1887

Abstract

A thermophilic, agar-degrading bacterium, strain FAB2, was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2 belonged to the family within the phylum . However, FAB2 was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for , 91.8 % for , 89.4 % for , 90.1 % for , and 89.0 % for . Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50–65 °C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 °C and pH 8.0–8.6. Growth was inhibited at pH≤7.0 and NaCl concentrations ≥2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C and C. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was -diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2 ( = NBRC 109510 = KCTC 33130) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed.

Funding
This study was supported by the:
  • JSPS KAKENHI (Award 20225775)
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2015-02-01
2021-10-27
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References

  1. Agbo J. A. C., Moss M. O. ( 1979 ). The isolation and characterization of agarolytic bacteria from a lowland river. . J Gen Microbiol 115, 355368. [View Article]
    [Google Scholar]
  2. Bacic A., Moody S. F., Clarke A. E. ( 1986 ). Structural analysis of secreted root slime from maize (Zea mays L.). . Plant Physiol 80, 771777. [View Article] [PubMed]
    [Google Scholar]
  3. Bannikova G. E., Lopatin S. A., Varlamov V. P., Kuznetsov B. B., Kozina I. V., Miroshnichenko M. L., Chernykh N. A., Turova T. P., Bonch-Osmolovskaya E. A. ( 2008 ). The thermophilic bacteria hydrolyzing agar: characterization of thermostable agarase. . Appl Biochem Microbiol 44, 366371. [View Article]
    [Google Scholar]
  4. Cai F., Wang Y., Qi H., Dai J., Yu B., An H., Rahman E., Fang C. ( 2010 ). Cohnella luojiensis sp. nov., isolated from soil of a Euphrates poplar forest. . Int J Syst Evol Microbiol 60, 16051608. [View Article] [PubMed]
    [Google Scholar]
  5. Chaboud A., Rougier M. ( 1984 ). Identification and localization of sugar components of rice (Oryza sativa L.) root cap mucilage. . J Plant Physiol 116, 323330. [View Article] [PubMed]
    [Google Scholar]
  6. Cho E. A., Lee J. S., Lee K. C., Jung H. C., Pan J. G., Pyun Y. R. ( 2007 ). Cohnella laeviribosi sp. nov., isolated from a volcanic pond. . Int J Syst Evol Microbiol 57, 29022907. [View Article] [PubMed]
    [Google Scholar]
  7. De Vos P. ( 2009 ). Order I. Bacillales . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol 3, p. 20. 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]
  8. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  9. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  10. Flores-Félix J. D., Carro L., Ramírez-Bahena M. H., Tejedor C., Igual J. M., Peix A., Velázquez E. ( 2014 ). Cohnella lupini sp. nov., an endophytic bacterium isolated from root nodules of Lupinus albus . . Int J Syst Evol Microbiol 64, 8387. [View Article] [PubMed]
    [Google Scholar]
  11. García-Fraile P., Velázquez E., Mateos P. F., Martínez-Molina E., Rivas R. ( 2008 ). Cohnella phaseoli sp. nov., isolated from root nodules of Phaseolus coccineus in Spain, and emended description of the genus Cohnella . . Int J Syst Evol Microbiol 58, 18551859. [View Article] [PubMed]
