[KSCI] Korea Science Citation Index Service

http://dx.doi.org/10.12651/JSR.2016.5.1.001

Report on 31 unrecorded bacterial species in Korea that belong to the phylum Actinobacteria

Choi, Jung-Hye (Department of Systems Biotechnology, Chung-Ang University)
Cha, Ju-Hee (Department of Systems Biotechnology, Chung-Ang University)
Bae, Jin-Woo (Department of Biology, Kyung Hee University)
Cho, Jang-Cheon (Department of Biological Sciences, Inha University)
Chun, Jongsik (School of Biological Sciences, Seoul National University)
Im, Wan-Taek (Department of Biotechnology, Hankyong National University)
Jahng, Kwang Yeop (Department of Life Sciences, Chonbuk National University)
Jeon, Che Ok (Department of Life Science, Chung-Ang University)
Joh, Kiseong (Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies)
Kim, Seung Bum (Department of Microbiology, Chungnam National University)
Seong, Chi Nam (Department of Biology, Sunchon National University)
Yoon, Jung-Hoon (Department of Food Science and Biotechnology, Sungkyunkwan University)
Cha, Chang-Jun (Department of Systems Biotechnology, Chung-Ang University)

Publication Information

Journal of Species Research / v.5, no.1, 2016 , pp. 1-13 More about this Journal

Abstract

To discover and characterize indigenous species in Korea, a total of 31 bacterial strains that belong to the phylum Actinobacteria were isolated from various niches in Korea. Each strain showed the high sequence similarity (>99.1%) with the closest bacterial species, forming a robust phylogenetic clade. These strains have not been previously recorded in Korea. According to the recently updated taxonomy of the phylum Actinobacteria based upon 16S rRNA trees, we report 25 genera of 13 families within 5 orders of the class Actinobacteria as actinobacterial species found in Korea. Cellular morphology, Gram staining, basic biochemical characteristics are described in the species description.

Keywords

16S rRNA gene; Actinobacteria; bacterial diversity; unrecorded species;

