Lysobacter agri sp. nov., a bacterium isolated from soil

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 108, Issue 3, 2015, Pages 553-561

  Singh, Hina ^a   Won, KyungHwa ^a   Du, Juan ^a   Yang, Jung Eun ^a   Akter, Shahina ^a   Kim, Ki Young ^a   Yi, Tae Hoo ^a  

^a Kyung Hee University   (South Korea)

Author keywords

Gram negative; Lysobacter agri; Polyphasic taxonomy; Ubiquinone Q 8

Indexed keywords

ACID PHOSPHATASE; ALKALINE PHOSPHATASE; ALPHA GALACTOSIDASE; ALPHA GLUCOSIDASE; ALPHA MANNOSIDASE; ARYL ACYLAMIDASE; BACTERIAL RNA; BETA GALACTOSIDASE; BETA GLUCOSIDASE; CARDIOLIPIN; CYSTINE ARYLAMIDASE; ESTERASE; LEUCINE ARYLAMIDASE; N ACETYL BETA GLUCOSAMINIDASE; NAPHTHOL AS BI PHOSPHOHYDROLASE; PHOSPHATASE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; RNA 16S; TRIACYLGLYCEROL LIPASE; UBIQUINONE; UNCLASSIFIED DRUG; VALINE ARYLAMIDASE; BACTERIAL DNA; FATTY ACID; PHOSPHOLIPID; QUINONE DERIVATIVE; RIBOSOME DNA; SODIUM CHLORIDE;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CONTROLLED STUDY; ENZYME ACTIVITY; GENE SEQUENCE; GENETIC SIMILARITY; LIPID ANALYSIS; LYSOBACTER; LYSOBACTER AGRI; LYSOBACTER ENZYMOGENES; LYSOBACTER NIASTENSIS; LYSOBACTER ORYZAE; LYSOBACTER PANACISOLI; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SOIL ACIDITY; SOIL MICROFLORA; SOUTH KOREA; STRAIN IDENTIFICATION; AEROBIC METABOLISM; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; CYTOSOL; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; LOCOMOTION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; PH; PHYSIOLOGY; TEMPERATURE;

BACTERIA (MICROORGANISMS); LYSOBACTER; LYSOBACTER ENZYMOGENES; NEGIBACTERIA;

AEROBIOSIS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CLUSTER ANALYSIS; CYTOSOL; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; HYDROGEN-ION CONCENTRATION; LOCOMOTION; LYSOBACTER; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHOSPHOLIPIDS; PHYLOGENY; QUINONES; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SODIUM CHLORIDE; SOIL MICROBIOLOGY; TEMPERATURE;

EID: 84938747615     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-015-0510-7     Document Type: Article

References (50)

