A molecular toolbox to estimate the number and diversity of Variovorax in the environment: Application in soils treated with the phenylurea herbicide linuron

FEMS Microbiology Ecology

Volumn 76, Issue 1, 2011, Pages 14-25

  Bers, Karolien ^a   Sniegowski, Kristel ^a   Albers, Pieter ^a   Breugelmans, Philip ^a   Hendrickx, Larissa ^b   De Mot, René ^a   Springael, Dirk ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b BELGIAN NUCLEAR RESEARCH CENTRE   (Belgium)

Author keywords

Agricultural soil; DGGE; Linuron; Real time PCR; Variovorax

Indexed keywords

BACTERIAL DNA; HERBICIDE; LINURON; PRIMER DNA; RNA 16S;

AGRICULTURAL SOIL; BACTERIUM; CULTIVATION; DEGRADATION; ELECTROKINESIS; MICROBIAL COMMUNITY; MICROCOSM; PHYLOGENETICS; POLYMERASE CHAIN REACTION; REAL TIME; SOIL MICROORGANISM; SPECIES DIVERSITY;

AGRICULTURE; ARTICLE; CHEMISTRY; COMAMONADACEAE; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA SEQUENCE; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SOIL; SPECIES DIFFERENCE;

AGRICULTURE; BASE SEQUENCE; COMAMONADACEAE; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA PRIMERS; DNA, BACTERIAL; ECOSYSTEM; HERBICIDES; LINURON; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; SPECIES SPECIFICITY;

ACIDOVORAX; VARIOVORAX;

EID: 79952341114     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2010.01028.x     Document Type: Article

References (37)

