Application of fluorescence in situ hybridization technique to detect simazine-degrading bacteria in soil samples

Chemosphere

Volumn 71, Issue 4, 2008, Pages 703-710

  Martín, Margarita ^a   Gibello, Alicia ^a   Lobo, Carmen ^b   Nande, Mar ^a   Garbi, Carlos ^a   Fajardo, Carmen ^a   Barra Caracciolo, Anna ^c   Grenni, Paola ^c   Martínez Iñigo, M José ^b  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b Instituto Madrileno de Investigacion y Desarrollo Rural   (Spain)

^c WATER RESEARCH INSTITUTE   (Italy)

Author keywords

Bacterial biodegradation; FISH; Natural attenuation; Simazine

Indexed keywords

BACTERIA; BIOREMEDIATION; DEGRADATION; GENE EXPRESSION; OLIGONUCLEOTIDES; OPTIMIZATION; SOILS;

BACTERIAL BIODEGRADATION; NATURAL ATTENUATION; SIMAZINE;

FLUORESCENCE;

HERBICIDE; SIMAZINE; TRIAZINE;

BACTERIA; BIOREMEDIATION; DEGRADATION; FLUORESCENCE; GENE EXPRESSION; OLIGONUCLEOTIDES; OPTIMIZATION; SOILS;

AGRICULTURAL SOIL; BACTERIUM; BIODEGRADATION; COMPARATIVE STUDY; DETECTION METHOD; PEPTIDE; PROBE; SIMAZINE;

AGAR GEL ELECTROPHORESIS; ARTICLE; ATZB GENE; BIOREMEDIATION; CELL VIABILITY; CONFOCAL LASER MICROSCOPY; DEAMINATION; DNA ISOLATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE; HYDROLYSIS; KLEBSIELLA; MICROBIAL DEGRADATION; MINERALIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PLASMID; POLYMERASE CHAIN REACTION; PSEUDOMONAS; SOIL POLLUTION; SOIL PROPERTY; SOIL TREATMENT;

AGRICULTURE; BACTERIA; BIODEGRADATION, ENVIRONMENTAL; DNA PROBES; IN SITU HYBRIDIZATION, FLUORESCENCE; POLYMERASE CHAIN REACTION; SIMAZINE; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 40049094067     PISSN: 00456535     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemosphere.2007.10.071     Document Type: Article

References (32)