1. Aslam Z, Yasir M, Jeon CO, Chung YR (2009) Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.). Int J Syst Evol Microbiol 59:675–680
2. Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070
3. Choi JH, Seok JH, Cha JH, Cha CJ (2014) Lysobacter panacisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 64:2193–2197
4. Christensen WB (1946) Urea decomposition as a means of differentiating Proteus and Paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 52:461–466
5. Christensen P, Cook FD (1978) Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28:367–393
6. Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354
7. 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
8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
10. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416
11. Fukuda W, Kimura T, Araki S, Miyoshi Y, Atomi H, Imanaka T (2013) Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica. Int J Syst Evol Microbiol 63:3313–3318
12. Gillis M, De Ley J, De Cleene M (1970) The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 12:143–153
13. 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
14. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469
15. 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
16. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
17. Lee JW, Im WT, Kim MK, Yang DC (2006) Lysobacter koreensis sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol 56:231–235
18. Lin SY, Hameed A, Wen CZ, Liu YC, Hsu YH, Lai WA, Young CC (2015) Lysobacter lycopersici sp. nov., isolated from tomato plant Solanum lycopersicum. Antonie van Leeuwenhoek. doi:10.1007/s10482-015-0419-1
19. Liu M, Liu Y, Wang Y, Luo X, Dai J, Fang C (2011) Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample. Int J Syst Evol Microbiol 61:433–437
20. Luo G, Shi Z, Wang G (2012) Lysobacter arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from iron-mined soil. Int J Syst Evol Microbiol 62:1659–1665
21. McConaughy BL, Laird CD, McCarthy BJ (1969) Nucleic acid reassociation in formamide. Biochemistry 8:3289–3295
22. Mesbah M, Premachandran U, Whitman WB (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 DE, ODonnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
24. Moore DD, Dowhan D (1995) Preparation and analysis of DNA. In: Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 2–11
25. Ngo HTT, Won K, Du J, Son HM, Park Y, MooChang K, Kim KY, Jin FX, Yi TH (2014) Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.067397-0
26. Park JH, Kim R, Aslam Z, Jeon CO, Chung YR (2008) Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter. Int J Syst Evol Microbiol 58:387–392
27. Reichenbach H (1992) The order Cytophagales. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, vol 4, 2nd edn. Springer, New York, pp 3631–3675
28. Romanenko LA, Uchino M, Tanaka N, Frolova GM, Mikhailov VV (2008) Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge. Int J Syst Evol Microbiol 58:370–374
29. Saddler GS, Bradbury JF (2005) Family I. Xanthomonadaceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 2, 2nd edn. Springer, New York, pp 63–122
30. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
31. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, Newark
32. Schmidt K, Connor A, Britton G (1994) Analysis of pigments: carotenoids and related polyenes. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 403–461
33. Singh H, Du J, Ngo HT, Won K, Yang JE, Kim KY, Yi TH (2015) Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant. Antonie van Leeuwenhoek. doi:10.1007/s10482-015-0439-x
34. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams and Wilkins, Baltimore
35. Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DC (2010) Lysobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 60:1543–1547
36. Stabili L, Gravili C, Tredici SM, Piraino S, Talà A, Boero F, Alifano P (2008) Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. Microb Ecol 56:625–636
37. Tamaoka J, Katayama-Fujiruma A, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36
38. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
39. Ten LN, Jung H, Im WT, Yoo SA, Oh HM, Lee ST (2009) Lysobacter panaciterrae sp. nov., isolated from soil of ginseng field. Int J Syst Evol Microbiol 59:958–963
40. 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 25:4876–4882
41. Wang Y, Dai J, Zhang L, Luo X, Li Y, Chen G, Tang Y, Meng Y, Fang C (2009) Lysobacter ximonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59:786–789
42. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore WEC, Murray RGE et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464
43. Wei DQ, Yu TT, Yao JC, Zhou EM, Song ZQ (2012) Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south-west China. Antonie van Leeuwenhoek 102:643–651
44. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
45. Weon HY, Kim BY, Baek YK, Yoo SH, Kwon SW, Stackebrandt E, Go SJ (2006) Two novel species Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. Int J Syst Evol Microbiol 56:947–951
46. Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW, Go SJ, Stackebrandt E (2007) Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 57:548–551
47. Yang SZ, Feng GD, Zhu HH, Wang YH (2014) Lysobacter mobilis sp. nov., isolated from abandoned lead–zinc ore. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.000026
48. Ye XM, Chu CW, Shi C, Zhu JC, He Q, He J (2014) Lysobacter caeni sp. nov., isolated from the sludge of pesticide manufacturing factory. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.000026
49. Yu TT, Zhou EM, Yin YR, Yao JC, Ming H, Dong L, Li S, Nie GX, Li WJ et al (2013) Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophiles Wei et al. 2012 as Vulcaniibacterium thermophilum comb. nov. Antonie Van Leeuwenhoek 104:369–376
50. Zhang L, Bai J, Wang Y, Wu JL, Dai J, Fang CX (2011) Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:2259–2265