Evidence for taxonomic and functional drift of an atrazine-degrading culture in response to high atrazine input

Applied Microbiology and Biotechnology

Volumn 90, Issue 4, 2011, Pages 1547-1554

  Udiković Kolić, Nikolina ^a   Devers Lamrani, Marion ^b   Petrić, Ines ^a   Hršak, Dubravka ^a   Martin Laurent, Fabrice ^b  

^a RUDER BO KOVI INSTITUTE   (Croatia)

^b UNIVERSITÉ DE BOURGOGNE   (France)

Author keywords

Atrazine; atz genes; Bacterial culture; Degradation; Evolution; trz genes

Indexed keywords

ATRAZINES; ATZ GENES; BACTERIAL CULTURE; EVOLUTION; TRZ GENES;

BACTERIOLOGY; CLONING; CONCENTRATION (PROCESS); DEGRADATION; GENES; POLYMERASE CHAIN REACTION; RNA;

HERBICIDES;

ATRAZINE; RNA 16S;

ATRAZINE; BACTERIUM; BIODEGRADATION; COMMUNITY DYNAMICS; CONCENTRATION (COMPOSITION); DOMINANCE; FUNCTIONAL CHANGE; GENETIC ANALYSIS; MICROBIAL COMMUNITY; MINERALIZATION; MOLECULAR ANALYSIS; POLYMERASE CHAIN REACTION; RELATIVE ABUNDANCE; TAXONOMY;

ACTINOBACTERIA; ARTICLE; BACTERIAL GENE; BACTERIUM CULTURE; BACTEROIDETES; BETAPROTEOBACTERIA; DEGRADATION; DNA SEQUENCE; GAMMAPROTEOBACTERIA; MINERALIZATION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RESTRICTION MAPPING; TAXONOMY;

ATRAZINE; BACTERIA; BIODEGRADATION, ENVIRONMENTAL; MOLECULAR SEQUENCE DATA; PESTICIDES; PHYLOGENY;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BETAPROTEOBACTERIA; GAMMAPROTEOBACTERIA;

EID: 79955551137     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-011-3198-2     Document Type: Article

References (41)

