Prevalence of the gene trzN and biogeographic patterns among atrazine-degrading bacteria isolated from 13 Colombian agricultural soils

FEMS Microbiology Ecology

Volumn 73, Issue 3, 2010, Pages 611-623

  Arbeli, Ziv ^a   Fuentes, Cilia ^a  

^a UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

Author keywords

atrazine; atzA; biodegradation; Colombia; Tropic; trzN

Indexed keywords

ATRAZINE; BACTERIAL DNA; BACTERIAL PROTEIN; HYDROLASE;

AGRICULTURAL SOIL; BACTERIUM; BIODEGRADATION; BIOGEOGRAPHY; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; MICROCOSM; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY;

AGRICULTURE; ARTICLE; BACTERIAL GENE; BACTERIUM; BIOREMEDIATION; COLOMBIA; DNA SEQUENCE; ENZYMOLOGY; GENETICS; GEOGRAPHY; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; BACTERIA;

AGRICULTURE; ATRAZINE; BACTERIA; BACTERIAL PROTEINS; BIODEGRADATION, ENVIRONMENTAL; COLOMBIA; DNA, BACTERIAL; GENES, BACTERIAL; GEOGRAPHY; HYDROLASES; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

COLOMBIA;

ANCYLOBACTER; ARTHROBACTER; BACTERIA (MICROORGANISMS); NEGIBACTERIA; NOCARDIOIDES; POSIBACTERIA;

EID: 77955251010     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2010.00905.x     Document Type: Article

References (67)

