Journal of Soils and Sediments

, Volume 16, Issue 9, pp 2263–2274 | Cite as

Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine degraders in a former pesticide mixing site and a machinery washing area

  • James F. Douglass
  • Mark Radosevich
  • Olli H. Tuovinen
Soils, Sec 5 • Soil and Landscape Ecology • Research Article

Abstract

Purpose

The purpose of this study was to determine the first-order rate constants and half-lives of aerobic and anaerobic biomineralization of atrazine in soil samples from an agricultural farm site that had been previously used for mixing pesticide formulations and washing application equipment. Atrazine catabolic genes and atrazine-degrading bacteria in the soil samples were analyzed by molecular methods.

Materials and methods

Biomineralization of atrazine was measured in soil samples with a [U-ring-14C]-atrazine biometer technique in soil samples. Enrichment cultures growing with atrazine were derived from soil samples and they were analyzed for bacterial diversity by constructing 16S rDNA clone libraries and sequencing. Bacterial isolates were also obtained and they were screened for atrazine catabolic genes.

Results and discussion

The soils contained active atrazine-metabolizing microbial communities and both aerobic and anaerobic biomineralization of [U-ring-14C]-atrazine to 14CO2 was demonstrated. In contrast to aerobic incubations, anaerobic biometers displayed considerable differences in the kinetics of atrazine mineralization between duplicates. Sequence analysis of 16S rDNA clone libraries constructed from the enrichment cultures revealed a preponderance of Variovorax spp. (51 %) and Schlesneria (16 %). Analysis of 16S rRNA gene sequences from pure cultures (n = 12) isolated from enrichment cultures yielded almost exclusively Arthrobacter spp. (83 %; 10/12 isolates). PCR screening of pure culture isolates for atrazine catabolic genes detected atzB, atzC, trzD, trzN, and possibly atzA. The presence of a complete metabolic pathway was not demonstrated by the amplification of catabolic genes among these isolates.

Conclusions

The soils contained active atrazine-metabolizing microbial communities. The anaerobic biometer data showed variable response of atrazine biomineralization to external electron acceptor conditions. Partial pathways are inevitable in soil microbial communities, with metabolites linking into other catabolic and assimilative pathways of carbon and nitrogen. There was no evidence for the complete set of functional genes of the known pathways of atrazine biomineralization among the isolates.

Keywords

Arthrobacter spp. Atz and trz genes Biodegradation of atrazine Herbicide biodegradation Pesticide biodegradation 

