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.

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2015-02-01
2019-10-17
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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:, 355–368. [CrossRef]
    [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:, 771–777. [CrossRef] [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:, 366–371. [CrossRef]
    [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:, 1605–1608. [CrossRef] [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:, 323–330. [CrossRef] [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:, 2902–2907. [CrossRef] [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:, 368–376. [CrossRef] [PubMed]
    [Google Scholar]
  9. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [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:, 83–87. [CrossRef] [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:, 1855–1859. [CrossRef] [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:, 2806–2812. [CrossRef] [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:, 168–177. [CrossRef]
    [Google Scholar]
  14. Hosoda A. , Sakai M. . ( 2006; ). Isolation of Asticcacaulis sp. SA7, a novel agar-degrading alphaproteobacterium. . Biosci Biotechnol Biochem 70:, 722–725. [CrossRef] [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:, 1048–1055. [CrossRef] [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:, 3320–3324.[PubMed] [CrossRef]
    [Google Scholar]
  17. Hunger W. , Claus D. . ( 1978; ). Reisolation and growth conditions of Bacillus agar-exedens. . Antonie van Leeuwenhoek 44:, 105–113. [CrossRef] [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:, 817–821. [CrossRef] [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:, 781–786. [CrossRef] [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:, 1811–1816. [CrossRef] [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:, 3169–3172. [CrossRef]
    [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:, 2284–2287. [CrossRef] [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:, 2913–2917. [CrossRef] [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:, 1921–1925. [CrossRef] [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:, 526–530. [CrossRef] [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:, 775–784. [CrossRef] [PubMed]
    [Google Scholar]
  27. Komagata K. , Suzuki K. . ( 1987; ). Lipid and cell-wall analysis in bacterial systematics. . Methods Micorbiol 19:, 161–207. [CrossRef]
    [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:, 612–616. [CrossRef] [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:, 2107–2111. [CrossRef] [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:, 369–374. [CrossRef] [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:, 2114–2121.[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:, 1128–1133. [CrossRef] [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:, 2857–2861. [CrossRef]
    [Google Scholar]
  34. Nakamura L. K. . ( 1987; ). Bacillus polymyxa (Prazmowski) Mace 1889 deoxyribonucleic acid relatedness and base composition. . Int J Syst Evol Microbiol 37:, 391–397.
    [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:, 1073–1081. [CrossRef] [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:, 531–540.
    [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:, 151–156. [CrossRef]
    [Google Scholar]
  38. Priest F. G. . ( 2009; ). Genus I. Paenibacillus . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol 3, pp. 269–295. 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:, 1850–1854. [CrossRef] [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:, 1049–1054. [CrossRef] [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:, 422–428. [CrossRef] [PubMed]
    [Google Scholar]
  42. 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]
  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:, 89–95. [CrossRef] [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:, 1344–1348. [CrossRef] [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. Stanier R. Y. . ( 1942; ). Agar-decomposing strains of the Actinomyces coelicolor species-group. . J Bacteriol 44:, 555–570.[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:, 2731–2739. [CrossRef] [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:, 249–266. [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:, 4673–4680. [CrossRef] [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:, 315–320. [CrossRef] [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:, 329–346. [CrossRef] [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:, 1473–1477. [CrossRef] [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:, 953–957. [CrossRef] [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:, 295–301. [CrossRef] [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:, 2339–2344. [CrossRef] [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:, 305–312. [CrossRef] [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:, 601–609. [CrossRef] [PubMed]
    [Google Scholar]
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