    [Google Scholar]
  12. Hameed A., Hung M. H., Lin S. Y., Hsu Y. H., Liu Y. C., Shahina M., Lai W. A., Huang H. C., Young L. S., Young C. C. ( 2013 ). Cohnella formosensis sp. nov., a xylanolytic bacterium isolated from the rhizosphere of Medicago sativa L.. Int J Syst Evol Microbiol 63, 28062812. [View Article] [PubMed]
    [Google Scholar]
  13. Hiraishi A., Muramatsu K., Ueda Y. ( 1996 ). Molecular genetic analyses of Rhodobacter azotoformans sp. nov. and related species of phototrophic bacteria. . Syst Appl Microbiol 19, 168177. [View Article]
    [Google Scholar]
  14. Hosoda A., Sakai M. ( 2006 ). Isolation of Asticcacaulis sp. SA7, a novel agar-degrading alphaproteobacterium. . Biosci Biotechnol Biochem 70, 722725. [View Article] [PubMed]
    [Google Scholar]
  15. Hosoda A., Sakai M., Kanazawa S. ( 2003 ). Isolation and characterization of agar-degrading Paenibacillus spp. associated with the rhizosphere of spinach. . Biosci Biotechnol Biochem 67, 10481055. [View Article] [PubMed]
    [Google Scholar]
  16. Huang Z., Yu Y. J., Bao Y. Y., Xia L., Sheng X. F., He L. Y. ( 2014 ). Cohnella nanjingensis sp. nov., an extracellular polysaccharide-producing bacterium isolated from soil. . Int J Syst Evol Microbiol 64, 33203324.[PubMed] [CrossRef]
    [Google Scholar]
  17. Hunger W., Claus D. ( 1978 ). Reisolation and growth conditions of Bacillus agar-exedens. . Antonie van Leeuwenhoek 44, 105113. [View Article] [PubMed]
    [Google Scholar]
  18. Jiang F., Dai J., Wang Y., Xue X., Xu M., Li W., Fang C., Peng F. ( 2012 ). Cohnella arctica sp. nov., isolated from Arctic tundra soil. . Int J Syst Evol Microbiol 62, 817821. [View Article] [PubMed]
    [Google Scholar]
  19. Kämpfer P., Rosselló-Mora R., Falsen E., Busse H. J., Tindall B. J. ( 2006 ). Cohnella thermotolerans gen. nov., sp. nov., and classification of ‘Paenibacillus hongkongensis’ as Cohnella hongkongensis sp. nov.. Int J Syst Evol Microbiol 56, 781786. [View Article] [PubMed]
    [Google Scholar]
  20. Kämpfer P., Glaeser S. P., McInroy J. A., Busse H. J. ( 2014 ). Cohnella rhizosphaerae sp. nov., isolated from the rhizosphere environment of Zea mays . . Int J Syst Evol Microbiol 64, 18111816. [View Article] [PubMed]
    [Google Scholar]
  21. Katayama-Fujimura Y., Komatsu Y., Kuraishi H., Kaneko T. ( 1984 ). Estimation of DNA base composition by high performance liquid chromatography of its nuclease P1 hydrolysate. . Agric Biol Chem 48, 31693172. [View Article]
    [Google Scholar]
  22. Khianngam S., Tanasupawat S., Akaracharanya A., Kim K. K., Lee K. C., Lee J. S. ( 2010a ). Cohnella thailandensis sp. nov., a xylanolytic bacterium from Thai soil. . Int J Syst Evol Microbiol 60, 22842287. [View Article] [PubMed]
    [Google Scholar]
  23. Khianngam S., Tanasupawat S., Akaracharanya A., Kim K. K., Lee K. C., Lee J. S. ( 2010b ). Cohnella xylanilytica sp. nov. and Cohnella terrae sp. nov., xylanolytic bacteria from soil. . Int J Syst Evol Microbiol 60, 29132917. [View Article] [PubMed]
    [Google Scholar]