Citations & Related Records

Reference

1	Huang, Y., N. Zhao, L. He, L. Wang, Z. Liu, M. You and F. Guan. 2005. Arthrobacter scleromae sp. nov. Isolated from Human Clinical Specimens. J Clin Microbiol 43:1451-1455. DOI
2	Huang, Z., X.-F. Sheng, F. Zhao, L.-Y. He, J. Huang and Q. Wang. 2012. Isoptericola nanjingensis sp. nov., a mineral- weathering bacterium. Int J Syst Evol Microbiol 62:971-976. DOI
3	Jukes, T.H. and C.R. Cantor. 1969. Mammalian Protein Metabolism in Evolution of protein molecules. H. N. Munro ed. Academic Press, New York.
4	Kampfer, P., O. Terenius, J.M. Lindh and I. Faye. 2006. Janibacter anophelis sp. nov., isolated from the midgut of Anopheles arabiensis. Int J Syst Evol Microbiol 56:389-392. DOI
5	Kampfer, P., C.-C. Young, H.-J. Busse, J.-N. Chu, P. Schumann, A.B. Arun, F.-T. Shen and P.D. Rekha. 2010. Microlunatus soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 60:824-827. DOI
6	Kageyama, A., A. Matsumoto, S. Omura and Y. Takahashi. 2008. Humibacillus xanthopallidus gen. nov., sp. nov. Int J Syst Evol Microbiol 58:1547-1551. DOI
7	Kageyama, A., Y. Takahashi, and S. Omura. 2006. Microbacterium deminutum sp. nov., Microbacterium pumilum sp. nov. and Microbacterium aoyamense sp. nov. Int J Syst Evol Microbiol 56:2113-2117. DOI
8	Kim, O.-S., Y.-J. Cho, K. Lee, S.-H. Yoon, M. Kim, H. Na, S.-C. Park, Y.S. Jeon, J.-H. Lee, H. Yi, S. Won and J. Chun. 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. DOI
9	Liu, X.-Y., B.-J. Wang, C.-Y. Jiang and S.-J. Liu. 2007. Micrococcus flavus sp. nov., isolated from activated sludge in a bioreactor. Int J Syst Evol Microbiol 57:66-69. DOI
10	Ludwig, W., and H.P. Klenk. 2005. Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. Pages 49-65 in Bergey's Manual of Systematic Bacteriology. Brenner, Krieg, Staley, and Garrity eds. Springer, New York.
11	Madhaiyan, M., S. Poonguzhali, J.-S. Lee, M. Senthilkumar, K.C. Lee and S. Sundaram. 2010. Leifsonia soli sp. nov., a yellow-pigmented actinobacterium isolated from teak rhizosphere soil. Int J Syst Evol Microbiol 60:1322-1327. DOI
12	Martinkova, L., B. Uhnakova, M. Patek, J. Nesvera and V. Kren. 2009. Biodegradation potential of the genus Rhodococcus. Environ Int 35:162-177. DOI
13	Miyadoh, S., S. Amano, H. Tohyama and T. Shomura. 1990. A taxonomic review of the genus Microbispora and a proposal to transfer two species to the genus Actinomadura and to combine ten species into Microbispora rosea. J Gen Microbiol 136:1905-1913. DOI
14	Nimaichand, S., S. Sanasam, L.-Q. Zheng, W.-Y. Zhu, L.-L. Yang, S.-K. Tang, D. S. Ningthoujam, and W.-J. Li. 2013. Rhodococcus canchipurensis sp. nov., an actinomycete isolated from a limestone deposit site. Int J Syst Evol Microbiol 63:114-118. DOI
15	Oren, A. and G.M. Garrity. 2014. Then and now: a systematic review of the systematics of prokaryotes in the last 80 years. Antonie van Leeuwenhoek 106:43-56. DOI
16	Parte, A.C. 2014. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613-616. DOI
17	Rivas, R., M.E. Trujillo, P.F. Mateos, E. Martínez-Molina and E. Velazquez. 2004. Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree. Int J Syst Evol Microbiol 54:533-536. DOI
18	Shibata, M., E. Higashide, H. Yamamoto and K. Nakazawa. 1962. Studies on Streptomycetes. Part I. Streptomyces atratus nov. sp., producing new antituberculous antibiotics rugomycin A and B. Agricultural and Biological Chemistry 26:228-233.
19	Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
20	Schumann, P., F.A. Rainey, J. Burghardt, E. Stackebrandt and N. Weiss. 1999. Reclassification of Brevibacterium oxydans (Chatelain and Second 1966) as Microbacterium oxydans comb. nov. Int J Syst Bacteriol 49:175-177. DOI
21	Stackebrandt, E., C. Koch, O. Gvozdiak and P. Schumann. 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. DOI
22	Takeuchi, M. and K. Hatano. 1998. Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium. Int J Syst Bacteriol 48:739-747. DOI
23	Takeuchi, M., K. Hatano, I. Sedlacek and Z. Pacova. 2002. Rhodococcus jostii sp. nov., isolated from a medieval grave. Int J Syst Evol Microbiol 52:409-413. DOI
24	Tamura, K., G. Stecher, D. Peterson, A. Filipski and S. Kumar. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725-2729. DOI
25	Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin and D.G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882. DOI
