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f gen. nov., sp. nov., a new member of the family isolated from a karst cave

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  • A Gram-stain-positive, aerobic, straight or slightly bent rod-shaped, non-motile, non-spore-forming bacterium, designated strain CC5-806, was isolated from a soil sample collected from a wild karst cave in the Wulong region, Chongqing, PR China and examined using a polyphasic approach to clarify its taxonomic position. This bacterium did not produce substrate mycelium or aerial hyphae, and no diffusible pigments were observed on the media tested. Strain CC5-806 grew optimally without NaCl at 20 °C and at pH 7.0. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain CC5-806 belonged to the family and showed the highest levels of 16S rRNA gene sequence similarities with EGI 6500707 (97.56 %), 801 (97.53 %) and MP203 (97.42 %). Phylogenetic trees revealed that strain CC5-806 did not show a clear affiliation to any genus within the family . The DNA G+C content of strain CC5-806 was 62.6 mol%. The cell-wall peptidoglycan contained -lysine as a diagnostic diamino acid. The predominant menaquinones were MK-11, MK-10 and MK-9. Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, four unidentified phospholipids and other polar lipids were detected in the polar lipid extracts. The major fatty acids were anteiso-C, iso-C and iso-C. On the basis of the phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, strain CC5-806 was distinguishable from phylogenetically related genera in the family . It represents a novel species of a novel genus, for which the name gen. nov., sp. nov. is proposed. The type strain is CC5-806 ( = DSM 27960 = CGMCC 1.14983).

  • The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain CC5-806 is KP411613.

  • Four supplementary figures and two supplementary tables are available with the online Supplementary Material.

