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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 65, Issue Pt_11

sp. nov., an actinobacterium () from forest soil Free

Abstract

The taxonomic position of an actinobacterium strain, C296001, isolated from a soil sample collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically, strain C296001 was closely associated with the genus and formed a distinct monophyletic clade with the only described species, NBRC 105296. The 16S rRNA gene sequence similarity between strain C296001 and was 98.7 %. DNA–DNA hybridization results showed that the relatedness of strain C296001 to was only 21.5 %. The DNA G+C content of strain C296001 was 71.7 mol%. Using a PacBio RS II system, whole genome sequences for strains C296001 and NBRC 105296 were obtained. The genome sizes of 4.5 Mbp and 5.4 Mbp determined were similar to those of other members of the family . The cell-wall peptidoglycan contained lysine, alanine, aspartic acid, glutamic acid and serine, representing the peptidoglycan type A4α -Lys--Ser--Asp. The major menaquinones were MK-8(H), MK-8 and MK-8(H). Phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and phosphoglycolipid were the polar lipids, while the whole-cell sugars were glucose, fucose and lesser amounts of ribose and galactose. The major fatty acids were iso-C, anteiso-C, iso-C H, anteiso-Cω9, iso-C and 10-methyl C. Chemotaxonomic analyses showed that C296001 had typical characteristics of members of the genus with the main differences occurring in phenotypic characteristics. On the basis of the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001 be classified as a representative of a novel species in the genus , for which the name sp. nov. is recommended. The type strain is C296001 ( = ATCC TSD-4 = JCM 30660).

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2015-11-01
2024-04-25
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References

