Bacterial diversity and bioaugmentation in floodwater of a paddy field in the presence of the herbicide molinate

Biodegradation

Volumn 22, Issue 2, 2011, Pages 445-461

  Barreiros, Luisa ^a,b   Manaia, Célia M ^b   Nunes, Olga C ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b UNIVERSIDADE CATÓLICA PORTUGUESA   (Portugal)

Author keywords

Bacterial community structure and composition; Bacterial diversity; Biodegradation; Floodwater; Molinate

Indexed keywords

BACTERIAL COMMUNITY; BACTERIAL COMMUNITY COMPOSITION; BACTERIAL COMMUNITY STRUCTURE; BACTERIAL DIVERSITY; BIO-AUGMENTATION; CULTIVABLE BACTERIA; ENVIRONMENTAL CONTAMINANT; FLOODWATER; HERBICIDE MOLINATE; MICROBIOTAS; MOLINATE; MOLINATE APPLICATION; MULTI VARIATE ANALYSIS; PADDY FIELDS; RICE PADDY; SAMPLING CAMPAIGNS; SHANNON'S INDICES; TEMPORAL VARIATION;

BACTERIOLOGY; BIODEGRADATION; BIOREMEDIATION; CELL CULTURE; DEGRADATION; HERBICIDES; MULTIVARIANT ANALYSIS; RATING; SOCIAL SCIENCES; STRUCTURE (COMPOSITION); WEED CONTROL;

BACTERIA;

AZEPINE DERIVATIVE; HERBICIDE; MOLINATE; THIOCARBAMIC ACID DERIVATIVE;

BACTERIUM; BIODEGRADATION; COMMUNITY STRUCTURE; FEASIBILITY STUDY; FLOOD; HERBICIDE; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MICROCOSM; MULTIVARIATE ANALYSIS; PADDY FIELD; TEMPORAL VARIATION; WATER POLLUTION;

AGRICULTURE; ARTICLE; BACTERIUM; CLASSIFICATION; ECOSYSTEM RESTORATION; GENETICS; METABOLISM; SOIL POLLUTANT; WATER POLLUTANT;

AGRICULTURE; AZEPINES; BACTERIA; ENVIRONMENTAL REMEDIATION; HERBICIDES; SOIL POLLUTANTS; THIOCARBAMATES; WATER POLLUTANTS, CHEMICAL;

BACTERIA (MICROORGANISMS);

EID: 79952184915     PISSN: 09239820     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10532-010-9417-1     Document Type: Article

References (75)