© 2015 IUMS | Published by the Microbiology Society

  • Cappuccino J.G. , Sherman N. . ( 2002;). Microbiology: A Laboratory Manual , 6th edn. San Francisco, CA: Benjamin Cummings Pearson Education;.
     [Google Scholar]
  • Cardinale M. , Grube M. , Berg G. . ( 2011;). Frondihabitans cladoniiphilus sp. nov., an actinobacterium of the family Microbacteriaceae isolated from lichen, and emended description of the genus Frondihabitans . Int J Syst Evol Microbiol 61: 3033––3038 [CrossRef] [PubMed].
     [Google Scholar]
  • Chun J. , Lee J.-H. , Jung Y. , Kim M. , Kim S. , Kim B.K. , Lim Y.-W. . ( 2007;). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57: 2259––2261 [CrossRef] [PubMed].
     [Google Scholar]
  • Collins M.D. , Pirouz T. , Goodfellow M. , Minnikin D.E. . ( 1977;). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100: 221––230 [CrossRef] [PubMed].
     [Google Scholar]
  • Dastager S.G. , Lee J.-C. , Ju Y.-J. , Park D.-J. , Kim C.-J. . ( 2008;). Frigoribacterium mesophilum sp. nov., a mesophilic actinobacterium isolated from Bigeum Island, Korea. Int J Syst Evol Microbiol 58: 1869––1872 [CrossRef] [PubMed].
     [Google Scholar]
  • Euzéby J.P. . ( 1997;). List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47: 590––592 [CrossRef] [PubMed].
     [Google Scholar]
  • Felsenstein J. . ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368––376 [CrossRef] [PubMed].
     [Google Scholar]
  • Felsenstein J. . ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783––791 [CrossRef].
     [Google Scholar]
  • Fitch W.M. . ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406––416 [CrossRef].
     [Google Scholar]
  • Gonzalez C. , Gutierrez C. , Ramirez C. . ( 1978;). Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24: 710––715 [CrossRef] [PubMed].
     [Google Scholar]
  • Gordon R.E. , Smith M.M. . ( 1955;). Proposed group of characters for the separation of Streptomyces and Nocardia . J Bacteriol 69: 147––150. [PubMed].
     [Google Scholar]
  • Greene A.C. , Euzéby J.P. , Tindall B.J. , Patel B.K. . ( 2009;). Proposal of Frondihabitans gen. nov. to replace the illegitimate genus name Frondicola Zhang et al. 2007. Int J Syst Evol Microbiol 59: 447––448. [PubMed].[CrossRef]
    [Google Scholar]
  • Guo L. , Tuo L. , Habden X. , Zhang Y. , Liu J. , Jiang Z. , Liu S. , Dilbar T. , Sun C. . ( 2015;). Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 65: 206––213 [CrossRef] [PubMed].
     [Google Scholar]
  • Hahn M.W. , Schmidt J. , Taipale S.J. , Doolittle W.F. , Koll U. . ( 2014;). Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome. Int J Syst Evol Microbiol 64: 3254––3263 [CrossRef] [PubMed].
     [Google Scholar]
  • Jang Y.-H. , Kim S.-J. , Hamada M. , Tamura T. , Ahn J.-H. , Weon H.-Y. , Suzuki K. , Kwon S.-W. . ( 2012;). Diaminobutyricimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 50: 1047––1052 [CrossRef] [PubMed].
     [Google Scholar]
  • Jang G.I. , Cho Y. , Cho B.C. . ( 2013a;). Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern. Int J Syst Evol Microbiol 63: 2124––2131 [CrossRef] [PubMed].
     [Google Scholar]
  • Jang Y.-H. , Kim S.-J. , Tamura T. , Hamada M. , Weon H.-Y. , Suzuki K. , Kwon S.-W. , Kim W.-G. . ( 2013b;). Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov. Int J Syst Evol Microbiol 63: 1403––1410 [CrossRef] [PubMed].
     [Google Scholar]
  • Kämpfer P. , Rainey F.A. , Andersson M.A. , Nurmiaho Lassila E.-L. , Ulrych U. , Busse H.-J. , Weiss N. , Mikkola R. , Salkinoja-Salonen M. . ( 2000;). Frigoribacterium faeni gen. nov., sp. nov., a novel psychrophilic genus of the family Microbacteriaceae . Int J Syst Evol Microbiol 50: 355––363 [CrossRef] [PubMed].
     [Google Scholar]
  • Kelly K.L. . ( 1964;). Inter-Society Color Council-National Bureau of Standards Color name Charts illustrated with Centroid Colors Washington, DC: US Government Printing Office;.
     [Google Scholar]
  • Kim H. , Park D.-S. , Oh H.-W. , Lee K.H. , Chung D.-H. , Park H.-Y. , Park H.-M. , Bae K.S. . ( 2012a;). Gryllotalpicola gen. nov., with descriptions of Gryllotalpicola koreensis sp. nov., Gryllotalpicola daejeonensis sp. nov. and Gryllotalpicola kribbensis sp. nov. from the gut of the African mole cricket, Gryllotalpa africana, and reclassification of Curtobacterium ginsengisoli as Gryllotalpicola ginsengisoli comb. nov. Int J Syst Evol Microbiol 62: 2363––2370 [CrossRef] [PubMed].
     [Google Scholar]
  • Kim S.-J. , Jang Y.H. , Hamada M. , Tamura T. , Ahn J.-H. , Weon H.-Y. , Suzuki K. , Kwon S.-W. . ( 2012b;). Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 50: 673––679 [CrossRef] [PubMed].
     [Google Scholar]
  • Kim S.-J. , Tamura T. , Hamada M. , Ahn J.-H. , Weon H.-Y. , Park I.-C. , Suzuki K. , Kwon S.-W. . ( 2012c;). Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost. Int J Syst Evol Microbiol 62: 2410––2416. [PubMed].[CrossRef]
    [Google Scholar]
  • Kim S.-J. , Moon J.-Y. , Hamada M. , Tamura T. , Weon H.Y. , Suzuki K. , Kwon S.W. . ( 2013;). Rudaibacter terrae gen. nov., sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol 63: 4052––4057 [CrossRef] [PubMed].
     [Google Scholar]
  • Kim S.-J. , Lim J.-M. , Ahn J.-H. , Weon H.-Y. , Hamada M. , Suzuki K. , Ahn T.-Y. , Kwon S.-W. . ( 2014a;). Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov. Int J Syst Evol Microbiol 64: 572––578 [CrossRef] [PubMed].