1. Amann R.I., Ludwig W., and Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59 (1995) 143-169
2. Bach H.J., Hartmann A., Schloter M.J., and Munch J.C. PCR primers and functional probes for amplification and detection of bacterial genes for extracellular peptidases in single strains and in soil. J. Microbiol. Methods 44 (2001) 1919-1925
3. Barra-Caracciolo A., Giuliano G., Grenni P., Cremisini C., Ciccoli R., and Ubaldi C. Effect of urea on degradation of terbuthylazine in soil. Environ. Toxicol. Chem. 134 (2005) 525-534
4. Barra-Caracciolo A., Grenni P., Ciccoli R., Di Landa G., and Cremisini C. Simazine biodegradation in soil: Analysis of bacterial community structure by in situ hybridization. Pest. Manage. Sci. 61 (2005) 917-921
5. Barra-Caracciolo A., Grenni P., Cupo C., and Rossetti S. In situ analysis of native microbial communities in complex samples with high particulate loads. FEMS Microbiol. Lett. 253 (2005) 55-58
6. Behki R., Topp E., Dick W., and Germon P. Metabolism of the herbicide atrazine by Rhodococcus strains. Appl. Environ. Microbiol. 59 (1993) 1955-1959
7. Christensen H., Hansen M., and Sorensen J. Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe. Appl. Environ. Microbiol. 65 (1999) 1753-1761
8. de Souza M.L., Wackett L.P., and Sadowsky M.J. The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 64 (1998) 2323-2326
9. Dedysh S.N., Derakshani M., and Liesack W. Detection and enumeration of methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris. Appl. Environ. Microbiol. 67 (2001) 4850-4857
10. Devers M., Soulas G., and Martin-Laurent F. Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil. J. Microbiol. Methods 56 (2004) 3-15
11. Devers M., Henry S., Hartmann A., and Martin-Laurent F. Horizontal gene transfer of atrazine-degrading genes (atz) from Agrobacterium tumefaciens St96-4 pADP1:Tn5 to bacteria of maize-cultivated soil. Pest Manage. Sci. 61 (2005) 870-880
12. Garbi C., Casasus L., Martinez-Alvarez R., Robla J.I., and Martin M. Biodegradation of oxadiazon by a soil isolated Pseudomonas fluorescens strain CG5, Implementation in an herbicide removal reactor and modelling. Water Res. 40 (2006) 1217-1223
13. Gibello A., Garbi C., Allende J.L., and Martin M. Improving dioxygenase stability by gene chromosome insertion: implementation in immobilized-cell systems. Curr. Microbiol. 49 (2004) 390-395
14. Girvan M.S., Campbell C.D., Killham K., Prosser J.I., and Glover L.A. Bacterial diversity promotes community stability and functional resilience after perturbation. Environ. Microbiol. 7 (2005) 301-313
15. Jen C.J., Chou C.H., Hsu P.C., Yu S.J., Chen W.E., Lay J.J., Huang C.C., and Wen F.S. Flow-FISH analyses and isolation of clostridial strains in an anaerobic semi-solid bio-hydrogen producing system by hydrogenase gene target. Appl. Microbiol. Biotechnol. 74 (2007) 1126-1134
16. Martinez B., Tomkins J., Wackett L.P., Wing R., and Sadowsky M.J. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J. Bacteriol. 183 (2001) 5684-5697
17. Martin-Laurent F., Piutti S., Hallet S., Wagschal I., Philippot L., Catroux G., and Soulas G. Monitoring of atrazine treatment on soil bacterial, fungal and atrazine-degrading communities by quantitative competitive PCR. Pest Manage. Sci. 59 (2003) 259-268
18. Martin-Montalvo D., Mengs G., Ferrer E., Allende J.L., Alonso R., and Martin M. Simazine degradation by immobilized and suspended soil bacterium. Int. Biodeter. Biodegr. 40 (1997) 93-99
19. Moran A.C., Muller A., Manzano M., and Gonzalez B. Simazine treatment history determines a significant herbicide degradation potential in soils that is not improved by bioaugmentation with Pseudomonas sp. ADP. J. Appl. Microbiol. 101 (2006) 35-36
20. Pernthaler A., and Amann R. Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol. 70 (2004) 5426-5433
21. Pernthaler A., and Pernthaler J. Simultaneous fluorescence in situ hybridization of mRNA and rRNA for the detection of gene expression in environmental microbes. Method Enzymol. 397 (2005) 352-371
22. Rhine E.D., Fuhrmann J.J., and Radosevich M. Microbial community responses to atrazine exposure and nutrient availability: linking degradation capacity to community structure. Microbial Ecol. 46 (2003) 145-160
23. Rousseaux S., Hartmann A., and Soulas G. Isolation and characterization of new Gram-negative and Gram-positive atrazine degrading bacteria from different French soils. FEMS Microbial. Ecol. 36 (2001) 211-222
24. Runes H.B., Jenkins J.J., Moore J.A., Bottomley P.J., and Wilson B.D. Treatment of atrazine in nursery irrigation runoff by a constructed wetland. Water Res. 37 (2003) 539-550
25. Sánchez M., Garbi C., Martínez-Alvarez R., Ortiz L.T., Allende J.L., and Martin M. Klebsiella planticola strain DSZ mineralizes simazine: Physiological adaptations involved in the process. Appl. Microbiol. Biotech. 66 (2005) 589-596
26. Santiago-Mora R., Martin-Laurent F., de Prado R., and Franco A.R. Degradation of simazine by microorganisms isolated from soils of Spanish olive fields. Pest Manage. Sci. 61 (2005) 917-921
27. Seffernick J., Aleem A., Osborne J., Johnson G., Sadowsky M., and Wackett L. Hydroxyatrazine N-ethylaminohydrolase (AtzB): An amidohydrolase superfamily enzyme catalyzing deamination and dechlorination. J. Bacteriol. 189 (2007) 6989-6997
28. Shapir N., Goux S., Mandelbaum R.T., and Pussemier I. The potential of soil microorganisms to mineralize atrazine as predicted by MCH-PCR followed by nested PCR. Can. J. Microbiol. 46 (2000) 425-432
29. Strong L.C., Rosendahl C., Johnson G., Sadowsky M.J., and Wackett L.P. Arthrobacter aurescens TC1 metabolizes diverse s-triazine ring compounds. Appl. Environ. Microbiol. 68 (2002) 5973-5980
30. Topp E., Zhu H., Nour S.M., Houot S., Lewis M., and Cuppels D. Characterization of an atrazine-degrading Pseudaminobacter sp. isolated from Canadian and French agricultural soils. Appl. Environ. Microbiol. 66 (2000) 2773-2782
31. Tsai Y.L., and Olson B.H. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol. 58 (1992) 2292-2295
32. Wilson I.G. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63 (1997) 3741-3751