1. Aislabie J, Bej AK, Ryburn J, Lloyd N Wilkins A (2005) Characterization of Arthrobacter nicotinovorans HIM, an atrazine-degrading bacterium, from agricultural soil New Zealand. FEMS Microbiol Ecol 52 : 279 286.
2. Altschul SF, Madden TL, Schaffer AA et al 1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 : 3389 3402.
3. Arbeli Z Fuentes CL (2007a) Accelerated biodegradation of pesticides: an overview of the phenomenon, its basis and possible solutions; and a discussion on the tropical dimension. Crop Prot 26 : 1733 1746.
4. Arbeli Z Fuentes CL (2007b) Improved purification and PCR amplification of DNA from environmental samples. FEMS Microbiol Lett 272 : 269 275.
5. Arbeli Z Ronen Z (2003) Enrichment of a microbial culture capable of reductive debromination of the flame retardant tetrabromobisphenol-A, and identification of the intermediate metabolites produced in the process. Biodegradation 14 : 385 395.
6. Barriuso E Houot S (1996) Rapid mineralization of the S-triazine ring of atrazine in soils in relation to soil management. Soil Biol Biochem 28 : 1341 1348.
7. Best JA Weber JB (1974) Disappearance of s-triazines as affected by soil pH using a balance-sheet approach. Weed Sci 22 : 364 373.
8. Boundy-Mills KL, de Souza ML, Mandelbaum RT, Wackett LP Sadowsky MJ (1997) The atzB gene of Pseudomonas sp. strain ADP encoded the second enzyme of a novel atrazine degradation pathway. Appl Environ Microb 63 : 916 923.
9. Bouquard C, Ouazzani J, Prome J, Michel-Briand Y Plesiat P (1997) Dechlorination of atrazine by a Rhizobium sp. isolate. Appl Environ Microb 63 : 862 866.
10. Cai B, Han Y, Liu B, Ren Y Jiang S (2003) Isolation and characterization of an atrazine-degrading bacterium from industrial wastewater in China. Lett Appl Microbiol 36 : 272 276.
11. Cohen S, Creager S, Carsel R Enfield C (1984) Potential pesticide contamination of groundwater from agricultural uses. Treatment and Disposal of Pesticide Waste (Krueger RF Seiber JN, eds), pp. 297 325. American Chemical Society, Washington, DC.
12. De Boer SH, Ward LJ, Li X Chittaranjan S (1995) Attenuation of PCR inhibition in the presence of plant compounds by addition of BLOTTO. Nucleic Acids Res 23 : 2567 2568.
13. de Souza ML, Wackett LP, Boundy-Mills KL, Mandelbaum RT Sadowsky MJ (1995) Cloning, characterization, and expression of a gene region from Pseudomonas sp. strain ADP involved in the dechlorination of atrazine. Appl Environ Microb 61 : 3373 3378.
14. de Souza ML, Sadowsky MJ Wackett LP (1996) Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization. J Bacteriol 178 : 4894 4900.
15. de Souza ML, Newcombe D, Alvey S, Crowley DE, Hay A, Sadowsky MJ Wackett LP (1998a) Molecular basis of a bacterial consortium: interspecies catabolism of atrazine. Appl Environ Microb 64 : 178 184.
16. de Souza ML, Seffernick J, Martinez B, Sadowsky MJ Wackett LP (1998b) The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol 180 : 1951 1954.
17. Devers M, Soulas G Martin-Laurent F (2004) Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil. J Microbiol Meth 56 : 3 15.
18. Devers M, El Azhari N, Kolic NU Martin-Laurent F (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.
19. Ghosh D, Roy K, Williamson KE, White DC, Wommack KE, Sublette KL Radosevich M (2008) Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA. Appl Environ Microb 74 : 495 502.
20. Gontang EA, Fenical W Jensen PR (2007) Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl Environ Microb 73 : 3272 3282.
21. Hernández M, Villalobos P, Morgante V, González M, Reiff C, Moore E Seeger M (2008) Isolation and characterization of a novel simazine-degrading bacterium from agricultural soil of central Chile, Pseudomonas sp. MHP41. FEMS Microbiol Lett 286 : 184 190.
22. Iwasaki A, Takagi K, Yoshioka Y, Fujii K, Kojima Y Harada N (2007) Isolation and characterization of a novel simazine-degrading beta-proteobacterium and detection of genes encoding s-triazine-degrading enzymes. Pest Manag Sci 63 : 261 268.
23. Kodama Y, Yamamoto H, Amano N Amachi T (1992) Reclassification of two strains of Arthrobacter oxydans and proposal of Arthrobacter nicotinovorans sp. nov. Int J Syst Evol Micr 42 : 234 239.
24. Kolić NU, Hršak D, Kolar AB, Petrić I, Stipièevic S, Soulas G Martin-Laurent F (2007) Combined metabolic activity within an atrazine-mineralizing community enriched from agrochemical factory soil. Int Biodeter Biodegr 60 : 299 307.
25. Krutz LJ, Zablotowicz RM, Reddy KN, Koger CH III. Weaver MA (2007) Enhanced degradation of atrazine under field conditions correlates with a loss of weed control in the glasshouse. Pest Manag Sci 63 : 23 31.
26. Kumar S, Tamura K Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5 : 150 163.
27. Lee SD (2007) Nocardioides furvisabuli sp. nov., isolated from black sand. Int J Syst Evol Micr 57 : 35 39.
28. Lee SD, Lee DW Kim JS (2008) Nocardioides hwasunensis sp. nov. Int J Syst Evol Micr 58 : 278 281.
29. Li Q, Li Y, Zhu X Cai B (2008) Isolation and characterization of atrazine-degrading Arthrobacter sp. AD26 and use of this strain in bioremediation of contaminated soil. J Environ Sci-China 20 : 1226 1230.
30. Ma L Selim HM (1996) Atrazine retention and transport in soils. Rev Environ Contam T 145 : 129 173.
31. Mandelbaum RT, Wackett LP Allan DL (1993) Rapid hydrolysis of atrazine to hydroxyatrazine by soil bacteria. Environ Sci Technol 27 : 1943 1946.
32. Mandelbaum RT, Allan DL Wackett LP (1995) Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl Environ Microb 61 : 1451 1457.
33. Martinez B, Tomkins J, Wackett LP, Wing R Sadowsky ML (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183 : 5684 5697.