1. Albanis TA, Hela DG, Sakellarides TM, Konstantinou IK (1998) Monitoring of pesticide residues and their metabolites in surface and underground waters of Imathia (N. Greece) by means of solid-phase extraction disks and gas chromatography. J Chromatogr A823(1-2): 59-71.
2. Asari N, Ishihara R, Nakajima Y, Kimura M, Asakawa S (2007) Succession and phylogenetic composition of eubacterial communities in rice straw during decomposition on the surface of paddy field soil. Soil Sci Plant Nutr 53(1): 56-65.
3. Bai Q, Gattinger A, Zelles L (2000) Characterization of microbial consortia in paddy rice soil by phospholipid analysis. Microb Ecol 39: 273-281.
4. Barreiros L, Nogales B, Manaia CM, Silva-Ferreira AC, Pieper DH, Reis MA, Nunes OC (2003) A novel pathway for mineralization of the thiocarbamate herbicide molinate by a defined bacterial mixed culture. Environ Microbiol 5(10): 944-953.
5. Barreiros L, Fernandes A, Silva-Ferreira AC, Pereira H, Bastos MMSM, Manaia CM, Nunes OC (2008) New insights into a bacterial metabolic and detoxifying association responsible for the mineralization of the thiocarbamate herbicide molinate. Microbiology 154(4): 1038-1046.
6. Benimeli CS, Fuentes MS, Abate CM, Amoroso MJ (2008) Bioremediation of lindane-contaminated soil by Streptomyces sp. M7 and its effects on Zea mays growth. Int Biodeterior Biodegrad 61: 233-239.
7. Blackwood CB, Paul EA (2003) Eubacterial community structure and population size within the soil light fraction, rhizosphere, and heavy fraction of several agricultural systems. Soil Biol Biochem 35(9): 1245-1255.
8. Bouchez T, Patureau D, Dabert P, Juretschko S, Dore J, Delgenes P, Molleta R, Wagner M (2000) Ecological study of a bioaugmentation failure. Environ Microbiol 2: 179-190.
9. Carvalho D, Mendes A, Magalhães FD, Nunes OC (2010) Treatment of waters containing the thiocarbamate herbicide molinate through an adsorption/bio-regeneration system using a low-cost adsorbent. Water Air Soil Pollut 207: 289-298.
10. Castro M, Silva-Ferreira AC, Manaia CM, Nunes OC (2005) A case study of molinate application in a Portuguese rice field: herbicide dissipation and proposal of a clean-up methodology. Chemosphere 59(7): 1059-1065.
11. Cerejeira MJ, Viana P, Batista S, Pereira T, Silva E, Valério MJ, Silva A, Ferreira M, Silva-Fernandes AM (2003) Pesticides in Portuguese surface and ground waters. Water Res 37(5): 1055-1063.
12. Chapalamadugu S, Chaudhry G (1992) Microbiological and biotechnological aspects of metabolism of carbamates and organophosphates. Crit Rev Biotechnol 12: 357-389.
13. Chen W-C, Yen J-H, Chang C-S, Wang Y-S (2009) Effects of herbicide butachlor on soil microorganisms and on nitrogen-fixing abilities in paddy soil. Ecotoxical Environ Safe 72: 120-127.
14. Claver A, Ormad P, Rodríguez L, Ovelleiro JL (2006) Study of the presence of pesticides in surface waters in the Ebro river basin (Spain). Chemosphere 64: 1437-1443.
15. Coelho C, Oliveira AS, Pereira MFR, Nunes OC (2006) The influence of activated carbon surface properties on the adsorption of the herbicide molinate and the bio-regeneration of the adsorbent. J Hazard Mater 138(2): 343-349.
16. Correia P, Boaventura RA, Reis MA, Nunes OC (2006) Effect of operating parameters on molinate biodegradation. Water Res 40: 331-340.
17. Curl EA, Truelove B (1986) The rhizosphere. Springer, Berlin.
18. Das K, Mukherjee AK (2007) Crude petroleum-oil biodegradation efficiency of Bacillus subtilis and Pseudomonas aeruginosa strains isolated from a petroleum-oil contaminated soil from North-East India. Bioresour Technol 98: 1339-1345.
19. Deuel LE, Turner FT, Brown KW, Price JD (1978) Persistence and factors affecting dissipation of molinate under flooded rice culture. J Environ Qual 7(3): 373-377.
20. Dorigo U, Bérard A, Humbert JF (2002) Comparison of eukaryotic phytobenthic community composition in a polluted river by partial 18S rRNA gene cloning and sequencing. Microb Ecol 44(4): 372-380.
21. Dorigo U, Bourrain X, Bérard A, Leboulanger C (2004) Seasonal changes in the sensitivity of river microalgae to atrazine and isoproturon along a contamination gradient. Sci Total Environ 318(1-3): 101-114.
22. Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S, Gillet F, Aragno M, Rossi P (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4: 634-643.
23. Gelsomino A, Cacco G (2006) Compositional shifts of bacterial groups in a solarized and amended soil as determined by denaturing gradient gel electrophoresis. Soil Biol Biochem 38(1): 91-102.
24. 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.
25. Hengstmann U, Chin KJ, Janssen PH, Liesack W (1999) Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. Appl Environ Microbiol 65(11): 5050-5058.
