Terriglobus tenax sp. nov., an exopolysaccharideproducing acidobacterium isolated from rhizosphere soil of a medicinal plant

International Journal of Systematic and Evolutionary Microbiology

Volumn 64, Issue PART 2, 2014, Pages 431-437

  Whang, Kyung Sook ^a   Lee, Jae Chan ^a   Lee, Hae Ran ^a   Han, Song Ih ^a   Chung, Sang Ho ^a  

^a Mokwon University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ACID PHOSPHATASE; AMINOPHOSPHOLIPID; ARABINOSE; ARBUTIN; ARYL ACYLAMIDASE; CHYMOTRYPSIN A; ESCULIN; ESTERASE; EXOPOLYSACCHARIDE; FRUCTOSE; GENOMIC DNA; GENTIOBIOSE; GLYCOGEN; INULIN; MALEIC ACID; MENAQUINONE; N ACETYLGLUCOSAMINE; PHOSPHATIDYLETHANOLAMINE; PHOSPHOLIPID; RIBOSE; RNA 16S; TREHALOSE; TRIACYLGLYCEROL LIPASE; TRYPSIN; XYLOSE;

ACIDOBACTERIA; ACIDOBACTERIUM; ANGELICA SINENSIS; ARTICLE; BACTERIAL CELL; BACTERIUM ISOLATION; GENE SEQUENCE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; LIPID COMPOSITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PHYLOGENY; PRIORITY JOURNAL; RHIZOSPHERE; TERRIGLOBUS TENAX;

ACIDOBACTERIA; ANGELICA SINENSIS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, BACTERIAL; FATTY ACIDS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHOSPHATIDYLETHANOLAMINES; PHOSPHOLIPIDS; PHYLOGENY; PLANTS, MEDICINAL; REPUBLIC OF KOREA; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; VITAMIN K 2;

EID: 84893431508     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.053769-0     Document Type: Article

References (37)

1. Coates, J. D., Ellis, D. J., Gaw, C. V. & Lovley, D. R. (1999). Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 49, 1615-1622.
2. Collins, M. D. & Jones, D. (1981). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45, 316-354.
3. Dedysh, S. N., Kulichevskaya, I. S., Serkebaeva, Y. M., Mityaeva, M. A., Sorokin, V. V., Suzina, N. E., Rijpstra, W. I. C. & Damsté, J. S. (2012). Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008. Int J Syst Evol Microbiol 62, 654-664.
4. DeLong, E. F. (1992). Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89, 5685-5689.
5. Eichorst, S. A., Breznak, J. A. & Schmidt, T. M. (2007). Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl Environ Microbiol 73, 2708-2717.
6. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224-229.
7. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
8. Felsenstein, J. (1985). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
9. Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406-416.
10. Fukunaga, Y., Kurahashi, M., Yanagi, K., Yokota, A. & Harayama, S. (2008). Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum 'Acidobacteria'. Int J Syst Evol Microbiol 58, 2597-2601.
11. Janssen, P. H. (2006). Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72, 1719-1728.
12. Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H. & other authors (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.
13. 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.
14. Kishimoto, N., Kosako, Y. & Tano, T. (1991). Acidobacteria capsulatum gen. nov., sp. nov.: an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol 22, 1-7.
15. Koch, I. H., Gich, F., Dunfield, P. F. & Overmann, J. (2008). Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. Int J Syst Evol Microbiol 58, 1114-1122.
16. Kulichevskaya, I. S., Suzina, N. E., Liesack, W. & Dedysh, S. N. (2010). Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria. Int J Syst Evol Microbiol 60, 301-306.
17. Kulichevskaya, I. S., Kostina, L. A., Valášková, V., Rijpstra, W. I. C., Damsté, J. S. S., Boer, W. & Dedysh, S. N. (2012). Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood.
18. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A. & other authors (2007). CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 23, 2947-2948.
19. Liesack, W., Bak, F., Kreft, J. U. & Stackebrandt, E. (1994). Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Arch Microbiol 162, 85-90.
20. Losey, N. A., Stevenson, B. S., Busse, H. J., Damsté, J. S., Rijpstra, W. I. C., Rudd, S. & Lawson, P. A. (2013). Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring. Int J Syst Evol Microbiol 63, 4149-4157.
21. Männistö, M. K., Rawat, S., Starovoytov, V. & Häggblom, M. M. (2011). Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil. Int J Syst Evol Microbiol 61, 1823-1828.
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.
23. 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.
24. Murray, R. G. E., Doetsch, R. N. & Robinow, F. (1994). Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology, pp. 21-41. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
25. Pankratov, T. A. & Dedysh, S. N. (2010). Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella. rosea sp. nov., novel acidophilic, polymer-degrading Acidobacteria from Sphagnum peat bogs. Int J Syst Evol Microbiol 60, 2951-2959.
26. Pankratov, T. A., Kirsanova, L. A., Kaparullina, E. N., Kevbrin, V. V. & Dedysh, S. N. (2012). Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991. Int J Syst Evol Microbiol 62, 430-437.
27. Parte, A. C. (2013). List of prokaryotic names with standing in nomenclature. http://www.bacterio.net/ [Last full update 23 October 2013].
28. Rosselló-Mora, R. & Amann, R. (2001). The species concept for prokaryotes. FEMS Microbiol Rev 25, 39-67.
29. Saito, H. & Miura, K. I. (1963). Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72, 619-629.
30. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
31. Sinninghe Damsté, J. S., Rijpstra, W. I. C., Hopmans, E. C., Weijers, J. W. H., Foesel, B. U., Overmann, J. & Dedysh, S. N. (2011). 13,16-Dimethyl octacosanedioic acid (iso-diabolic acid), a common membrane-spanning lipid of Acidobacteria subdivisions 1 and 3. Appl Environ Microbiol 77, 4147-4154.
32. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607-654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
33. Stackebrandt, E. & Ebers, J. (2006). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33, 152-155.
34. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
35. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A., Kämpfer, P., Maiden, M. C., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors (2002). Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
36. Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125-128.
37. 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.