1887

Abstract

An actinomycete strain, TKZ-21, was isolated from a freshwater alga () collected from the Takizawa River, Yamanashi, Japan, and examined using a polyphasic taxonomic approach. Cells were Gram-stain positive, aerobic, non-sporulating, motile, and coccoid or short rod-shaped. The strain grew in the presence of 0–4 % (w/v) NaCl, between pH 6–9.4, and over a temperature range of 15–40 °C, with optimum growth at 30 °C. The peptidoglycan type of strain TKZ-21 was A4β, containing -ornithine as diagnostic diamino acid and -glutamic acid as the interpeptide bridge. The predominant menaquinone was MK-9(H). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, ninhydrin-positive glycolipid, and unidentified phospholipids. The major cellular fatty acids were anteiso-C and anteiso-C, and the DNA G+C content was 75.6 mol%. On the basis of 16S rRNA gene sequence analysis, strain TKZ-21 was closely related to (98.5 % sequence similarity) and (98.3 %). The genome orthoANI value between strain TKZ-21 and and were 84.7 and 84.2 %, respectively. On the basis of fatty acid and MALDI-TOF MS profile analysis, phylogenetic analyses, genomic analysis, and phenotypic data, it is proposed that the isolate be classified as a representative of a novel species of the genus , with the name sp. nov. The type strain is TKZ-21 (=NBRC 112905=TBRC 8129).

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2019-09-01
2019-10-14
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References