26. Hong Q, Zhang Z, Hong Y, Li S (2007) A microcosm study on bioremediation of fenitrothion-contaminated soil using Burkholderia sp. FDS-1. Int Biodeterior Biodegrad 59: 55-61.
27. Hoque MM, Inubushi K, Miura S, Kobayashi K, Kim HY, Okada M, Yabashi S (2001) Biological dinitrogen fixation and soil microbial biomass carbon as influenced by free-air carbon dioxide enrichment (FACE) at three levels of nitrogen fertilization in a paddy field. Biol Fertil Soils 34: 453-459.
28. Inubushi IC, Watanabe I (1986) Dynamics of available nitrogen in paddy soils. II. Mineralized N of chloroform-fumigated soil as nutrient source for rice. Soil Sci Plant Nutr 32: 561-577.
29. 2 enrichment (FACE) on microbial biomass in paddy field soil. Soil Sci Plant Nutr 47: 737-745.
30. Johnson WG, Lavy TL (1995) Organic chemicals in the environment. Persistence of carbofuran and molinate in flooded rice culture. J Environ Qual 24(3): 487-493.
31. Kikuchi H, Watanabe T, Jia Z, Kimura M, Asakawa S (2007) Molecular analyses reveal stability of bacterial communities in bulk soil of a Japanese paddy field: estimation by denaturing gradient gel electrophoresis of 16S rRNA genes amplified from DNA accompanied with RNA. Soil Sci Plant Nutr 53(4): 448-458.
32. Kim MC, Ahn JH, Shin HC, Kim T, Ryu TH, Kim DH, Song HG, Lee GH, Ka JO (2008) Molecular analysis of bacterial community structures in paddy soils for environmental risk assessment with two varieties of genetically modified rice, Iksan 483 and Milyang 204. J Microbiol Biotechnol 18(2): 207-218.
33. Kimura M, Shibagaki T, Nakajima Y, Matsuya K, Ikenaga M (2002) Community structure of the microbiota in the flood water of a Japanese paddy field estimated by restriction fragment length polymorphism and denaturing gradient gel electrophoresis pattern analysis. Biol Fertil Soils 36(4): 306-312.
34. Knapp CW, Caquet T, Hanson ML, Lagadic L, Graham DW (2005) Response of water column microbial communities to sudden exposure to deltamethrin in aquatic mesocosms. FEMS Microbiol Ecol 54(1): 157-165.
35. Köck M, Farré M, Martínez E, Gajda-Schrantz K, Ginebreda A, Navarro A, López de Alda M, Barceló D (2010) Integrated ecotoxicological and chemical approach for the assessment of pesticide pollution in the Ebro River delta (Spain). J Hydrol 383: 73-82.
36. Kong CH, Wang P, Zhao H, Xu XH, Zhu YD (2008) Impact of allelochemical exuded from allelopathic rice on soil microbial community. Soil Biol Biochem 40: 1862-1869.
37. Kuivila KM, Jennings BE (2007) Input, flux, and persistence of six select pesticides in San Francisco Bay. Int J Environ Anal Chem 87: 897-911.
38. Leps J, Smilauer P (2003) Multivariate analysis of ecological data using CANOCO. Cambridge University Press, Cambridge.
39. Liesack W, Schnell S, Revsbech NP (2000) Microbiology of flooded rice paddies. FEMS Microbiol Rev 24(5): 625-645.
40. Lima D, Viana P, André S, Chelinho S, Costa C, Ribeiro R, Sousa JP, Fialho AM, Viegas CA (2009) Evaluating a bioremediation tool for atrazine contaminated soils in open soil microcosms: the effectiveness of bioaugmentation and biostimulation approaches. Chemosphere 74: 187-192.
41. Lu Y, Watanabe A, Kimura M (2002) Contribution of plant-derived carbon to soil microbial biomass dynamics in a paddy rice microcosm. Biol Fertil Soils 36: 136-142.
42. Lynch JM, Whipps JM (1990) Substrate flow in the rhizosphere. Plant Soil 129: 1-10.
43. Mabury SA, Cox JS, Crosby DG (1996) Environmental fate of rice pesticides in California. Rev Environ Contam Toxicol 147: 71-117.
44. Manaia CM, Nogales B, Weiss N, Nunes OC (2004) Gulosibacter molinativorax gen. nov., sp. nov., a molinate degrading bacterium, and classification of "Brevibacterium helvolum" DSM 20419 as Pseudoclavibacter helvolus gen. nov., sp. nov. Int J Syst Evol Microbiol 54(3): 783-789.
45. Manuel CM, Nunes OC, Melo LF (2007) Dynamics of drinking water biofilm in flow/non-flow conditions. Water Res 41(3): 551-562.
46. Mohanty G, Mukherji S (2008) Biodegradation rate of diesel range n-alkanes by bacterial cultures Exiguobacterium aurantiacum and Burkholderia cepacia. Int Biodeterior Biodegrad 61: 240-250.
47. Murase J, Shimizu M, Hayashi M, Matsuya K, Kimura M (2005) Vertical changes in bacterial communities in percolating water of a Japanese paddy field as revealed by PCR-DGGE. Soil Sci Plant Nutr 51(1): 83-90.
48. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
49. Nagy I, Schoofs G, Compernolle F, Proost P, Vanderleyden J, De Mot R (1995) Degradation of the thiocarbamate herbicide EPTC (S-Ethyl diproylcarbamothioate) and biosafening by Rhodococcus sp. strain NI86/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase. J Bacteriol 177: 676-687.