     [Google Scholar]
  • Kim T.-S. , Han J.-H. , Joung Y. , Kim S.B. . ( 2014b;). Conyzicola lurida gen. nov., sp. nov., isolated from the root of Conyza canadensis . Int J Syst Evol Microbiol 64: 2753––2757 [CrossRef] [PubMed].
     [Google Scholar]
  • 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 [CrossRef] [PubMed].
     [Google Scholar]
  • Lee S.D. . ( 2010;). Frondihabitans peucedani sp. nov., an actinobacterium isolated from rhizosphere soil, and emended description of the genus Frondihabitans Greene et al. 2009. Int J Syst Evol Microbiol 60: 1740––1744 [CrossRef] [PubMed].
     [Google Scholar]
  • Li W.-J. , Xu P. , Schumann P. , Zhang Y.-Q. , Pukall R. , Xu L.-H. , Stackebrandt E. , Jiang C.-L. . ( 2007;). Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 57: 1424––1428 [CrossRef] [PubMed].
     [Google Scholar]
  • Li H.-R. , Yu Y. , Luo W. , Zeng Y.-X. . ( 2010;). Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic. Int J Syst Evol Microbiol 60: 2535––2539 [CrossRef] [PubMed].
     [Google Scholar]
  • Li A.-H. , Liu H.-C. , Xin Y.-H. , Kim S.-G. , Zhou Y.-G. . ( 2014;). Glaciihabitans tibetensis gen. nov., sp. nov., a psychrotolerant bacterium of the family Microbacteriaceae, isolated from glacier ice water. Int J Syst Evol Microbiol 64: 579––587 [CrossRef] [PubMed].
     [Google Scholar]
  • Magee C.M. , Rodeheaver G. , Edgerton M.T. , Edlich R.F. . ( 1975;). A more reliable gram staining technic for diagnosis of surgical infections. Am J Surg 130: 341––346 [CrossRef] [PubMed].
     [Google Scholar]
  • Männistö M.K. , Schumann P. , Rainey F.A. , Kämpfer P. , Tsitko I. , Tiirola M.A. , Salkinoja-Salonen M.S. . ( 2000;). Subtercola boreus gen. nov., sp. nov. and Subtercola frigoramans sp. nov., two new psychrophilic actinobacteria isolated from boreal groundwater. Int J Syst Evol Microbiol 50: 1731––1739. [PubMed].[CrossRef]
    [Google Scholar]
  • Marmur J. . ( 1961;). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3: 208––218 [CrossRef].
     [Google Scholar]
  • 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 [CrossRef].
     [Google Scholar]
  • Minnikin D.E. , O'Donnell A.G. , Goodfellow M. , Alderson G. , Athalye M. , Schaal A. , Parlett J.H. . ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2: 233––241 [CrossRef].
     [Google Scholar]
  • Park Y.H. , Suzuki K. , Yim D.G. , Lee K.C. , Kim E. , Yoon J. , Kim S. , Kho Y.H. , Goodfellow M. , Komagata K. . ( 1993;). Suprageneric classification of peptidoglycan group B actinomycetes by nucleotide sequencing of 5S ribosomal RNA. Antonie van Leeuwenhoek 64: 307––313 [CrossRef] [PubMed].
     [Google Scholar]
  • 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]
  • Sasser M. . ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI inc;.
     [Google Scholar]
  • Schleifer K.H. . ( 1985;). Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18: 123––156 [CrossRef].
     [Google Scholar]
  • Schleifer K.H. , Kandler O. . ( 1972;). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36: 407––477. [PubMed].
     [Google Scholar]
  • Schumann P. . ( 2011;). Peptidoglycan structure. Methods Microbiol 38: 101––129 [CrossRef].
     [Google Scholar]
  • Schumann P. , Zhang D.-C. , Redzic M. , Margesin R. . ( 2012;). Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 62: 2724––2730 [CrossRef] [PubMed].
     [Google Scholar]
  • Shirling E.B. , Gottlieb D. . ( 1966;). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16: 313––340 [CrossRef].
     [Google Scholar]
  • Skerman V.B.D. . ( 1967;). A Guide to the Identification of the Genera of Bacteria , 2nd edn.. Baltimore, MD: Williams, Wilkins;.
     [Google Scholar]
  • Stackebrandt E. , Rainey F.A. , Ward-Rainey N.L. . ( 1997;). Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47: 479––491 [CrossRef].
     [Google Scholar]
  • 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]
  • Thompson J.D. , Gibson T.J. , Plewniak F. , Jeanmougin F. , Higgins D.G. . ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876––4882 [CrossRef] [PubMed].
     [Google Scholar]
  • Waksman S.A. . ( 1961;). Classification, Identification and Description of Genera and Species, vol. 2, The Actinomycetes Baltimore, MD: Williams & Wilkins;.
     [Google Scholar]
  • Wang H.-F. , Zhang Y.-G. , Chen J.-Y. , Guo J.-W. , Li L. , Hozzein W. , Zhang Y.-M. , Wadaan M. , Li W.-J. . ( 2015;). Frigoribacterium endophyticum sp. nov., an endophytic actinobacterium isolated from root of Anabasis elatior (C. A. Mey.) Schischk. Int J Syst Evol Microbiol 65: 1207––1212 [CrossRef].
     [Google Scholar]
  • Weon H.-Y. , Kim S.-J. , Jang Y.-H. , Hamada M. , Tamura T. , Ahn J.-H. , Suzuki K. , Kwon S.-W. . ( 2013;). Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air. Int J Syst Evol Microbiol 63: 2436––2441 [CrossRef] [PubMed].
     [Google Scholar]
  • Xu P. , Li W.-J. , Tang S.-K. , Zhang Y.-Q. , Chen G.-Z. , Chen H.-H. , Xu L.-H. , Jiang C.-L. . ( 2005;). Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55: 1149––1153 [CrossRef] [PubMed].
     [Google Scholar]
  • Zhi X.-Y. , Li W.-J. , Stackebrandt E. . ( 2009;). An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59: 589––608. [PubMed].[CrossRef]
    [Google Scholar]
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