  24. Khianngam S., Tanasupawat S., Akaracharanya A., Kim K. K., Lee K. C., Lee J. S. ( 2012 ). Cohnella cellulosilytica sp. nov., isolated from buffalo faeces. . Int J Syst Evol Microbiol 62, 19211925. [View Article] [PubMed]
    [Google Scholar]
  25. Kim S. J., Weon H. Y., Kim Y. S., Anandham R., Jeon Y. A., Hong S. B., Kwon S. W. ( 2010 ). Cohnella yongneupensis sp. nov. and Cohnella ginsengisoli sp. nov., isolated from two different soils. . Int J Syst Evol Microbiol 60, 526530. [View Article] [PubMed]
    [Google Scholar]
  26. Knee E. M., Gong F. C., Gao M., Teplitski M., Jones A. R., Foxworthy A., Mort A. J., Bauer W. D. ( 2001 ). Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source. . Mol Plant Microbe Interact 14, 775784. [View Article] [PubMed]
    [Google Scholar]
  27. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Micorbiol 19, 161207. [View Article]
    [Google Scholar]
  28. Lee J. C., Yoon K. H. ( 2008 ). Paenibacillus woosongensis sp. nov., a xylanolytic bacterium isolated from forest soil. . Int J Syst Evol Microbiol 58, 612616. [View Article] [PubMed]
    [Google Scholar]
  29. Lee J. S., Lee K. C., Chang Y. H., Hong S. G., Oh H. W., Pyun Y. R., Bae K. S. ( 2002 ). Paenibacillus daejeonensis sp. nov., a novel alkaliphilic bacterium from soil. . Int J Syst Evol Microbiol 52, 21072111. [View Article] [PubMed]
    [Google Scholar]
  30. Lee K. C., Kim K. K., Eom M. K., Kim M. J., Lee J. S. ( 2011 ). Fontibacillus panacisegetis sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 61, 369374. [View Article] [PubMed]
    [Google Scholar]
  31. Logan N. A., Berge O., Bishop A. H., Busse H.-J., De Vos P., Fritze D., Heyndrickx M., Kämpfer P., Rabinovitch L. & other authors ( 2009 ). Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. . Int J Syst Evol Microbiol 59, 21142121.[PubMed] [CrossRef]
    [Google Scholar]
  32. Miyazaki M., Nogi Y., Ohta Y., Hatada Y., Fujiwara Y., Ito S., Horikoshi K. ( 2008 ). Microbulbifer agarilyticus sp. nov. and Microbulbifer thermotolerans sp. nov., agar-degrading bacteria isolated from deep-sea sediment. . Int J Syst Evol Microbiol 58, 11281133. [View Article] [PubMed]
    [Google Scholar]
  33. Moody S. F., Clarke A. E., Bacic A. ( 1988 ). Structural analysis of secreted slime from wheat and cowpea roots. . Phytochemistry 27, 28572861. [View Article]
    [Google Scholar]
  34. Nakamura L. K. ( 1987 ). Bacillus polymyxa (Prazmowski) Mace 1889 deoxyribonucleic acid relatedness and base composition. . Int J Syst Evol Microbiol 37, 391397.
    [Google Scholar]
  35. Ohta Y., Nogi Y., Miyazaki M., Li Z., Hatada Y., Ito S., Horikoshi K. ( 2004 ). Enzymatic properties and nucleotide and amino acid sequences of a thermostable β-agarase from the novel marine isolate, JAMB-A94. . Biosci Biotechnol Biochem 68, 10731081. [View Article] [PubMed]
    [Google Scholar]
  36. Pettersson B., Rippere K. E., Yousten A. A., Priest F. G. ( 1999 ). Transfer of Bacillus lentimorbus and Bacillus popilliae to the genus Paenibacillus with emended descriptions of Paenibacillus lentirnorbus comb. nov. and Paenibacillus popilliae comb. nov.. Int J Syst Evol Microbiol 49, 531540.