26	Umezawa, H., T. Tazaki, Y. Okami and S. Fukuyama. 1950. On the new source of chloromycetin, Streptomyces omiyaensis. J Antibiotics 3:292-296.
27	Xiao, J., Y. Luo, S. Xie and J. Xu. 2011. Serinicoccus profundi sp. nov., an actinomycete isolated from deep-sea sediment, and emended description of the genus Serinicoccus. Int J Syst Evol Microbiol 61:16-19. DOI
28	Ventura, M., C. Canchaya, G.F. Fitzgerald, R.S. Gupta and D. van Sinderen. 2007. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie van Leeuwenhoek 91:351-372. DOI
29	Whitman, W.B., D.C. Coleman and W.J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578-6583. DOI
30	Willumsen, P., U. Karlson, E. Stackebrandt and R.M. Kroppenstedt. 2001. Mycobacterium frederiksbergense sp. nov., a novel polycyclic aromatic hydrocarbon-degrading Mycobacterium species. Int J Syst Evol Microbiol 51:1715-1722. DOI
31	Yam, K.C., S. Okamoto, J.N. Roberts and L.D. Eltis. 2011. Adventures in Rhodococcus-from steroids to explosives. Can J Microbiol 57:155-168. DOI
32	Yamada, K. and K. Komagata. 1972. Taxonomic studies on coryneform bacteria. V. Classification of coryneform bacteria. J Gen Appl Microbiol 18:417-431. DOI
33	Yassin, A.F., H. Hupfer and K.P. Schaal. 2006. Dietzia cinnamea sp. nov., a novel species isolated from a perianal swab of a patient with a bone marrow transplant. Int J Syst Evol Microbiol 56:641-645. DOI
34	Yassin, A.F., F.A. Rainey, J. Burghardt, H. Brzezinka, S. Schmitt, P. Seifert, O. Zimmermann, H. Mauch, D. Gierth, I. Lux and K.P. Schaal. 1997. Tsukamurella tyrosinosolvens sp. nov. Int J Syst Bacteriol 47:607-614. DOI
35	Zhang, J., Y. Zhang, C. Xiao, Z. Liu and M. Goodfellow. 2002. Rhodococcus maanshanensis sp. nov., a novel actinomycete from soil. Int J Syst Evol Microbiol 52:2121-2126.
36	Behrendt, U., A. Ulrich, P. Schumann, D. Naumann and K.-i. Suzuki. 2002. Diversity of grass-associated Microbacteriaceae isolated from the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov. Int J Syst Evol Microbiol 52:1441-1454.
37	Zhi, X.-Y., W.-J. Li and E. Stackebrandt. 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. DOI
38	Zlamala, C., P. Schumann, P. Kampfer, R. Rossello-Mora, W. Lubitz and H.-J. Busse. 2002. Agrococcus baldri sp. nov., isolated from the air in the 'Virgilkapelle' in Vienna. Int J Syst Evol Microbiol 52:1211-1216.
39	Amann, R.I., W. Ludwig and K.H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169.
40	Baldacci, E. and A. Grein. 1966. Streptomyces avellaneus and Streptomyces libani: two new species characterized by a hazel-nut brown (avellaneus) aerial mycelium. Giorn Microbiol 14:185-198.
41	Brown, J.M., A.G. Steigerwalt, R.E. Morey, M.I. Daneshvar, L.-J. Romero and M.M. McNeil. 2006. Characterization of clinical isolates previously identified as Oerskovia turbata: proposal of Cellulosimicrobium funkei sp. nov. and emended description of the genus Cellulosimicrobium. Int J Syst Evol Microbiol 56:801-804. DOI
42	Conn, H.J. and I. Dimmick. 1947. Soil Bacteria Similar in Morphology to Mycobacterium and Corynebacterium. J Bacteriol 54:291-303.
43	Buczolits, S., P. Schumann, G. Weidler, C. Radax and H.-J. Busse. 2003. Brachybacterium muris sp. nov., isolated from the liver of a laboratory mouse strain. Int J Syst Evol Microbiol 53:1955-1960. DOI
44	Chater, K.F. 2006. Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics. Philos Trans R Soc Lond B Biol Sci 361:761-768. DOI
45	Chater, K.F., S. Biro, K.J. Lee, T. Palmer and H. Schrempf. 2010. The complex extracellular biology of Streptomyces. FEMS Microbiol Rev 34:171-198. DOI
46	Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of molecular evolution 17:368-376. DOI
47	Fierer, N. and R.B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626-631. DOI
48	Gao, B. and R.S. Gupta. 2012. Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria. Microbiol Mol Biol Rev 76:66-112. DOI
49	Goodfellow, M. and G. Alderson. 1977. The Actinomycete-genus Rhodococcus: A Home for the 'rhodochrous' Complex. J Gen Microbiol 100:99-122. DOI
50	Hahn, M.W. 2009. Description of seven candidate species affiliated with the phylum Actinobacteria, representing planktonic freshwater bacteria. Int J Syst Evol Microbiol 59:112-117. DOI
51	Hopwood, D.A. 2007. Streptomyces in nature and medicine. Oxford University Press, New York, NY.