Centimetre-scale vertical variability of phenoxy acid herbicide mineralization potential in aquifer sediment relates to the abundance of tfdA genes

FEMS Microbiology Ecology

Volumn 80, Issue 2, 2012, Pages 331-341

  Batioǧlu Pazarbaşi, Meriç ^a,b   Bælum, Jacob ^a,c   Johnsen, Anders R ^a   Sørensen, Sebastian R ^a   Albrechtsen, Hans Jørgen ^b   Aamand, Jens ^a  

^a GEOLOGICAL SURVEY OF DENMARK AND GREENLAND   (Denmark)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c Chalmers University of Technology   (Denmark)

Author keywords

Radiorespirometric analysis; Spatial variability; TaqMan probe based quantitative real time PCR; TfdA diversity

Indexed keywords

2 (4 CHLORO 2 METHYLPHENOXY)ACETIC ACID; 2,4 DICHLOROPHENOXYACETATE ALPHA KETOGLUTARATE DIOXYGENASE; 2,4 DICHLOROPHENOXYACETIC ACID; 2,4-DICHLOROPHENOXYACETATE-ALPHA-KETOGLUTARATE DIOXYGENASE; DRUG DERIVATIVE; GROUND WATER; HERBICIDE; MECOPROP; MIXED FUNCTION OXIDASE;

ACETIC ACID; AGRICULTURAL SOIL; AQUIFER; BIODEGRADATION; GENE EXPRESSION; GROUNDWATER; HERBICIDE; MINERALIZATION; ORGANIC CARBON; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SEDIMENT ANALYSIS; SEDIMENT CHEMISTRY; SPATIAL VARIATION; WATER TABLE;

ARTICLE; BACTERIAL GENE; BACTERIUM; BIOREMEDIATION; CHEMISTRY; GENETICS; METABOLISM; MICROBIOLOGY; SEDIMENT; WATER POLLUTANT;

2,4-DICHLOROPHENOXYACETIC ACID; 2-METHYL-4-CHLOROPHENOXYACETIC ACID; BACTERIA; BIODEGRADATION, ENVIRONMENTAL; GENES, BACTERIAL; GEOLOGIC SEDIMENTS; GROUNDWATER; HERBICIDES; MIXED FUNCTION OXYGENASES; WATER MICROBIOLOGY; WATER POLLUTANTS, CHEMICAL;

EID: 84859626335     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2012.01300.x     Document Type: Article

References (44)

