Abstract
A novel nocardioform actinomycete, designated strain NEAU-GQTH2-3T, was isolated from muddy soil collected from a stream in Qitaihe, Heilongjiang Province, northeast China and characterized using a polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that the organism should be assigned to the genus Kribbella and forms a clade with Kribbella catacumbae JCM 14968T (99.2 % sequence similarity), Kribbella koreensis JCM 10977T (99.1 %), Kribbella ginsengisoli JCM 16928T (98.6 %) and Kribbella sancticallisti JCM 14969T (98.4 %), although with low bootstrap support. Morphological and chemotaxonomic properties of the isolate are in agreement with the description of the genus Kribbella. Chemotaxonomic characteristics include LL-diaminopimelic acid in the cell-wall peptidoglycan; glucose and ribose as the characteristic whole-cell hydrolysates; diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, a glycerolipid and an unidentified phospholipid as the predominant polar lipids; the major menaquinones MK-9(H4) and MK-9(H2); as well as iso-C15:0, iso-C16:0 and C17:1 ω7c being the predominant fatty acid components. Mycolic acids were not detected. Furthermore, the strain could be clearly distinguished by the combination of DNA–DNA hybridization results and some phenotypic characteristics from the closest phylogenetic relatives. Therefore, it is proposed that strain NEAU-GQTH2-3T represents a novel species of the genus Kribbella, for which the name Kribbella qitaiheensis sp. nov. is proposed. The type strain is NEAU-GQTH2-3T (=CGMCC 4.7215T =JCM 30343T).
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References
Ara I, Kudo T (2007) Sphaerosporangium gen. nov., a new member of the family Streptosporangiaceae, with descriptions of three new species as Sphaerosporangium melleum sp. nov., Sphaerosporangium rubeum sp. nov. and Sphaerosporangium cinnabarinum sp. nov., and transfer of Streptosporangium viridialbum Nonomura and Ohara 1960 to Sphaerosporangium viridialbum comb. nov. Actinomycetologica 21:11–21
Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London, pp 267–284
De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142
Everest GJ, Curtis SM, De Leo F, Urzì C, Meyers PR (2013) Kribbella albertanoniae sp. nov., isolated from a Roman catacomb, and emended description of the genus Kribbella. Int J Syst Evol Microbiol 63:3591–3596
Everest GJ, Curtis SM, De Leo F, Urzì C, Meyers PR (2014) Description of Kribbella italica sp. nov., isolated from a Roman catacomb. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.070672-0
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Gao RX, Liu CX, Zhao JW, Jia FY, Yu C, Yang LY, Wang XJ, Xiang WS (2014) Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie Van Leeuwenhoek 105:307–315
Gordon RE, Barnett DA, Handerhan JE, Pang C (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63
Hayakawa M, Nonomura H (1987) Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65:501–509
Huss VAR, Festl H, Schleifer KH (1983) Studies on the spectrometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192
Kaewkla O, Franco CMM (2013) Kribbella endophytica sp. nov., an endophytic actinobacterium isolated from the surface-sterilized leaf of a native apricot tree. Int J Syst Bacteriol 63:1249–1253
Kelly KL (1964) Inter-society color council-national bureau of standards color-name charts illustrated with centroid colors published in US
Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow M (2000) Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 50:2031–2036
Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721
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
Lechevalier MP, Lechevalier HA (1980) The chemotaxonomy of actinomycetes. In: Dietz A, Thayer DW (eds) Actinomycete taxonomy special publication, vol 6. Society of Industrial Microbiology, Arlington, pp 227–291
Lee SD, Kang SO, Hah YC (2000) Hongia gen. nov., a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 50:191–199
Mandel M, Marmur J (1968) Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195–206
McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM, Brooks P, Se-viour RJ (2000) A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 30:178–182
Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M (1980) Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr 188:221–233
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal K, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Mohammadipanah F, Hamedi J, Göker M, Fiebig A, Pukall R, Spröer C, Klenk HP (2013) Kribbella shirazensis sp. nov., isolated from soil of Shiraz in Iran. Int J Syst Evol Microbiol 63:3369–3374
Park YH, Yoon JH, Shin YK, Suzuki K, Kudo T, Seino A, Kim HJ, Lee JS, Lee ST (1999) Classification of “Nocardioides fulvus” IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 49:743–752
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) methods for general and molecular bacteriology. American Society for Microbiology, Washington DC, pp 607–654
Sohn K, Hong SG, Bae KS, Chun J (2003) Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov. Int J Syst Evol Microbiol 53:1005–1007
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
Urzì C, De Leo F, Schumann P (2008) Kribbella catacumbae sp. nov. and Kribbella sancticallisti sp. nov., isolated from whitish-grey patinas in the catacombs of St Callistus in Rome Italy. Int J Syst Evol Microbiol 58:2090–2097
Waksman SA (1961) The Actinomycetes, vol 2, Classification, identification and descriptions of genera and species. Williams and Wilkins, Baltimore
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (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
Wu C, Lu X, Qin M, Wang Y, Ruan J (1989) Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 16:176–178
Xiang WS, Liu CX, Wang XJ, Du J, Xi LJ, Huang Y (2011) Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 61:1165–1169
Yokota A, Tamura T, Hasegawa T, Huang LH (1993) Catenuloplanes japonicas gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 43:805–812
Yoon JH, Park YH (2006) The genus Nocardioides. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The Prokaryotes, vol 3. Springer, New York, pp 1099–1113
Acknowledgments
This work was supported in part by grants from the National Outstanding Youth Foundation (No. 31225024), the National Key Project for Basic Research (No. 2010CB126102), the National Key Technology R&D Program (No. 2012BAD19B06), the Program for New Century Excellent Talents in University (NCET-11-0953), the National Natural Science Foundation of China (Nos. 31372006, 31171913 and 31071750), the Outstanding Youth Foundation of Heilongjiang Province (JC201201), the Chang Jiang Scholar Candidates Program for Provincial Universities in Heilongjiang (CSCP), the Science and Technology Research Project of Heilongjiang Provincial Educational Commission (No. 12541001) and the Youth Science Foundation of Heilongjiang Province (No. QC2014C013).
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Guo, L., Zhao, J., Liu, C. et al. Kribbella qitaiheensis sp. nov., a novel actinomycete isolated from soil. Antonie van Leeuwenhoek 107, 1533–1539 (2015). https://doi.org/10.1007/s10482-015-0446-y
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DOI: https://doi.org/10.1007/s10482-015-0446-y