  1. Anzai K., Sugiyama T., Sukisaki M., Sakiyama Y., Otoguro M., Ando K. ( 2011;). Flexivirga alba gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae . J Antibiot (Tokyo) 64 613–616 [View Article] [PubMed].
     [Google Scholar]
  2. Ara I., Yamamura H., Tsetseg B., Daram D., Ando K. ( 2010;). Luteipulveratus mongoliensis gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae . Int J Syst Evol Microbiol 60 574–579 [View Article] [PubMed].
     [Google Scholar]
  3. Becker K., Schumann P., Wüllenweber J., Schulte M., Weil H.P., Stackebrandt E., Peters G., von Eiff C. ( 2002;). Kytococcus schroeteri sp. nov., a novel Gram-positive actinobacterium isolated from a human clinical source. Int J Syst Evol Microbiol 52 1609–1614 [View Article] [PubMed].
     [Google Scholar]
  4. Bligh E.G., Dyer W.J. ( 1959;). A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37 911–917 [View Article] [PubMed].
     [Google Scholar]
  5. Blin K., Medema M.H., Kazempour D., Fischbach M.A., Breitling R., Takano E., Weber T. ( 2013;). antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41 (W1), W204–W212 [View Article] [PubMed].
     [Google Scholar]
  6. Cashion P., Holder-Franklin M.A., McCully J., Franklin M. ( 1977;). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81 461–466 [View Article] [PubMed].
     [Google Scholar]
  7. Chin C.S., Alexander D.H., Marks P., Klammer A.A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., other authors. ( 2013;). Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10 563–569 [View Article] [PubMed].
     [Google Scholar]
  8. Cordero M.R., Zumalacárregui J.M. ( 2000;). Characterization of micrococcaceae isolated from salt used for Spanish dry-cured ham. Lett Appl Microbiol 31 303–306 [View Article] [PubMed].
     [Google Scholar]
  9. De la Rosa M.C., Mohino M.R., Mohino M., Mosso M.A. ( 1990;). Characteristics of micrococci and staphylococci isolated from semi-preserved meat products. Food Microbiol 7 207–215 [View Article].
     [Google Scholar]
  10. De Ley J., Cattoir H., Reynaerts A. ( 1970;). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12 133–142 [View Article] [PubMed].
     [Google Scholar]
  11. Delcher A.L., Bratke K.A., Powers E.C., Salzberg S.L. ( 2007;). Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23 673–679 [View Article] [PubMed].
     [Google Scholar]
  12. Difco ( 1998). Difco Manual , 11th edn.. Detroit, MI: Difco Laboratories;.
     [Google Scholar]
  13. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783–791 [View Article].
     [Google Scholar]
  14. Groth I., Schumann P., Rainey F.A., Martin K., Schuetze B., Augsten K. ( 1997;). Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 47 1129–1133 [View Article] [PubMed].
     [Google Scholar]
  15. Hall T.A. ( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41 95–98.
     [Google Scholar]
  16. Huss V.A.R., Festl H., Schleifer K.H. ( 1983;). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4 184–192 [View Article] [PubMed].
     [Google Scholar]
  17. Kämpfer P., Kroppenstedt R.M. ( 1996;). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42 989–1005 [View Article].
     [Google Scholar]
  18. Kim S.J., Jang Y.H., Ahn J.H., Weon H.Y., Schumann P., Chun S.C., Kwon S.W., Kim W.G. ( 2013;). Rudaeicoccus suwonensis gen. nov., sp. nov., an actinobacterium isolated from the epidermal tissue of a root of a Phalaenopsis orchid. Int J Syst Evol Microbiol 63 1291–1296 [View Article] [PubMed].
     [Google Scholar]
  19. Kuykendall L.D., Roy M.A., O'Neill J.J., Devine T.E. ( 1988;). Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradorhizobium japonicum . Int J Syst Bacteriol 38 358–361 [View Article].
     [Google Scholar]
  20. Lee S.D. ( 2013;). Tamlicoccus marinus gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 63 1951–1954 [View Article] [PubMed].
     [Google Scholar]
  21. Lee L.H., Cheah Y.K., Sidik S.M., Xie Q.Y., Tang Y.L., Lin H.P., Mutalib N.S.A., Hong K. ( 2013;). Barrientosiimonas humi gen. nov., sp. nov., an actinobacterium of the family Dermacoccaceae . Int J Syst Evol Microbiol 63 241–248 [View Article] [PubMed].
     [Google Scholar]
  22. 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]
  23. Miller L.T. ( 1982;). A 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]
  24. Mincer T.J., Jensen P.R., Kauffman C.A., Fenical W. ( 2002;). Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68 5005–5011 [View Article] [PubMed].
     [Google Scholar]
  25. Muramatsu H., Shahab N., Tsurumi Y., Hino M. ( 2003;). A comparative study of Malaysian and Japanese actinomycetes using simple identification method based on partial 16S rRNA sequence. Actinomycetologica 17 33–43 [View Article].
     [Google Scholar]
  26. Papamanoli E., Kotzekidou P., Tzanetakis N., Litopoulou-Tzanetaki E. ( 2002;). Characterization of Micrococcaceae isolated from dry fermented sausage. Food Microbiol 19 441–449 [View Article].
     [Google Scholar]
  27. Rhuland L.E., Work E., Denman R.F., Hoare D.S. ( 1955;). The behaviour of the isomers of 2,6-diaminopimelic acid on paper chromatograms. J Am Chem Soc 77 4844–4846 [View Article].
     [Google Scholar]
  28. Ruckmani A., Kaur I., Schumann P., Klenk H.P., Mayilraj S. ( 2011;). Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae . Int J Syst Evol Microbiol 61 2419–2424 [View Article] [PubMed].
     [Google Scholar]
  29. 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]
  30. Schleifer K.H. ( 1985;). Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18 123–156 [View Article].
     [Google Scholar]
  31. Schleifer K.H., Kandler O. ( 1972;). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36 407–477 [PubMed].
     [Google Scholar]
  32. Schumann P. ( 2011;). Peptidoglycan structure. Methods Microbiol 38 101–129 [View Article].
     [Google Scholar]
  33. Shirling E.B., Gottlieb D. ( 1966;). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16 313–340 [View Article].
     [Google Scholar]
  34. Sims D., Brettin T., Detter J.C., Han C., Lapidus A., Copeland A., Glavina Del Rio T., Nolan M., Chen F., other authors. ( 2009;). Complete genome sequence of Kytococcus sedentarius type strain (541). Stand Genomic Sci 1 12–20 [View Article] [PubMed].
     [Google Scholar]
  35. Stackebrandt E., Ebers J. ( 2006;). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33 152–155.
     [Google Scholar]
  36. Stackebrandt E., Koch C., Gvozdiak O., Schumann P. ( 1995;). Taxonomic dissection of the genus Micrococcus. Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 45 682–692 [View Article] [PubMed].
     [Google Scholar]
  37. Sugimoto S., Kato T., Ito M., Sakata N., Tsuchida T., Matsumoto A., Takahashi Y. ( 2011;). Branchiibius hedensis gen. nov., sp. nov., an actinobacterium isolated from a Japanese codling (Physiculus japonicus). Int J Syst Evol Microbiol 61 1195–1200 [View Article] [PubMed].
     [Google Scholar]
  38. Tamaoka J., Komagata K. ( 1984;). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25 125–128 [View Article].
     [Google Scholar]
  39. Tamura K., Nei M., Kumar S. ( 2004;). Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101 11030–11035 [View Article] [PubMed].
     [Google Scholar]
  40. 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]
  41. Tang S.K., Wu J.Y., Wang Y., Schumann P., Li W.J. ( 2010;). Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae . Int J Syst Evol Microbiol 60 659–663 [View Article] [PubMed].
     [Google Scholar]
  42. Tindall B.J. ( 1990a;). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13 128–130 [View Article].
     [Google Scholar]
  43. Tindall B.J. ( 1990b;). Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66 199–202 [View Article].
     [Google Scholar]
  44. Tindall B.J., Sikorski J., Smibert R.M., Krieg N.R. ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology, pp. 330–393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. , 3rd edn.., Washington, DC: American Society for Microbiology; [View Article].
     [Google Scholar]
  45. 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 [View Article] [PubMed].
     [Google Scholar]
  46. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., Murray R.G.E., other authors. ( 1987;). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 463–464. [CrossRef]
    [Google Scholar]
  47. Yeo T.C., Naming M., Manurung R. ( 2014;). Building a discovery partnership with Sarawak Biodiversity Centre: a gateway to access natural products from the rainforests. Comb Chem High Throughput Screen 17 192–200 [View Article] [PubMed].
     [Google Scholar]
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Luteipulveratus halotolerans sp. nov., an actinobacterium (Dermacoccaceae) from forest soil
Int J Syst Evol Microbiol 65, 4113 (2015); https://doi.org/10.1099/ijsem.0.000548
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