34. McDonald IR, Kämpfer P, Topp E et al 2005) Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments. Int J Syst Evol Micr 55 : 1827 1832.
35. Monard C, Martin-Laurent F, Devers-Lamrani M, Lima O, Vandenkoornhuyse P Binet F (2010) atz gene expressions during atrazine degradation in the soil drilosphere. Mol Ecol 19 : 749 759.
36. Mulbry WW, Zhu H, Nour SM Topp E (2002) The triazine hydrolase gene trzN from Nocardioides sp. strain C190: cloning and construction of gene-specific primers. FEMS Microbiol Lett 206 : 75 79.
37. O'Donnell AG, Goodfellow M Minnikin DE (1982) Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) Lochhead in the genus Nocardioides (Prauser) emend. O'Donnell et al. as Nocardioides simplex comb. nov. Arch Microbiol 133 : 323 329.
38. Piutti S, Semon E, Landry D, Hartmann A, Dousset S, Lichtfouse E, Topp E, Soulas G Martin-Laurent F (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.
39. Rousseaux S, Hartmann A Soulas G (2001) Isolation and characterization of new gram-negative and gram positive atrazine degrading bacteria from different French soils. FEMS Microbial Ecol 36 : 211 222.
40. Sadowsky MJ, Tong Z, de Souza M Wackett LP (1998) AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-degrading enzymes. J Bacteriol 180 : 152 158.
41. Santiago-Mora R, Martin-Laurent F, de Prado R Franco AR (2005) Degradation of simazine by microorganisms isolated from soils of Spanish olive fields. Pest Manag Sci 61 : 917 921.
42. Satsuma K (2006) Characterisation of new strains of atrazine degrading Nocardioides sp. isolated from Japanese riverbed sediment using naturally derived river ecosystem. Pest Manag Sci 62 : 340 349.
43. Satsuma K (2009) Complete biodegradation of atrazine by a microbial community isolated from a naturally derived river ecosystem (microcosm). Chemosphere 77 : 590 596.
44. Scott C, Jackson CJ, Coppin CW, Mourant RG, Hilton ME, Sutherland TD, Russell RJ Oakeshott JG (2009) Catalytic improvement and evolution of atrazine chlorohydrolase. Appl Environ Microb 75 : 2184 2191.
45. Seffernick JL Wackett LP (2001) Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase. Biochemistry 40 : 12747 12753.
46. Shapir N, Rosendahl C, Johnson G, Andreina M, Sadowsky MJ Wackett LP (2005) Substrate specificity and colorimetric assay for recombinant TrzN derived from Arthrobacter aurescens TC1. Appl Environ Microb 71 : 2214 2220.
47. Shapir N, Mongodin EF, Sadowsky MJ, Daugherty SC, Nelson KE Wackett LP (2007) Evolution of catabolic pathways: genomic insights into microbial s-triazine metabolism. J Bacteriol 189 : 674 682.
48. Singh P, Suri CR Cameotra SS (2004) Isolation of a member of Acinetobacter species involved in atrazine degradation. Biochem Bioph Res Co 317 : 697 702.
49. 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.
50. Stamper DM, Radosevich M, Hallberg KB, Traina SJ Tuovinen OH (2002) Ralstonia basilensis M91-3, a denitrifying soil bacterium capable of using s-triazines as nitrogen sources. Can J Microbiol 48 : 1089 1098.
51. Strong LC, Rosendahl C, Johnson G, Sadowsky MJ Wackett LP (2002) Arthrobacter aurescens TC1 metabolizes diverse s-triazine ring compounds. Appl Environ Microb 68 : 5973 5980.
52. Struthers JK, Jayachandran K Moorman TB (1998) Biodegradation of atrazine by Agrobacterium radiobacter J14a and use of this strain in bioremediation of contaminated soil. Appl Environ Microb 64 : 3368 3375.
53. Thompson JD, Higgins DG Gibson TJ (1994) Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 : 4673 4680.
54. Topp E, Mulbry WM, Zhu H, Nour SM Cuppels D (2000a) Characterization of s-triazine herbicide metabolism by a Nocardioides sp. isolated from agriculture soils. Appl Environ Microb 66 : 3134 3141.
55. Topp E, Zhu H, Nour SM, Houot S, Lewis M Cuppels D (2000b) Characterization of an atrazine-degrading Pseudaminobacter sp. isolated from Canadian and French agricultural soils. Appl Environ Microb 66 : 2773 2782. (Pubitemid 30497580)
56. Vaishampayan PA, Kanekar PP Dhakephalkar PK (2007) Isolation and characterization of Arthrobacter sp. strain MCM B-436, an atrazine-degrading bacterium, from rhizospheric soil. Int Biodeter Biodegr 60 : 273 278.
57. Vanderheyden V, Debongnie P Pussemier L (1997) Accelerated degradation and mineralization of atrazine in surface and subsurface soil materials. Pest Sci 49 : 237 242.
58. Versalovic J, Koeuth T Lupski JR (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19 : 6823 6831.
59. Versalovic J, Schneider M, de Bruijn FJ Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5 : 25 40.
60. Vibber LL, Pressler MJ Colores GM (2007) Isolation and characterization of novel atrazine-degrading microorganisms from an agricultural soil. Appl Microbiol Biot 75 : 921 928.
61. Walker A Welch SJ (1991) Enhanced degradation of some soil-applied herbicides. Weed Res 31 : 49 57.
62. Weisburg WG, Barns SM, Pelletier DA Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 : 697 703.
63. Widdel F Bak F (1991) Gram-negative mesophilic sulfate-reducing bacteria. The Prokaryotes (Balows A, Truper HG, Dworkin M, Hander W Schleifer KH, eds), pp. 3352 3378. Springer-Verlag, New York.
64. Xin YH, Zhou YG Chen WX (2006) Ancylobacter polymorphus sp. nov. and Ancylobacter vacuolatus sp. nov. Int J Syst Evol Micr 56 : 1185 1188.
65. Yamazaki K, Fujii K, Iwasaki A, Takagi K, Satsuma K, Harada N Uchimura T (2008) Different substrate specificities of two triazine hydrolases (TrzNs) from Nocardioides species. FEMS Microbiol Lett 286 : 171 177.
66. Yoon JH, Lee JK, Jung SY, Kim JA, Kim HK Oh TK (2006) Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium. Int J Syst Evol Micr 56 : 1783 1787.
67. Zhou J, Bruns MA Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microb 62 : 316 322.