Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 105, Issue 5, 2014, Pages 915-924

  Kim, Kwang Kyu ^a   Lee, Keun Chul ^a   Eom, Mi Kyung ^a   Kim, Jong Shik ^b   Kim, Dae Shin ^c   Ko, Suk Hyung ^c   Kim, Byung Hyuk ^a   Lee, Jung Sook ^a  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b Gyeongbuk Institute for Marine Bio Industry (GIMB)   (South Korea)

^c Research Institute for Hallasan   (South Korea)

Author keywords

Proteobacteria; Taxonomy; Variibacter gotjawalensis gen. nov., sp. nov.

Indexed keywords

CARDIOLIPIN; FATTY ACID; GLUCOSE; PEPTIDOGLYCAN; PHOSPHATIDYLCHOLINE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; QUINONE DERIVATIVE; RHAMNOSE; RIBOSE; RNA 16S; BACTERIAL DNA; CARBOHYDRATE; DIAMINOPIMELIC ACID; PHOSPHOLIPID; RIBOSOME DNA;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; BRADYRHIZOBIACEAE; BRADYRHIZOBIUM OLIGOTROPHICUM; DNA BASE COMPOSITION; GENE SEQUENCE; NEW GENUS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RHIZOBIALES; SEQUENCE HOMOLOGY; SOIL MICROFLORA; VARIIBACTER GOTJAWALENSIS; BACTERIUM IDENTIFICATION; CELL WALL; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; FOREST; GENETICS; GRAM NEGATIVE AEROBIC RODS AND COCCI; ISOLATION AND PURIFICATION; KOREA; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY;

BACTERIA (MICROORGANISMS); BRADYRHIZOBIUM; NEGIBACTERIA; PROTEOBACTERIA; RHIZOBIALES;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CARBOHYDRATES; CELL WALL; CLUSTER ANALYSIS; DIAMINOPIMELIC ACID; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; FORESTS; GRAM-NEGATIVE AEROBIC RODS AND COCCI; KOREA; MOLECULAR SEQUENCE DATA; PHOSPHOLIPIDS; PHYLOGENY; QUINONES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

EID: 84900798131     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-014-0146-z     Document Type: Article

References (40)

