 °C. The pH range for growth was 5.0–7.5, with an optimum at pH 6.0 (slightly acidophilic). Strain KC3 fermented cellobiose to lactate, butyrate, acetate, formate, hydrogen and carbon dioxide. The major cellular fatty acids (>10 %) were C, C and C cyclo 11,12 dimethylacetal. The DNA G+C content of strain KC3 was 37.5 mol%. 16S rRNA gene sequence analysis revealed that strain KC3 shared low sequence similarity (<93 %) with type strains of the genus ( rRNA cluster I). Analyses of the DNA gyrase A and ATP synthase beta subunit sequences supported the affiliation of strain KC3 to the genus The evidence presented here indicates that strain KC3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of is KC3 ( = DSM 28571 = NBRC 110163).

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2015-03-01
2024-04-19
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References

  1. Broda D. M., Lawson P. A., Bell R. G., Musgrave D. R. ( 1999 ). Clostridium frigidicarnis sp. nov., a psychrotolerant bacterium associated with ‘blown pack’ spoilage of vacuum-packed meats. . Int J Syst Bacteriol 49, 1539–1550. [View Article]
    [Google Scholar]
  2. Bru K., Blazy V., Joulian C., Trably E., Latrille E., Quemeneur M., Dictor M. C. ( 2012 ). Innovative CO2 pretreatment for enhancing biohydrogen production from the organic fraction of municipal solid waste (OFMSW). . Int J Hydrogen Energy 37, 14062–14071. [View Article]
    [Google Scholar]
  3. Collins M. D., Lawson P. A., Willems A., Cordoba J. J., Fernandez-Garayzabal J., Garcia P., Cai J., Hippe H., Farrow J. A. ( 1994 ). The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. . Int J Syst Bacteriol 44, 812–826. [View Article] [PubMed]
    [Google Scholar]
  4. Duda V. I., Lebedinsky A. V., Mushegjan M. S., Mitjushina L. L. ( 1987 ). A new anaerobic bacterium, forming up to five endospores per cell – Anaerobacter polyendosporus gen. et spec. nov.. Arch Microbiol 148, 121–127. [View Article]
    [Google Scholar]
  5. Edgar R. C. ( 2004 ). muscle: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32, 1792–1797. [View Article] [PubMed]
    [Google Scholar]
  6. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  7. Glissmann K., Conrad R. ( 2000 ). Fermentation pattern of methanogenic degradation of rice straw in anoxic paddy soil. . FEMS Microbiol Ecol 31, 117–126. [View Article] [PubMed]
    [Google Scholar]
  8. Goodwin S., Zeikus J. G. ( 1987 ). Physiological adaptations of anaerobic bacteria to low pH: metabolic control of proton motive force in Sarcina ventriculi . . J Bacteriol 169, 2150–2157.[PubMed]
    [Google Scholar]
  9. Gu X., Fu Y. X., Li W. H. ( 1995 ). Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. . Mol Biol Evol 12, 546–557.[PubMed]
    [Google Scholar]
  10. Guo P., Zhu W., Wang H., Lü Y., Wang X., Zheng D., Cui Z. ( 2010 ). Functional characteristics and diversity of a novel lignocelluloses degrading composite microbial system with high xylanase activity. . J Microbiol Biotechnol 20, 254–264.[PubMed]
    [Google Scholar]
  11. Gupta R. S., Gao B. ( 2009 ). Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). . Int J Syst Evol Microbiol 59, 285–294. [View Article] [PubMed]
    [Google Scholar]
  12. Hengstmann U., Chin K. J., Janssen P. H., Liesack W. ( 1999 ). Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. . Appl Environ Microbiol 65, 5050–5058.[PubMed]
    [Google Scholar]
  13. Holdeman L. V., Cato E. P., Moore W. E. C. ( 1977 ). Anaerobe Laboratory Manual, , 4th edn.. Blacksburg, VA:: Virginia Polytechnic Institute and State University;.