1. Abou-Shanab RAI, van Berkum P & Angle JS (2007) Heavy metal resistance and genotypic analysis of metal resistance genes in gram-positive and gram-negative bacteria present in Ni-rich serpentine soil and in the rhizosphere of Alyssum murale. Chemosphere 68: 360-367.
2. Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Ashelford KE, Weightman AJ & Fry JC (2002) Primrose: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 30: 3481-3489.
4. Breugelmans P, D'Huys PJ, De Mot R & Springael D (2007) Characterization of novel linuron-mineralizing bacterial consortia enriched from long-term linuron-treated agricultural soils. FEMS Microbiol Ecol 62: 374-385.
5. Clark IM & Hirsch PR (2008) Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted broadbalk experiment. Soil Biol Biochem 40: 1090-1102.
6. Cole JR, Wang Q, Cardenas E et al. (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
7. Dejonghe W, Berteloot E, Goris J, Boon N, Crul K, Maertens S, Hofte M, De Vos P, Verstraete W & Top EM (2003) Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading Variovorax strain. Appl Environ Microb 69: 1532-1541.
8. El-Fantroussi S (2000) Enrichment and molecular characterization of a bacterial culture that degrades methoxy-methyl urea herbicides and their aniline derivatives. Appl Environ Microb 66: 5110-5115.
9. El-Fantroussi S, Verschuere L, Verstraete W & Top EM (1999) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl Environ Microb 65: 982-988.
10. Eriksson M, Sodersten E, Yu ZT, Dalhammar G & Mohn WW (2003) Degradation of polycyclic aromatic hydrocarbons at low temperature under aerobic and nitrate-reducing conditions in enrichment cultures from northern soils. Appl Environ Microb 69: 275-284.
11. Green SJ & Minz D (2005) Suicide polymerase endonuclease restriction, a novel technique for enhancing PCR amplification of minor DNA templates. Appl Environ Microb 71: 4721-4727.
12. Greene EA, Beatty PH & Fedorak PM (2000) Sulfolane degradation by mixed cultures and a bacterial isolate identified as a Variovorax sp. Arch Microbiol 174: 111-119.
13. Haest PJ, Philips J, Springael D & Smolders E (2010) The reactive transport of trichloroethene is influenced by residence time and microbial numbers. J Contam Hydrol, in press.
14. Humphries JA, Ashe AMH, Smiley JA & Johnston CG (2005) Microbial community structure and trichloroethylene degradation in groundwater. Can J Microbiol 51: 433-439.
15. Hussain S, Sørensen SR, Devers-Lamrani M, El-Sebai T & Martin-Laurent F (2009) Characterization of an isoproturon mineralizing bacterial culture enriched from a French agricultural soil. Chemosphere 77: 1052-1059.
16. Hutalle-Schmelzer KML & Grossart HP (2009) Changes in the bacterioplankton community of oligotrophic lake Stechlin (northeastern Germany) after humic matter addition. Aquat Microb Ecol 55: 155-167.
17. Kim BY, Weon HY, Yoo SH, Lee SY, Kwon SW, Go SJ & Stackebrandt E (2006) Variovorax soli sp. nov., isolated from greenhouse soil. Int J Syst Evol Micr 56: 2899-2901.
18. Leys NM, Ryngaert A, Bastiaens L, Wattiau P, Top EM, Verstraete W & Springael D (2005) Occurrence and community composition of fast-growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons. FEMS Microbiol Ecol 51: 375-388.
19. Massart DL, Vandeginste BGM & Deming SN (1990) Chemometrics: a textbook. Data Handling in Science and Technology, Vol. 2 (Vandeginste BGM & Kaufman L, eds), pp. 112-113. Elsevier, Amsterdam.
20. Miwa H, Ahmed I, Yoon J, Yokota A & Fujiwara T (2008) Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil. Int J Syst Evol Micr 58: 286-289.
21. Myers RM, Fischer SG, Lerman LS & Maniatis T (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel-electrophoresis. Nucleic Acids Res 13: 3131-3145.
22. Okano Y, Hristova KR, Leutenegger CM, Jackson LE, Denison RF, Gebreyesus B, Lebauer D & Scow KM (2004) Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Appl Environ Microb 70: 1008-1016.
23. Palumbo JD, O'Keeffe TL & Abbas HK (2007) Isolation of maize soil and rhizosphere bacteria with antagonistic activity against Aspergillus flavus and Fusarium verticillioides. J Food Protect 70: 1615-1621.
24. Polz MF & Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microb 64: 3724-3730.
25. Saul DJ, Aislabie JM, Brown CE, Harris L & Foght JM (2005) Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiol Ecol 53: 141-155.
26. Segawa T, Miyamoto K, Ushida K, Agata K, Okada N & Kohshima S (2005) Seasonal change in bacterial flora and biomass in mountain snow from the Tateyama mountains, Japan, analyzed by 16S rRNA gene sequencing and real-time PCR. Appl Environ Microb 71: 123-130.
27. Sheffield VC, Cox DR, Lerman LS & Myers RM (1989) Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain-reaction results in improved detection of single-base changes. P Natl Acad Sci USA 86: 232-236.
28. Smith D, Alvey S & Crowley DE (2005) Cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil. FEMS Microbiol Ecol 53: 265-273.
29. Sniegowski K (2010) Pesticide-degrading organisms and their application in the processing of spray residues of crop protection products. PhD Thesis, Katholieke Universiteit, Leuven, Belgium.
30. Sniegowski K, Mertens J, Diels J, Smolders E & Springael D (2009) Inverse modeling of pesticide degradation and pesticide-degrading population size dynamics in a bioremediation system: parameterizing the Monod model. Chemosphere 75: 726-731.
31. Sørensen SR, Rasmussen J, Jacobsen CS, Jacobsen OS, Juhler RK & Aamand J (2005) Elucidating the key member of a linuron-mineralizing bacterial community by PCR and reverse transcription-PCR denaturing gradient gel electrophoresis 16S rRNA gene fingerprinting and cultivation. Appl Environ Microb 71: 4144-4148.
32. Suss J, Schubert K, Sass H, Cypionka H, Overmann J & Engelen B (2006) Widespread distribution and high abundance of Rhizobium radiobacter within mediterranean subsurface sediments. Environ Microbiol 8: 1753-1763.
33. Tamura K, Dudley J, Nei M & Kumar S (2007) Mega4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
34. Uyttebroek M, Breugelmans P, Janssen M et al. (2006) Distribution of the Mycobacterium community and polycyclic aromatic hydrocarbons (PAHs) among different size fractions of a long-term PAH-contaminated soil. Environ Microbiol 8: 836-847.
35. Wang YP & Gu JD (2006) Degradability of dimethyl terephthalate by Variovorax paradoxus T4 and Sphingomonas yanoikuyae DOS01 isolated from deep-ocean sediments. Ecotoxicology 15: 549-557.
36. Young RF, Cheng SM & Fedorak PM (2006) Aerobic biodegradation of 2, 2'-dithiodibenzoic acid produced from dibenzothiophene metabolites. Appl Environ Microb 72: 491-496.
37. Zaitsev GM, Uotila JS & Haggblom MM (2007) Biodegradation of methyl tert-butyl ether by cold-adapted mixed and pure bacterial cultures. Appl Microbiol Biot 74: 1092-1102.