1. Auling G, Busse J, Hahn M, Hennecke H, Kropprnstedt RM, Probst A, Stackebrandt E (1988) Phylogenetic heterogeneity and chemotaxonomic properties of certain Gramnegative aerobic carboxydobacteria. Syst Appl Microbiol 10:264-272
2. Brenner DJ, Hollis DG, Moss CW, English CK, Hall GS, Vincent J, Radosevic J, Birkness KA, Bibb WF, Quinn FD (1991) Proposal of Afipia gen. nov. with Afipia felis sp. Nov. (formerly the cat scratch disease bacillus) Afipia clevelandensis sp. nov. (formerly the Cleveland Clinic Foundation strain) Afipia broomeae sp. nov. and three unnamed genospecies. J Clin Microbiol 29:2450-2460
3. Das SK, Mishra AK, Tindall BJ, Rainey FA, Stackebrandt E (1996) Oxidation of thiosulfate by a new bacterium, Bosea thiooxidans (strain BI-42) gen. nov., sp. nov.: analysis of phylogeny based on chemotaxonomy and 16S ribosomal DNA sequencing. Int J Syst Bacteriol 46:981-987 (Pubitemid 26339224)
4. De Meyer SE, Coorevits A, Willems A (2012) Tardiphaga robiniae gen. nov., sp. nov., a new genus in the family Bradyrhizobiaceae isolated from Robinia pseudoacacia in Flanders (Belgium). Syst Appl Microbiol 35:205-214
5. Felsenstein J (1981) Evolutionary trees from DNA sequences, a maximum likelihood approach. J Mol Evol 17:368-376
6. Felsenstein J (1985) Confidence limits on phylogenies, an approach using the bootstrap. Evolution 39:783-791
7. Felsenstein J (2009) PHYLIP (phylogeny inference package) version 369. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
8. Fitch WM (1971) Toward defining the course of evolution, minimum change for a specific tree topology. Syst Zool 20:406-416
9. Garrity GE, Bell JA, Lilnurn T (2005) Family VII. Bradyrhizobiaceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey's manual of systematic bacteriology, part C, vol 2, 2nd edn. Springer, New York
10. Gomori G (1955) Preparation of buffers for use in enzyme studies. Methods Enzymol 1:138-146
11. Hall TA (1999) BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98
12. Hiraishi A, Ueda Y (1994) Rhodoplanes gen. nov., a new genus of phototrophic bacteria including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov. Int J Syst Bacteriol 29:56-58
13. Hiraishi A, Kuraishi H, Kawahara K (2000) Emendation of the description of Blastomonas natatoria (Sly 1985) Sly and Cahill 1997 as an aerobic photosynthetic bacterium and reclassification of Erythromonas ursincola Yurkov et al. 1997 as Blastomonas ursincola comb. nov. Int J Syst Evol Microbiol 50:1113-1118
14. Jordan DC (1982) Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing root nodule bacteria from leguminous plants. Int J Syst Bacteriol 32:136-139
15. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic Press, New York, pp 21-132
16. Kampfer P, Young C-C, Arun AB, Shen F-T, Jackel U, Rossello-Mora R, Lai W-A, Rekha PD (2006) Pseudolabrys taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from soil. Int J Syst Evol Microbiol 56:2469-2472 (Pubitemid 44566826)
17. Kaur J, Verma M, Lal R (2011) Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Muller 1986 as Rhizobium aggregatum comb. nov. Int J Syst Evol Microbiol 61:1218-1225
18. Kuykendall LD (2005) Order VI. Rhizobiales ord. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey's manual of systematic bacteriology, part C, vol 2, 2nd edn. Springer, New York
19. Lányí B (1987) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1-67
20. Lee KC, Kim KK, Eom MK, Kim MJ, Lee JS (2011) Fontibacillus panacisegetis sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 61:369-374
21. Liu JH, Wang YX, Zhang XX, Wang ZG, Chen YG, Wen ML, Xu LH, Peng Q, Cui XL (2010) Salinarimonas rosea gen. nov., sp. nov., a new member of the alpha-2 subgroup of the Proteobacteria. Int J Syst Evol Microbiol 60:55-60
22. Meyer O, Stackebrandt E, Auling G (1993) Reclassification of ubiquinone Q-10 containing carboxidotrophic bacteria: transfer of "[Pseudomonas] carboxydovorans" OM5T to Oligotropha gen. nov. as Oligotropha carboxidovorans comb. nov., transfer of "[Alcaligenes] carboxydus" DSM 1086T to Carbophilus gen. nov. as Carbophilus carboxidus comb. nov., transfer of "[Pseudomonas] compransoris" DSM 1231T to Zavarzinia gen. nov. as Zavarzinia compransoris comb. nov. and amended descriptions of the new genera. Syst Appl Microbiol 16:390-395 (Pubitemid 24010290)
23. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104-117 (Pubitemid 8112397)
24. Ohta H, Hattori T (1983) Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. Antonie Van Leeuwenhoek 49:429-446
25. Omar AMN, Richard C, Weinhard P, Balandreau J (1989) Using the spermosphere model technique to describe the dominant nitrogen-fixing microflora associated with wetland rice in two Egyptian soils. Biol Fertil Soils 7:158-163
26. Ramana VV, Chakravarthy SK, Raj PS, Kumar BV, Shobha E, Ramaprasad EVV, Sasikala C, RamanaCV(2012) Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov. and emended description of Rhodopseudomonas palustris. Int J Syst Evol Microbiol 62:1790-1798
27. Ramírez-Bahena MH, Chahboune R, Peix A, Velázquez E (2013) Reclassification of Agromonas oligotrophica into the genus Bradyrhizobium as Bradyrhizobium oligotrophicum comb. nov. Int J Syst Evol Microbiol 63:1013-1016
28. Saitou N, Nei M (1987) The neighbour-joining method; a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
29. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101 Newark, DE, MIDI Inc
30. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407-477
31. T. J Microbiol Biotechnol 6:68-69
32. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams Wilkins, Baltimore
33. Spieck E, Bock E (2005) Genus VI. Nitrobacter Winogradsky 1892. In: Brenner G (ed) Bergey's manual of systematic bacteriology, part C, vol 2, 2nd edn. Springer, New York, pp 461-468
34. Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin layer chromatography. Appl Microbiol 28:226-231
35. Tamaoka J, Komagata K (1984) Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125-128 (Pubitemid 15217312)
36. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882 (Pubitemid 28022245)
37. Van Berkum P, Leibold JM, Eardly BD (2006) Proposal for combining Bradyrhizobium spp. (Aeschynomene indica) with Blastobacter denitrificans and to transfer Blastobacter denitrificans (Hirsh and Muller, 1985) to the genus Bradyrhizobium as Bradyrhizobium denitrificans (comb. nov.). Syst Appl Microbiol 29:207-215
38. Weon HY, Kwon SW, Son JA, Jo EH, Kim SJ, Kim YS, Kim BY, Ka JO (2010) Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga. Int J Syst Evol Microbiol 60:2596-2600
39. Yang KS, Kim SB, Kim SY, Lee GE, Kim WT (2006) Community analysis of the moths in the Gotjawal terrains of Jeju Island Korea. J Ecol Field Biol 29:365-379
40. Zehr JP, Melion M, Braun S, Litaker W, Steppe T, Paerl HW (1995) Diversity of heterotrophic nitrogen fixation genes in a marine cyanobacterial mat. Appl Environ Microbiol 61:2527-2532