References

  1. Abigail MEA, Lakshmi V, Das N (2012) Biodegradation of atrazine by Cryptococcus laurentii isolated from contaminated agricultural soil. J Microbiol Biotechnol Res 2:450–457Google Scholar
  2. Abigail MEA, Salam JA, Das N (2013) Atrazine degradation in liquid culture and soil by a novel yeast Pichia kudriavzevii strain Atz-EN-01 and its potential application for bioremediation. J Appl Pharmaceut Sci 3(6):35–40Google Scholar
  3. Arthur EL, Perkovich BS, Anderson TA, Coats JR (2000) Degradation of an atrazine and metolachlor herbicide mixture in pesticide-contaminated soils from two agrochemical dealerships in Iowa. Water Air Soil Pollut 119:75–90CrossRefGoogle Scholar
  4. 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 52:279–286CrossRefGoogle Scholar
  5. Bastos AC, Magan N (2009) Trametes versicolor: potential for atrazine bioremediation in calcareous clay soil, under low water availability conditions. Int Biodeter Biodegr 63:389–394CrossRefGoogle Scholar
  6. Boundy-Mills KL, de Souza ML, Mandelbaum RT, Wackett LP, Sadowsky MJ (1997) The atzB gene of Pseudomonas sp. strain ADP encodes the second enzyme of a novel atrazine degradation pathway. Appl Environ Microbiol 63:916–923Google Scholar
  7. Cheng G, Shapir N, Sadowsky MJ, Wackett LP (2005) Allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism. Appl Environ Microbiol 71:4437–4445CrossRefGoogle Scholar
  8. Chirnside AEM, Ritter WF, Radosevich M (2007) Isolation of a selected microbial consortium from a pesticide-contaminated mix-load site soil capable of degrading the herbicides atrazine and alachlor. Soil Biol Biochem 39:3056–3065CrossRefGoogle Scholar
  9. Chirnside AEM, Ritter WF, Radosevich M (2009) Biodegradation of aged residues of atrazine and alachlor in a mixed-load site soil. Soil Biol Biochem 41:2484–2492CrossRefGoogle Scholar
  10. 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 Microbiol 61:3373–3378Google Scholar
  11. de Souza ML, Seffernick J, Martinez B, Sadowsky MJ, Wackett LP (1998) The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol 180:1951–1954Google Scholar
  12. de Wilde T, Spanoghe P, Debaer C, Ryckeboer J, Springael D, Jaeken P (2007) Overview of on-farm bioremediation systems to reduce the occurrence of point source contamination. Pest Manag Sci 63:111–128CrossRefGoogle Scholar
  13. del Pilar Castillo M, Torstensson L, Stenström J (2008) Biobeds for environmental protection from pesticide use—a review. J Agric Food Chem 56:6206–6219CrossRefGoogle Scholar
  14. 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 56:3–15CrossRefGoogle Scholar
  15. Devers M, El Azhari N, Kolic N-U, 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 273:78–86CrossRefGoogle Scholar
  16. Donnelly PK, Entry JA, Crawford DL (1993) Degradation of atrazine and 2,4-dichlorophenoxyacetic acid by mycorrhizal fungi at three nitrogen concentrations in vitro. Appl Environ Microbiol 59:2642–2647Google Scholar
  17. Douglass JF, Radosevich M, Tuovinen OH (2014) Mineralization of atrazine in the river water intake and sediments of a constructed flow-through wetland. Ecol Eng 72:35–39CrossRefGoogle Scholar
  18. Douglass JF, Radosevich M, Tuovinen OH (2015) Molecular analysis of atrazine-degrading bacteria and catabolic genes in the water column and sediment of a created wetland in an agricultural/urban watershed. Ecol Eng 83:405–412CrossRefGoogle Scholar
  19. Eaton RW, Karns JS (1991) Cloning and analysis of s-triazine catabolic genes from Pseudomonas sp. strain NRRLB-12227. J Bacteriol 173:1215–1222Google Scholar
  20. El Sebaï T, Devers-Lamrani M, Changey F, Rouard N, Martin-Laurent F (2011) Evidence of atrazine mineralization in a soil from the Nile Delta: isolation of Arthrobacter sp. TES6, an atrazine-degrading strain. Int Biodeter Biodegrad 65:1249–1255CrossRefGoogle Scholar
  21. Ettema CH, Wardle DA (2002) Spatial soil ecology. Trends Ecol Evol 17:177–183CrossRefGoogle Scholar
  22. Fan X, Song F (2014) Bioremediation of atrazine: recent advances and promises. J Soils Sedim 14:1727–1737CrossRefGoogle Scholar