50. Nakayama N, Okabe A, Toyota K, Kimura M, Asakawa S (2006) Phylogenetic distribution of bacteria isolated from the flood water of a Japanese paddy field. Soil Sci Plant Nutr 52(3): 305-312.
51. Normander B, Prosser JI (2000) Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions. Appl Environ Microbiol 66(10): 4372-4377.
52. Okabe A, Toyota K, Kimura M (2000) Seasonal variations of phospholipid fatty acid composition in the flood water of a Japanese paddy field under a long-term fertilizer trial. Soil Sci Plant Nutr 46(1): 177-188.
53. Pesce S, Fajon C, Bardot C, Bonnemoy F, Portelli C, Bohatier J (2006) Effects of the phenylurea herbicide diuron on natural riverine microbial communities in an experimental study. Aquat Toxicol 78(4): 303-314.
54. Pesce S, Fajon C, Bardot C, Bonnemoy F, Portelli C, Bohatier J (2008) Longitudinal changes in microbial planktonic communities of a French river in relation to pesticide and nutrient inputs. Aquat Toxicol 86(3): 352-360.
55. Phyu YL, Warne MStJ, Lim RP (2005) Effect of river water, sediment and time on the toxicity and bioavailability of molinate to the marine bacterium Vibrio fischeri (Microtox). Water Res 39: 2738-2746.
56. Pielou EC (1966) The measurement of diversity in different types of biological collections. J Theor Biol 13: 131-144.
57. Quayle WC, Oliver DP, Zrna S (2006) Field dissipation and environmental hazard assessment of clomazone, molinate, and thiobencarb in Australian rice culture. J Agric Food Chem 54(19): 7213-7220.
58. Ross LJ, Sava RJ (1986) Fate of thiobencarb and molinate in rice fields. J Environ Qual 15(3): 220-224.
59. Saeki M, Toyota K (2004) Effect of bensulfuron-methyl (a sulfonylurea herbicide) on the soil bacterial community of a paddy soil microcosm. Biol Fertil Soils 40(2): 110-118.
60. Shannon CE, Weaver W (1963) The mathematical theory of communication. University of Illinois Press, Urbana.
61. Shibagaki-Shimizu T, Nakayama N, Nakajima Y, Matsuya K, Kimura M, Asakawa S (2006) Phylogenetic study on a bacterial community in the flood water of a Japanese paddy field estimated by sequencing 16S rDNA fragments after denaturing gradient gel electrophoresis. Biol Fertil Soils 42(4): 362-365.
62. Silva E, Fialho AM, Sá-Correia I, Burns RG, Shaw LJ (2004a) Combined bioaugmentation and biostimulation to cleanup soil contaminated with high concentrations of atrazine. Environ Sci Technol 38(2): 632-637.
63. Silva M, Fernandes A, Mendes A, Manaia CM, Nunes OC (2004b) Preliminary feasibility study for the use of an adsorption/bio-regeneration system for molinate removal from effluents. Water Res 38: 2677-2684.
64. Singh S, Ladha JK, Gupta RK, Bhushan L, Rao AN (2008) Weed management in aerobic rice systems under varying establishment methods. Crop Prot 27(3-5): 660-671.
65. Soderquist CJ, Bowers JB, Crosby DG (1977) Dissipation of molinate in a rice field. J Agric Food Chem 25(4): 940-945.
66. Son HV, Ishihara S, Watanabe H (2006) Exposure risk assessment and evaluation of the best management practice for controlling pesticide runoff from paddy fields. Part 1: Paddy watershed monitoring. Pest Manag Sci 62(12): 1193-1206.
67. Sudo M, Okubo T, Kaneki R (2005) Paddy herbicide inputs in the entire river inflow reaching Lake Biwa, Japan. Limnology 6: 91-99.
68. ter Braak CJF (1994) Canonical community ordination. Part I: Basic theory and linear methods. Ecoscience 1: 127-140.
69. ter Braak CJF, Smilauer P (2002) CANOCO reference manual and CanoDraw for Windows user's guide: software for canonical community ordination (version 4. 5). Microcomputer Power, Ithaca.
70. Tomlin C (2000) The pesticide manual: a world compendium, 12th edn. The British Crop Protection Council, Farnham.
71. Valle A, Boschin G, Negri M, Abbruscato P, Sorlini C, D'Agostina A, Zanardini E (2006) The microbial degradation of azimsulfuron and its effect on the soil bacterial community. J Appl Microbiol 101(2): 443-452.
72. Wakelin SA, Macdonald LM, Rogers SL, Gregg AL, Bolger TP, Baldock JA (2008) Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils. Soil Biol Biochem 40(3): 803-813.
73. Wang G, Zhang QC, Witt C, Buresh RJ (2007) Opportunities for yield increases and environmental benefits through site-specific nutrient management in rice systems of Zhejiang province, China. Agric Syst 94(3): 801-806.
74. Wenderoth DF, Rosenbrock P, Abraham W-R, Pieper DH, Höfle MG (2003) Bacterial community dynamics during biostimulation and bioaugmentation experiments aiming at chlorobenzene degradation in groundwater. Microb Ecol 46: 161-176.
75. Yamazaki M, Hamada Y, Ibuka T, Momii T, Kimura M (2001) Seasonal variations in the community structure of aquatic organisms in a paddy field under a long-term fertilizer trial. Soil Sci Plant Nutr 47(3): 587-599.