     [Google Scholar]
  14. Hungate R. E. ( 1969 ). A roll-tube method for cultivation of strict anaerobes. . Methods Microbiol 3B, 117–132. [View Article]
    [Google Scholar]
  15. Inglett K. S., Bae H. S., Aldrich H. C., Hatfield K., Ogram A. V. ( 2011 ). Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil. . Int J Syst Evol Microbiol 61, 2626–2631. [CrossRef]
    [Google Scholar]
  16. Jones D. T., Taylor W. R., Thornton J. M. ( 1992 ). The rapid generation of mutation data matrices from protein sequences. . Comput Appl Biosci 8, 275–282.[PubMed]
    [Google Scholar]
  17. Keis S., Shaheen R., Jones D. T. ( 2001 ). Emended descriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clostridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov.. Int J Syst Evol Microbiol 51, 2095–2103. [View Article] [PubMed]
    [Google Scholar]
  18. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111–120. [View Article] [PubMed]
    [Google Scholar]
  19. Miller L. T. ( 1982 ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16, 584–586.[PubMed]
    [Google Scholar]
  20. Montville T. J., Parris N., Conway L. K. ( 1985 ). Influence of pH on organic acid production by Clostridium sporogenes in test tube and fermentor cultures. . Appl Environ Microbiol 49, 733–736.[PubMed]
    [Google Scholar]
  21. Rainey F. A., Hollen B. J., Small A. ( 2009 ). Genus I. Clostridium Prazmowski 1880, 23AL . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 3, pp. 738–828. Edited by De Vos P., Garrity G. M., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schleifer K. H., Whitman W. B. . New York:: Springer;.
     [Google Scholar]
  22. 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]
  23. Schütz H., Holzapfel-Pschorn A., Conrad R., Rennenberg H., Seiler W. ( 1989 ). A 3-year continuous record on the influence of daytime, season, and fertilizer treatment on methane emission rates from an Italian rice paddy. . J Geophys Res Atmos 94 (D13), 16405–16416. [View Article]
    [Google Scholar]
  24. She D., Nie X. N., Xu F., Geng Z. C., Jia H. T., Jones G. L., Baird M. S. ( 2012 ). Physico-chemical characterization of different alcohol-soluble lignins from rice straw. . Cellulose Chem Technol 46, 207–219.
     [Google Scholar]
  25. Silva E. M., Yang S.-T. ( 1995 ). Kinetics and stability of a fibrous-bed bioreactor for continuous production of lactic acid from unsupplemented acid whey. . J Biotechnol 41, 59–70. [View Article]
    [Google Scholar]
  26. Sleat R., Mah R. A., Robinson R. ( 1984 ). Isolation and characterization of an anaerobic, cellulolytic bacterium, Clostridium cellulovorans sp. nov.. Appl Environ Microbiol 48, 88–93.[PubMed]
    [Google Scholar]
  27. 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. [View Article]
    [Google Scholar]
  28. Sugano A., Tsuchimoto H., Tun C. C., Asakawa S., Kimura M. ( 2005 ). Succession and phylogenetic profile of eubacterial communities in rice straw incorporated into a rice field: estimation by PCR-DGGE analysis. . Soil Sci Plant Nutr 51, 51–60. [View Article]
    [Google Scholar]
  29. 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. [View Article] [PubMed]
    [Google Scholar]
  30. Tsutsuki K., Ponnamperuma F. N. ( 1987 ). Behavior of anaerobic decomposition products in submerged soils. . Soil Sci Plant Nutr 33, 13–33. [View Article]
    [Google Scholar]
  31. Watanabe A., Katoh K., Kimura M. ( 1993 ). Effect of rice straw application on CH4 emission from paddy fields. . Soil Sci Plant Nutr 39, 707–712. [View Article]
    [Google Scholar]
  32. Weber S., Stubner S., Conrad R. ( 2001 ). Bacterial populations colonizing and degrading rice straw in anoxic paddy soil. . Appl Environ Microbiol 67, 1318–1327. [View Article] [PubMed]
    [Google Scholar]
  33. Wiegel J., Tanner R., Rainey F. ( 2006 ). An introduction to the family Clostridiaceae . . In The Prokaryotes, , 3rd edn., vol. 4, pp. 654–678. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E. . New York:: Springer;. [View Article]
    [Google Scholar]
  34. Zhao J., Zhang R., Xue C., Xun W., Sun L., Xu Y., Shen Q. ( 2014 ). Pyrosequencing reveals contrasting soil bacterial diversity and community structure of two main winter wheat cropping systems in China. . Microb Ecol 67, 443–453. [View Article] [PubMed]
    [Google Scholar]
  35. Zhu Y., Yang S. T. ( 2004 ). Effect of pH on metabolic pathway shift in fermentation of xylose by Clostridium tyrobutyricum . . J Biotechnol 110, 143–157. [View Article] [PubMed]
    [Google Scholar]
  36. Zuckerkandl E., Pauling L. ( 1965 ). Evolutionary divergence and convergence in proteins. . In Evolving Genes and Proteins, pp. 97–166. Edited by Bryson V., Vogel H. J. . New York:: Academic Press;. [View Article]
    [Google Scholar]
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Clostridium oryzae sp. nov., from soil of a Japanese rice field
Int J Syst Evol Microbiol 65, 943 (2015); https://doi.org/10.1099/ijs.0.000042
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