  23. Fenner K, Canonica S, Wackett LP, Elsner M (2013) Evaluating pesticide degradation in the environment: blind spots and emerging opportunities. Science 341:752–758CrossRefGoogle Scholar
  24. Ghosh D, Roy K, Srinivasan V, Mueller T, Tuovinen OH, Sublette K, Peacock A, Radosevich M (2009) In-situ enrichment and analysis of atrazine-degrading microbial communities using atrazine-containing porous beads. Soil Biol Biochem 41:1331–1334CrossRefGoogle Scholar
  25. Grigg BC, Assaf NA, Turco RF (1997) Removal of atrazine contamination in soil and liquid systems using bioaugmentation. Pestic Sci 50:211–220CrossRefGoogle Scholar
  26. Guerin WF, Boyd SA (1992) Differential bioavailability of soil-sorbed naphthalene to two bacterial species. Appl Environ Microbiol 58:1142–1152Google Scholar
  27. Karns JS, Eaton RW (1997) Genes encoding s-triazine degradation are plasmid-borne in Klebsiella pneumoniae strain 99. J Agric Food Chem 45:1017–1022CrossRefGoogle Scholar
  28. Krutz LJ, Shaner DL, Weaver MA, Webb RMT, Zablotowicz RM, Reddy KN, Huang Y, Thomson SJ (2010) Agronomic and environmental implications of enhanced s-triazine degradation. Pest Manag Sci 66:461–481CrossRefGoogle Scholar
  29. Krutz LJ, Zablotowicz RM, Reddy KN (2012) Selection pressure, cropping system, and rhizosphere proximity affect atrazine degrader populations and activity in s-triazine-adapted soil. Weed Sci 60:516–524CrossRefGoogle Scholar
  30. Kulichevskaya IS, Ivanova AO, Belova SE, Baulina OI, Bodelier PLE, Rijpstra WIC, Damsté JSS, Zavarzin GA, Dedysh SN (2007) Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomycetales, from Sphagnum-dominated boreal wetlands. Int J System Evol Microbiol 57:2680–2687CrossRefGoogle Scholar
  31. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acid Techniques in Bacterial Systematics. Wiley, Chichester, pp 115–175Google Scholar
  32. Lazorko-Connon S, Achari G (2009) Atrazine: its occurrence and treatment in water. Environ Rev 17:199–214CrossRefGoogle Scholar
  33. Lian B, Jiang J, Zhang J, Zhao Y, Li S (2012) Horizontal transfer of dehalogenase genes involved in the catalysis of chlorinated compounds: evidence and ecological role. Crit Rev Microbiol 38:95–110CrossRefGoogle Scholar
  34. Liu X, Hui C, Bi L, Romantschuk M, Kontro M, Strömmer R, Hui N (2016) Bacterial community structure in atrazine treated reforested farmland in Wuying China. Appl Soil Ecol 98:39–46CrossRefGoogle Scholar
  35. Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183:5684–5697CrossRefGoogle Scholar
  36. Masaphy S, Levanon D, Henis Y (1996) Degradation of atrazine by the lignocellulolytic fungus Pleurotus pulmonarius during solid-state fermentation. Bioresour Technol 56:207–214CrossRefGoogle Scholar
  37. Mougin C, Laugero C, Asther M, Dubroca J, Frasse P, Asther M (1994) Biotransformation of the herbicide atrazine by the white rot fungus Phanerochaete chrysosporium. Appl Environ Microbiol 60:705–708Google Scholar
  38. Mudhoo A, Garg VK (2011) Sorption, transport and transformation of atrazine in soils, minerals and composts: a review. Pedosphere 21:11–25CrossRefGoogle Scholar
  39. Mueller TC, Steckel LE, Radosevich M (2010) Effect of soil pH and previous atrazine use history on atrazine degradation in a Tennessee field soil. Weed Sci 58:478–483CrossRefGoogle Scholar
  40. 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 206:75–79CrossRefGoogle Scholar
  41. 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 59:695–700Google Scholar
  42. O’Donnell AG, Young IM, Rushton SP, Shirley MD, Crawford JW (2007) Visualization, modelling and prediction in soil microbiology. Nature Rev Microbiol 5:689–699CrossRefGoogle Scholar
  43. Omotayo AE, Ilori MO, Amund OO, Ghosh D, Roy K, Radosevich M (2011) Establishment and characterization of atrazine degrading cultures from Nigerian agricultural soil using traditional and Bio-Sep bead enrichment techniques. Appl Soil Ecol 48:63–70CrossRefGoogle Scholar
  44. Pussemier L, Goux S, Vanderheyden V, Debongnie P, Tresinie I, Foucart G (1997) Rapid dissipation of atrazine in soils taken from various maize fields. Weed Res 37:171–179CrossRefGoogle Scholar
  45. Radosevich M, Traina SJ, Hao Y-L, Tuovinen OH (1995) Degradation and mineralization of atrazine by a soil bacterial isolate. Appl Environ Microbiol 61:297–302Google Scholar