    [Google Scholar]
  37. Pitcher D. G., Saunders N. A., Owen R. J. ( 1989 ). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. . Lett Appl Microbiol 8, 151156. [View Article]
    [Google Scholar]
  38. Priest F. G. ( 2009 ). Genus I. Paenibacillus . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol 3, pp. 269295. 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]
  39. Rivas R., García-Fraile P., Zurdo-Piñeiro J. L., Mateos P. F., Martínez-Molina E., Bedmar E. J., Sánchez-Raya J., Velázquez E. ( 2008 ). Saccharibacillus sacchari gen. nov., sp. nov., isolated from sugar cane. . Int J Syst Evol Microbiol 58, 18501854. [View Article] [PubMed]
    [Google Scholar]
  40. Roux V., Raoult D. ( 2004 ). Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures. . Int J Syst Evol Microbiol 54, 10491054. [View Article] [PubMed]
    [Google Scholar]
  41. Saha P., Krishnamurthi S., Bhattacharya A., Sharma R., Chakrabarti T. ( 2010 ). Fontibacillus aquaticus gen. nov., sp. nov., isolated from a warm spring. . Int J Syst Evol Microbiol 60, 422428. [View Article] [PubMed]
    [Google Scholar]
  42. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  43. Sakai M., Hosoda A., Ogura K., Ikenaga M. ( 2014 ). The growth of Steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to Rhizobiales . . Microbes Environ 29, 8995. [View Article] [PubMed]
    [Google Scholar]
  44. Shiratori H., Tagami Y., Beppu T., Ueda K. ( 2010 ). Cohnella fontinalis sp. nov., a xylanolytic bacterium isolated from fresh water. . Int J Syst Evol Microbiol 60, 13441348. [View Article] [PubMed]
    [Google Scholar]
  45. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  46. Stanier R. Y. ( 1942 ). Agar-decomposing strains of the Actinomyces coelicolor species-group. . J Bacteriol 44, 555570.[PubMed]
    [Google Scholar]
  47. 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, 27312739. [View Article] [PubMed]
    [Google Scholar]
  48. Tindall B. J., Rosselló-Móra R., Busse H. J., Ludwig W., Kämpfer P. ( 2010 ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60, 249266. [CrossRef]
    [Google Scholar]
  49. Thompson J. D., Higgins D. G., Gibson T. J. ( 1994 ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22, 46734680. [View Article] [PubMed]
    [Google Scholar]
  50. Touzel J. P., O’Donohue M., Debeire P., Samain E., Breton C. ( 2000 ). Thermobacillus xylanilyticus gen. nov., sp. nov., a new aerobic thermophilic xylan-degrading bacterium isolated from farm soil. . Int J Syst Evol Microbiol 50, 315320. [View Article] [PubMed]
    [Google Scholar]
  51. van der Meulen H. J., Harder W., Veldkamp H. ( 1974 ). Isolation and characterization of Cytophaga flevensis sp. nov., a new agarolytic flexibacterium. . Antonie van Leeuwenhoek 40, 329346. [View Article] [PubMed]
    [Google Scholar]
  52. Watanabe K., Nagao N., Yamamoto S., Toda T., Kurosawa N. ( 2007 ). Thermobacillus composti sp. nov., a moderately thermophilic bacterium isolated from a composting reactor. . Int J Syst Evol Microbiol 57, 14731477. [View Article] [PubMed]
    [Google Scholar]
  53. Yang S. Y., Liu H., Liu R., Zhang K. Y., Lai R. ( 2009 ). Saccharibacillus kuerlensis sp. nov., isolated from a desert soil. . Int J Syst Evol Microbiol 59, 953957. [View Article] [PubMed]
    [Google Scholar]
  54. Yoon J. H., Oh H. M., Yoon B. D., Kang K. H., Park Y. H. ( 2003 ). Paenibacillus kribbensis sp. nov. and Paenibacillus terrae sp. nov., bioflocculants for efficient harvesting of algal cells. . Int J Syst Evol Microbiol 53, 295301. [View Article] [PubMed]
    [Google Scholar]
  55. Yoon J. H., Kang S. J., Yeo S. H., Oh T. K. ( 2005 ). Paenibacillus alkaliterrae sp. nov., isolated from an alkaline soil in Korea. . Int J Syst Evol Microbiol 55, 23392344. [View Article] [PubMed]
    [Google Scholar]
  56. Zhilina T. N., Zavarzin G. A., Rainey F., Kevbrin V. V., Kostrikina N. A., Lysenko A. M. ( 1996 ). Spirochaeta alkalica sp. nov., Spirochaeta africana sp. nov., and Spirochaeta asiatica sp. nov., alkaliphilic anaerobes from the Continental Soda Lakes in Central Asia and the East African Rift. . Int J Syst Bacteriol 46, 305312. [View Article] [PubMed]
    [Google Scholar]
  57. Zhou Y., Gao S., Wei D. Q., Yang L. L., Huang X., He J., Zhang Y. J., Tang S. K., Li W. J. ( 2012 ). Paenibacillus thermophilus sp. nov., a novel bacterium isolated from a sediment of hot spring in Fujian province, China. . Antonie van Leeuwenhoek 102, 601609. [View Article] [PubMed]
    [Google Scholar]
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