1. Albrechtsen HJ, Mills MS, Aamand J & Bjerg PL (2001) Degradation of herbicides in shallow Danish aquifers: an integrated laboratory and field study. Pest Manag Sci 57: 341-350.
2. Bælum J & Jacobsen CS (2009) TaqMan probe-based real-time PCR assay for detection and discrimination of class I, II, and III tfdA genes in soils treated with phenoxy acid herbicides. Appl Environ Microbiol 75: 2969-2972.
3. Bælum J, Henriksen T, Hansen HCB & Jacobsen CS (2006) Degradation of 4-chloro-2-methylphenoxyacetic acid in top- and sub-soil is quantitatively linked to the class III tfdA gene. Appl Environ Microbiol 72: 1476-1486.
4. Bælum J, Nicolaisen MH, Holben WE, Strobel BW, Sorensen J & Jacobsen CS (2008) Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil. ISME J 2: 677-687.
5. Baker KL, Langenheder S, Nicol GW, Ricketts D, Killham K, Campbell CD & Prosser JI (2009) Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies. Soil Biol Biochem 41: 2292-2298.
6. Becker JM, Parkin T, Nakatsu CH, Wilbur JD & Konopka A (2006) Bacterial activity, community structure, and centimeter-scale spatial heterogeneity in contaminated soil. Microb Ecol 51: 220-231.
7. Berkowitz B, Silliman SE & Dunn AM (2004) Impact of the capillary fringe on local flow, chemical migration, and microbiology. Vadose Zone J 3: 534-548.
8. Brad T, van Breukelen BM, Braster M, van Straalen NM & Röling WFM (2008) Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer. FEMS Microbiol Ecol 65: 534-543.
9. Bundt M, Widmer F, Pesaro M, Zeyer J & Blaser P (2001) Preferential flow paths: biological 'hot spots' in soils. Soil Biol Biochem 33: 729-738.
10. European Parliament and Council (2006). Directive 2006/118/EC of the European Parliament and of the Council of 12 December 2006 on the protection of groundwater against pollution and deterioration.
11. Feris K, Ramsey P, Frazar C, Moore JN, Gannon JE & Holben WE (2003) Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient. Appl Environ Microbiol 69: 5563-5573.
12. Feris K, Ramsey P, Frazar C, Rillig M, Moore JN, Gannon JE & Holben WE (2004) Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient. Appl Environ Microbiol 70: 2323-2331.
13. Flury M, Flühler H, Jury WA & Leuenberger J (1994) Susceptibility of soils to preferential flow of water: a field study. Water Resour Res 30: 1945-1954.
14. Franklin RB & Mills AL (2003) Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol Ecol 44: 335-346.
15. Franklin RB & Mills AL (2009) Importance of spatially structured environmental heterogeneity in controlling microbial community composition at small spatial scales in an agricultural field. Soil Biol Biochem 41: 1833-1840.
16. Fukumori F & Hausinger RP (1993a) Alcaligenes eutrophus JMP134 "2, 4-Dichlorophenoxyacetate monooxygenase" is an α-ketoglutarate-dependent dioxygenase. J Bacteriol 175: 2083-2086.
17. Fukumori F & Hausinger RP (1993b) Purification and characterization of 2, 4-Dichlorophenoxyacetate alpha-ketoglutarate dioxygenase. J Biol Chem 268: 24311-24317.
18. Goldscheider N, Hunkeler D & Rossi P (2006) Review: microbial biocenoses in pristine aquifers and an assessment of investigative methods. Hydrogeol J 14: 926-941.
19. Gonod LV, Chenu C & Soulas G (2003) Spatial variability of 2, 4-Dichlorophenoxyacetic acid (2, 4-D) mineralization potential at a millimetre scale in soil. Soil Biol Biochem 35: 373-382.
20. Gonod LV, Chadoeuf J & Chenu C (2006) Spatial distribution of microbial 2, 4-dichlorophenoxy acetic acid mineralization from field to microhabitat scales. Soil Sci Soc Am J 70: 64-71.
21. Griffiths RI, Whiteley AS, O'Donnell AG & Bailey MJ (2003) Influence of depth and sampling time on bacterial community structure in an upland grassland soil. FEMS Microbiol Ecol 43: 35-43.
22. International Organization for Standardization (1994). Soil Quality - Determination of pH. ISO 10390.
23. Itoh K, Kanda R, Sumita Y, Kim H, Kamagata Y, Suyama K, Yamamoto H, Hausinger RP & Tiedje JM (2002) tfdA-like genes in 2, 4-dichlorophenoxyacetic acid-degrading bacteria belonging to the Bradyrhizobium-Agromonas-Nitrobacter-Afipia cluster in α-Proteobacteria. Appl Environ Microbiol 68: 3449-3454.