1. C Accinelli C Screpanti G Dinelli A Vicari 2002 Short-time effects of pure and formulated herbicides on soil microbial activity and biomass Int J Environ Anal Chem 82 519 527 10.1080/03067310290009514 1:CAS:528: DC%2BD38Xptl2rs78%3D (Pubitemid 35464963)
2. Z Arbeli C Fuentes 2010 Prevalence of the gene trzN and biogeographic patterns among atrazine-degrading bacteria isolated from 13 Colombian agricultural soils FEMS Microbiol Ecol 73 611 623 1:CAS:528:DC%2BC3cXhtFajtLbJ
3. J Baelum T Henriksen HCB Hansen CS Jacobsen 2006 Degradation of 4-chloro-2-methylphenoxyacetic acid in top- and subsoil is quantitatively linked to the class III tfdA gene Appl Environ Microbiol 72 1476 1486 10.1128/AEM.72.2.1476-1486.2006 1:CAS:528:DC%2BD28Xhs1Ghtbs%3D (Pubitemid 43271262)
4. J Baelum MH Nicolaisen WE Holben BW Strobel J Sorensen CS Jacobsen 2008 Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil ISME J 2 677 687 10.1038/ismej.2008.21 1:CAS:528:DC%2BD1cXotFejtbw%3D (Pubitemid 351793253)
5. E Barriuso S Houot 1996 Rapid mineralisation of s-triazine ring of atrazine in soils in relation to soil management Soil Biol Biochem 28 1341 1348 10.1016/S0038-0717(96)00144-7 1:CAS:528:DyaK2sXos1SgsQ%3D%3D (Pubitemid 27126569)
6. KL Boundy-Mills ML De Souza RT Mandelbaum LP Wackett MJ Sadowsky 1997 The atzB gene of Pseudomonas sp. strain ADP encodes the second enzyme of a novel atrazine degradation pathway Appl Environ Microbiol 63 916 923 1:CAS:528:DyaK2sXhsV2mtbk%3D (Pubitemid 27098472)
7. Y-J Chang AKM Anwar Hussain JR Stephen MD Mullen DC White A Peacock 2001 Impact of herbicides on the abundance and structure of indigenous β-subgroup ammonia-oxidizer communities in soil microcosms Environ Toxicol Chem 20 2462 2468 10.1002/etc.5620201110 1:CAS:528:DC%2BD38XjtVekuw%3D%3D (Pubitemid 34117866)
8. D Chèneby L Philippot A Hartmann C Henault JC Germon 2000 16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils FEMS Microbiol Ecol 34 121 128
9. ML De Souza MJ Sadowsky LP Wackett 1996 Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization J Bacteriol 178 4894 4900 (Pubitemid 26321290)
10. ML De Souza D Newcombe S Alvey DE Crowley A Hay MJ Sadowsky LP Wackett 1998 Molecular basis of a bacterial consortium: interspecies catabolism of atrazine Appl Environ Microbiol 64 178 184 (Pubitemid 28040310)
11. ML De Souza J Seffernick B Martinez MJ Sadowsky LP Wackett 1998 The atrazine catabolism genes atzABC are widespread and highly conserved J Bacteriol 180 1951 1954 (Pubitemid 28173080)
12. M Devers G Soulas F Martin-Laurent 2004 Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil J microbiol methods 56 3 15 10.1016/j.mimet.2003.08.015 1:CAS:528:DC%2BD2cXoslWn (Pubitemid 38045441)
13. M Devers NE Azhari NU Kolic F Martin-Laurent 2007 Detection and organization of atrazine-degrading genetic potential of seventeen bacterial isolates belonging to divergent taxa indicate a recent common origin of their catabolic functions FEMS Microbiol Lett 273 78 86 10.1111/j.1574-6968.2007. 00792.x 1:CAS:528:DC%2BD2sXotlGntbc%3D (Pubitemid 47024900)
14. S El-Fantroussi 2000 Enrichment and molecular characterization of a bacterial culture that degrades methoxy-methyl urea herbicides and their aniline derivatives Appl Environ Microbiol 66 5110 5115 10.1128/AEM.66.12.5110-5115. 2000 1:CAS:528:DC%2BD3MXjsVyhtLo%3D (Pubitemid 32217105)
15. Fournier JC, Soulas G, Parekh R (1997) Main microbial mechanisms of pesticide degradation in soils. In: Tarradellas J, Bitton G, Rossel D (eds) Soil ecotoxicology. CRC, Boca Raton, pp 85-116
16. C Gaggi G Sbrilli AM Hasab El Naby M Bucci M Duccini E Bacci 1995 Toxicity and hazard ranking of s-triazine herbicides using Microtox®, two green algal species and a marine crustacean Environ Toxicol Chem 14 1065 1069 1:CAS:528:DyaK2MXlvVGgsL4%3D
17. D Ghosh K Roy V Srinivasan T Mueller OH Tuovinen K Sublette A Peacock M Radosevich 2009 In-situ enrichment and analysis of atrazine-degrading microbial communities using atrazine-containing porous beads Soil Biol Biochem 41 1331 1334 10.1016/j.soilbio.2008.12.027 1:CAS:528:DC%2BD1MXmtVGku7c%3D
18. S Houot E Topp A Yassir G Soulas 2000 Dependence of accelerated degradation of atrazine on soil pH in French and Canadian soils Soil Biol Biochem 32 615 625 10.1016/S0038-0717(99)00188-1 1:CAS:528:DC%2BD3cXjtlKjsrk%3D (Pubitemid 30263862)
19. S Hussain SR Sørensen M Devers-Lamrani T El-Sebai F Martin-Laurent 2009 Characterization of an isoproturon mineralising bacterial culture enriched from a French agricultural soil Chemosphere 77 1052 1059 10.1016/j.chemosphere. 2009.09.020 1:CAS:528:DC%2BD1MXhtlWnsL7P
20. JS Karns 1999 Gene sequence and properties of an s-triazine ring cleavage enzyme from Pseudomonas sp. strain NRRLB-12227 Appl Environ Microbiol 65 3512 3517 1:CAS:528:DyaK1MXltVOlsbs%3D (Pubitemid 29398979)