  1. McCormick PV, Cairns J. Algae as indicators of environmental change. J Appl Phycol 1994;6:509–526 [CrossRef]
    [Google Scholar]
  2. Stevenson J. Ecological assessments with algae: a review and synthesis. J Phycol 2014;50:437–461 [CrossRef][PubMed]
    [Google Scholar]
  3. Stackebrandt E, Prauser H. Assignment of the Genera Cellulomonas, Oerskovia, Promicromonospora and Jonesia to Cellulomonadaceae fam. nov. Syst Appl Microbiol 1991;14:261–265 [CrossRef]
    [Google Scholar]
  4. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Bergey’s Manual of Determinative Bacteriology Baltimore: Williams &Wilkins; 1923
    [Google Scholar]
  5. Hatayama K, Esaki K, Ide T. Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013;63:60–65 [CrossRef][PubMed]
    [Google Scholar]
  6. Ahmed I, Kudo T, Abbas S, Ehsan M, Iino T et al. Cellulomonas pakistanensis sp. nov., a moderately halotolerant Actinobacteria. Int J Syst Evol Microbiol 2014;64:2305–2311 [CrossRef][PubMed]
    [Google Scholar]
  7. Kang MS, Im WT, Jung HM, Kim MK, Goodfellow M et al. Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost. Int J Syst Evol Microbiol 2007;57:1256–1260 [CrossRef][PubMed]
    [Google Scholar]
  8. Rivas R, Trujillo ME, Mateos PF, Martínez-Molina E, Velázquez E. Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree. Int J Syst Evol Microbiol 2004;54:533–536 [CrossRef][PubMed]
    [Google Scholar]
  9. Zhang G, Cao T, Ying J, Yang Y, Ma L. Diversity and novelty of actinobacteria in Arctic marine sediments. Antonie van Leeuwenhoek 2014;105:743–754 [CrossRef][PubMed]
    [Google Scholar]
  10. Rusznyák A, Tóth EM, Schumann P, Spröer C, Makk J et al. Cellulomonas phragmiteti sp. nov., a cellulolytic bacterium isolated from reed (Phragmites australis) periphyton in a shallow soda pond. Int J Syst Evol Microbiol 2011;61:1662–1666 [CrossRef][PubMed]
    [Google Scholar]
  11. Stackebrandt E, Schumann P. The family Cellulomonadaceae. In Dworkin Martin. (editor) The Prokaryotes Berlin: Heidelberg: Springer; 2014; pp.163–184
    [Google Scholar]
  12. Saxena S, Bahadur J, Varma A. Production and localisation of carboxymethylcellulase, xylanase and β-glucosidase from Cellulomonas and Micrococcus spp. Appl Microbiol Biotechnol 1991;34:668–670 [CrossRef]
    [Google Scholar]
  13. Siddiqui KS, Rashid MH, Ghauri TM, Durrani IS, Rajoka MI. Purification and characterization of an intracellular β-glucosidase from Cellulomonas biazotea. World J Microbiol Biotechnol 1997;13:245–247 [CrossRef]
    [Google Scholar]
  14. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 1987;65:501–509 [CrossRef]
    [Google Scholar]
  15. Hsing W, Canale-Parola E. Cellobiose chemotaxis by the cellulolytic bacterium Cellulomonas gelida. J Bacteriol 1992;174:7996–8002 [CrossRef][PubMed]
    [Google Scholar]
  16. Gerhardt P. Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981
    [Google Scholar]
  17. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  18. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain. Int J Syst Bacteriol 1974;24:54–63 [CrossRef]
    [Google Scholar]
  19. Sun X, Li J, du J, Xiao H, Ni J. Cellulomonas macrotermitis sp. nov., a chitinolytic and cellulolytic bacterium isolated from the hindgut of a fungus-growing termite. Antonie van Leeuwenhoek 2018;111:471–478 [CrossRef][PubMed]
    [Google Scholar]
  20. Kiska DL, Hicks K, Pettit DJ. Identification of medically relevant Nocardia species with an abbreviated battery of tests. J Clin Microbiol 2002;40:1346–1351 [CrossRef][PubMed]
    [Google Scholar]
  21. Mellmann A, Cloud J, Maier T, Keckevoet U, Ramminger I et al. Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J Clin Microbiol 2008;46:1946–1954 [CrossRef][PubMed]
    [Google Scholar]
  22. Hamada M, Yamamura H, Komukai C, Tamura T, Suzuki K et al. Luteimicrobium album sp. nov., a novel actinobacterium isolated from a lichen collected in Japan, and emended description of the genus Luteimicrobium. J Antibiot 2012;65:427–431 [CrossRef][PubMed]
    [Google Scholar]
  23. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  24. Yassin AF, Haggenel B, Budzikiewicz H, Schaal KP. Fatty acid and polar lipid composition of the genus Amycolatopsis: application of fast atom bombardment-mass spectrometry to structure analysis of underivatized phospholipids. Int J Syst Bacteriol 1993;43:414–420 [CrossRef]
    [Google Scholar]
  25. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963;72:619–629 [CrossRef][PubMed]
    [Google Scholar]
  26. Hatano K, Nishii T, Kasai H. Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA-DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev. Int J Syst Evol Microbiol 2003;53:1519–1529 [CrossRef][PubMed]
    [Google Scholar]
  27. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984;25:125–128 [CrossRef]
    [Google Scholar]
  28. Tamura T, Hatano K. Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. 1986 and 'Actinoplanes aurantiacus' to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov. Int J Syst Evol Microbiol 2001;51:2119–2125 [CrossRef][PubMed]
    [Google Scholar]
  29. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  30. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  31. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  32. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  33. Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 2000;17:1251–1258 [CrossRef][PubMed]
    [Google Scholar]
  34. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  35. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  37. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821–829 [CrossRef][PubMed]
    [Google Scholar]
  38. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018;34:1037–1039 [CrossRef][PubMed]
    [Google Scholar]
  39. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  40. Brown JM, Frazier RP, Morey RE, Steigerwalt AG, Pellegrini GJ et al. Phenotypic and genetic characterization of clinical isolates of CDC coryneform group A-3: proposal of a new species of Cellulomonas, Cellulomonas denverensis sp. nov. J Clin Microbiol 2005;43:1732–1737 [CrossRef][PubMed]
    [Google Scholar]
  41. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972;36:407–477[PubMed]
    [Google Scholar]
  42. Abt B, Foster B, Lapidus A, Clum A, Sun H et al. Complete genome sequence of Cellulomonas flavigena type strain (134T). Stand Genomic Sci 2010;3:15–25 [CrossRef][PubMed]
    [Google Scholar]
  43. Ndongo S, Bittar F, Beye M, Robert C, di Pinto F et al. 'Cellulomonas timonensis' sp. nov., taxonogenomics description of a new bacterial species isolated from human gut. New Microbes New Infect 2018;23:7–16 [CrossRef][PubMed]
    [Google Scholar]
  44. Lagier JC, Ramasamy D, Rivet R, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov. Stand Genomic Sci 2012;7:258–270 [CrossRef][PubMed]
    [Google Scholar]
  45. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
  46. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–351 [CrossRef][PubMed]
    [Google Scholar]
  47. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014;64:316–324 [CrossRef][PubMed]
    [Google Scholar]
  48. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  49. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef][PubMed]
    [Google Scholar]
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