24. Itoh K, Tashiro Y, Uobe K, Kamagata Y, Suyama K & Yamamoto H (2004) Root nodule Bradyrhizobium spp. harbor tfdA alpha and cadA, homologous with genes encoding 2, 4 dichlorophenoxyacetic acid-degrading proteins. Appl Environ Microbiol 70: 2110-2118.
25. Jacobsen OS, Brüsch W, Fomsgaard IS, Helweg A, Vinther FP, Spliid NH, Bossi R & Mogensen BB (1998) In Leaching and Degradation of Selected Pesticides in a Sandy Watershed. Ministry of Environment and Energy, Danish EPA, Copenhagen, Denmark.
26. Janniche GS, Mouvet C & Albrechtsen HJ (2011) Vertical small scale variations of sorption and mineralization of three herbicides in subsurface limestone and sandy aquifer. J Contam Hydrol 123: 167-177.
27. Jensen PH, Hansen HCB, Rasmussen J & Jacobsen OS (2004) Sorption-controlled degradation kinetics of MCPA in soil. Environ Sci Technol 38: 6662-6668.
28. 14C]-compounds in a 96-well microplate format. J Microbiol Meth 79: 114-116.
29. Juhler RK, Henriksen TH, Ernstsen V, Vinther FP & Rosenberg P (2008) Impact of basic soil parameters on pesticide disappearance investigated by multivariate partial least square regression and statistics. J Environ Qual 37: 1719-1732.
30. Kamagata Y, Fulthorpe RR, Tamura K, Takami H, Forney LJ & Tiedje JM (1997) Pristine environments harbor a new group of oligotrophic 2, 4-dichlorophenoxyacetic acid-degrading bacteria. Appl Environ Microbiol 63: 2266-2272.
31. Kitagawa W, Takami S, Miyauchi K, Masai E, Kamagata Y, Tiedje JM & Fukuda M (2002) Novel 2, 4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment. J Bacteriol 184: 509-518.
32. Larsen L, Sørensen SR & Aamand J (2000) Mecoprop, isoproturon, and atrazine in and above a sandy aquifer: Vertical distribution of mineralization potential. Environ Sci Technol 34: 2426-2430.
33. Lipthay JR, Tuxen N, Johnsen K, Hansen LH, Albrechtsen HJ, Bjerg PL & Aamand J (2003) In situ exposure to low herbicide concentrations affects microbial population composition and catabolic gene frequency in an aerobic shallow aquifer. Appl Environ Microbiol 69: 461-467.
34. McGowan C, Fulthorpe R, Wright A & Tiedje JM (1998) Evidence for interspecies gene transfer in the evolution of 2, 4-dichlorophenoxyacetic acid degraders. Appl Environ Microbiol 64: 4089-4092.
35. Philippot L, Bru D, Saby NPA, Cuhel J, Arrouays D, Šimek M & Hallin S (2009) Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree. Environ Microbiol 11: 3096-3104.
36. Rodriguez-Cruz MS, Bælum J, Shawc LJ, Sørensen SR, Shi S, Aspray T, Jacobsen CS & Bending GD (2009) Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes. Soil Biol Biochem 42: 32-39.
37. Sebai T, Lagacherie B, Soulas G & Martin-Laurent F (2007) Spatial variability of isoproturon mineralizing activity within an agricultural field: geostatistical analysis of simple physicochemical and microbiological soil parameters. Environ Pollut 145: 680-690.
38. Sjøholm OR, Aamand J, Sørensen J & Nybroe O (2010) Degrader density determines spatial variability of 2, 6-dichlorobenzamide mineralization in soil. Environ Pollut 158: 292-298.
39. Stamm C, Flühler H, Gächter R, Leuenberger J & Wunderli H (1998) Preferential transport of phosphorus in drained grassland soils. J Environ Qual 27: 515-522.
40. Starr RC & Ingleton RA (1992) A new method for collecting core samples without a drilling rig. Ground Water Monit Rev 12: 91-95.
41. Vervier P & Gibert J (1991) Dynamics of surface-water groundwater ecotones in a karstic aquifer. Freshw Biol 26: 241-250.
42. Williams DD (1993) Changes in fresh-water meiofauna communities along the groundwater hyporheic water ecotone. Trans Am Microsc Soc 112: 181-194.
43. Wood M, Issa S, Albuquerque M & Johnson AC (2002) Spatial variability in herbicide degradation in the subsurface environment of a groundwater protection zone. Pest Manag Sci 58: 3-9.
44. Zakaria D, Lappin-Scott H, Burton S & Whitby C (2007) Bacterial diversity in soil enrichment cultures amended with 2(2-methyl-4-chlorophenoxy)propionic acid (mecoprop). Environ Microbiol 9: 2575-2587.