  46. Radosevich M, Traina SJ, Tuovinen OH (1996) Biodegradation of atrazine in surface soils and subsurface sediments collected from an agricultural research farm. Biodegradation 7:137–149CrossRefGoogle Scholar
  47. Romero MC, Urrutia MI, Reinoso EH, Vedoval RD, Reynaldi FJ (2014) Atrazine degradation by wild filamentous fungi. Global Res J Microbiol 4:10–16Google Scholar
  48. Rousseaux S, Hartmann A, Soulas G (2001) Isolation and characterisation of new Gram-negative and Gram-positive atrazine degrading bacteria from different French soils. FEMS Microbiol Ecol 36:211–222CrossRefGoogle Scholar
  49. 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-metabolizing enzymes. J Bacteriol 180:152–158Google Scholar
  50. Sajjaphan K, Shapir N, Wackett LP, Palmer M, Blackmon B, Tomkins J, Sadowsky MJ (2004) Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli. Appl Environ Microbiol 70:4402–4407CrossRefGoogle Scholar
  51. Sajjaphan K, Heepngoen P, Sadowsky MJ, Boonkerd N (2010) Arthrobacter sp. strain KU001 isolated from a Thai soil degrades atrazine in the presence of inorganic nitrogen sources. J Microbiol Biotechnol 20:602–608Google Scholar
  52. Singh B, Singh K (2016) Microbial degradation of herbicides. Crit Rev Microbiol 42:245–261Google Scholar
  53. Smith D, Alvey S, Crowley DE (2005) Cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil. FEMS Microbiol Ecol 53:265–273CrossRefGoogle Scholar
  54. Spanoghe P, Maes A, Steurbaut W (2009) Limitation of point source pesticide pollution: results of bioremediation system. Comm Appl Biol Sci Ghent Univ 74(2):1–14Google Scholar
  55. 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 48:1089–1098CrossRefGoogle Scholar
  56. Tuovinen OH, Desmukh V, Özkaya B, Radosevich M (2015) Kinetics of aerobic and anaerobic biomineralization of atrazine in surface and subsurface agricultural soils in Ohio. J Environ Sci Health B50:718–726CrossRefGoogle Scholar
  57. Udiković N, Hršak D, Mendaš G, Filipčić D (2003) Enrichment and characterization of atrazine degrading microbial communities. Food Technol Biotechnol 41:211–217Google Scholar
  58. Udiković Kolić N, Hršak D, Kolar AB, Petrić I, Stipičevic S, Soulas G, Martin-Laurent F (2007) Combined metabolic activity within an atrazine-mineralizing community enriched from agrochemical factory soil. Int Biodeter Biodegrad 60:299–307CrossRefGoogle Scholar
  59. Udiković-Kolić N, Hršak D, Devers M, Klepac-Ceraj V, Petrič I, Martin-Laurent F (2010) Taxonomic and functional diversity of atrazine-degrading bacterial communities enriched from agrochemical factory soil. J Appl Microbiol 109:355–367Google Scholar
  60. Udiković-Kolić N, Scott C, Martin-Laurent F (2012) Evolution of atrazine-degrading capabilities in the environment. Appl Microbiol Biotechnol 96:1175–1189CrossRefGoogle Scholar
  61. Vargha M, Takátsc Z, Márialigeti K (2005) Degradation of atrazine in a laboratory scale model system with Danube river sediment. Water Res 39:1560–1568CrossRefGoogle Scholar
  62. 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 60:273–278CrossRefGoogle Scholar
  63. Vibber LL, Pressler MJ, Colores GM (2007) Isolation and characterization of novel atrazine-degrading microorganisms from an agricultural soil. Appl Microbiol Biotechnol 75:921–928CrossRefGoogle Scholar
  64. Zhang Y, Jiang Z, Cao B, Hu M, Wang Z, Dong X (2011) Metabolic ability and gene characteristics of Arthrobacter sp. strain DNS10, the sole atrazine-degrading strain in a consortium isolated from black soil. Int Biodeter Biodegrad 65:1140–1144CrossRefGoogle Scholar
  65. Zhang Y, Cao B, Jiang Z, Dong X, Hu M, Wang Z (2012) Metabolic ability and individual characteristics of an atrazine-degrading consortium DNC5. J Hazard Mater 237–238:376–381CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • James F. Douglass
    • 1
  • Mark Radosevich
    • 2
  • Olli H. Tuovinen
    • 1
  1. 1.Department of MicrobiologyOhio State UniversityColumbusUSA
  2. 2.Biosystems Engineering and Soil ScienceUniversity of TennesseeKnoxvilleUSA

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