21. NU Kolić D Hršak AB Kolar I Petrić S Stipičević G Soulas F Martin-Laurent 2007 Combined metabolic activity within an atrazine-mineralizing community enriched from agrochemical factory soil Int Biodeterior Biodegrad 60 299 307 10.1016/j.ibiod.2007.05.004 (Pubitemid 350101224)
22. NU Kolić F Martin-Laurent M Devers I Petrić AB Kolar D Hršak 2008 Genetic potential, diversity and activity of an atrazine-degrading community enriched from a herbicide factory effluent J Appl Microbiol 105 1334 1343 10.1111/j.1365-2672.2008.03890.x
23. BC Kross A Vergara LE Raue 1992 Toxicity assessment of atrazine, alachlor, and carbofuran and their respective environmental metabolites using Microtox J Toxicol Environ Health 37 149 159 10.1080/15287399209531662 1:CAS:528:DyaK38XmsVKrsbk%3D
24. B Martinez J Tomkins LP Wackett R Wing MJ Sadowsky 2001 Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP J Bacteriol 183 5684 5697 10.1128/JB.183.19. 5684-5697.2001 1:CAS:528:DC%2BD3MXmvF2msL0%3D (Pubitemid 32898616)
25. F Martin-Laurent L Cornet L Ranjard J-C Lopez-Gutierrez L Philippot C Schwartz R Chaussod G Catroux G Soulas 2004 Estimation of atrazine-degrading genetic potential and activity in three French agricultural soils FEMS Microbiol Ecol 48 425 435 10.1016/j.femsec.2004.03.008 1:CAS:528:DC%2BD2cXktF2ku78%3D (Pubitemid 38648929)
26. C Monard F Martin-Laurent M Devers-Lamrani O Lima P Vandenkoornhuyse F Binet 2010 atz gene expressions during atrazine degradation in the soil drilosphere Mol Ecol 19 749 759 10.1111/j.1365-294X.2009.04503.x 1:CAS:528:DC%2BC3cXjsFekurg%3D
27. WW Mulbry H Zhu SM Nour E Topp 2002 The triazine hydrolase gene trzN from Nocardioides sp. strain C190: cloning and construction of gene-specific primers FEMS Microbiol Lett 206 75 79 10.1111/j.1574-6968.2002.tb10989.x 1:CAS:528:DC%2BD38XitFahsA%3D%3D (Pubitemid 34084941)
28. G Neumann R Teras L Monson M Kivisaar F Schauer HJ Heipieper 2004 Simultaneous degradation of atrazine and phenol by Pseudomonas sp. strain ADP: effects of toxicity and adaptation Appl Environ Microbiol 70 1907 1912 10.1128/AEM.70.4.1907-1912.2004 1:CAS:528:DC%2BD2cXjtlOit7o%3D (Pubitemid 38500486)
29. D Paul G Pandey C Meier JR van der Meer RK Jain 2006 Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation FEMS Microbiol Ecol 57 116 127 10.1111/j.1574-6941.2006.00103.x 1:CAS:528:DC%2BD28XntFaqtb0%3D (Pubitemid 43876444)
30. O Pelz M Tesar R-M Wittich ERB Moore KN Timmis W-R Abraham 1999 Towards elucidation of microbial community metabolic pathways: unravelling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry Environ Microbiol 1 167 174 10.1046/j.1462-2920.1999.00023.x 1:CAS:528:DyaK1MXktFykurs%3D (Pubitemid 129640039)
31. SF Pesce DA Wunderlin 2004 Biodegradation of lindane by a native bacterial consortium isolated from contaminated river sediment Int Biodeterior Biodegrad 54 255 260 10.1016/j.ibiod.2004.02.003 1:CAS:528:DC%2BD2cXntVOjtbw%3D (Pubitemid 39151686)
32. S Piutti E Semon D Landry A Hartmann S Dousset E Lichtfouse E Topp G Soulas F Martin-Laurent 2003 Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil FEMS Microbiol Lett 221 111 117 10.1016/S0378- 1097(03)00168-X 1:CAS:528:DC%2BD3sXivFCru74%3D (Pubitemid 36407760)
33. L Ranjard F Poly S Nazaret 2000 Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment Res Microbiol 151 167 177 10.1016/S0923-2508(00)00136-4 1:CAS:528: DC%2BD3cXltFSis7o%3D (Pubitemid 30353405)
34. MJ Sadowsky ZK Tong M De Souza LP Wackett 1998 AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes J Bacteriol 180 152 158 1:CAS:528:DyaK1cXotVWm (Pubitemid 28023795)
35. D Seghers K Verthe D Reheul R Bulcke SD Siciliano W Verstraete EM Top 2003 Effect of long-term herbicide applications on the bacterial community structure and function in an agricultural soil FEMS Microbiol Ecol 1566 1 8
36. N Udiković D Hršak G Mendaš D Filipčić 2003 Enrichment and characterization of atrazine degrading bacterial communities Food technol biotechnol 41 211 217 (Pubitemid 37085961)
37. N Udiković-Kolić D Hršak M Devers V Klepac-Ceraj I Petrić F Martin-Laurent 2010 Taxonomic and functional diversity of atrazine-degrading bacterial communities enriched from agrochemical factory soil J Appl Microbiol 109 355 367
38. JR Van der Meer 2006 Environmental pollution promotes selection of microbial degradation pathways Front Ecol Environ 4 35 42 10.1890/1540- 9295(2006)004[0035:EPPSOM]2.0.CO;2 (Pubitemid 43227727)
39. M-C Wang Y-H Liu Q Wang M Gong X-M Hua Y-J Pang S Hu Y-H Yang 2008 Impacts of methamidophos on the biochemical, catabolic, and genetic characteristics of soil microbial communities Soil Biol Biochem 40 778 788 10.1016/j.soilbio.2007.10.012 1:CAS:528:DC%2BD1cXisFKrsA%3D%3D
40. YF Ye H Min YF Du 2004 Characterization of a strain of Sphingobacterium sp. and its degradation to herbicide mefenacet J Environ Sci (China) 16 343 347 1:CAS:528:DC%2BD2cXivFGlurY%3D (Pubitemid 38403658)
41. MH Zwietering I Jongenburger FM Rombouts K Van't Riet 1990 Modeling of the bacterial-growth curve Appl Environ Microbiol 56 1875 1881 1:STN:280:DC%2BC3crotFKrsg%3D%3D