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Genomic tools in bioremediation: A case study with atrazine as pollutant (GENOTOOLS)

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Basic project information


Contamination of both soil and groundwater with pesticides is an increasing global problem. In India the annual consumption of atrazine amounts to 340 MT. In Finland and in most of the European Union countries atrazine was used widely, but was banned in the 1990's. However, atrazine and its degradation products are among the most commonly found pesticides in groundwater still today, and so far there are not many technical solutions available for cleanup. Bioremediation with or without the use of microbial inoculants offers sustainable solutions to this problem. However, successful up-scaling of bioremediation actions from the laboratory to pilot and field scale is still a big challenge, and knowledge on the microbial community and its dynamics in the soil is of great importance for the success of bioremediation. Since atrazine is banned in Finland the clean-up needs are mainly for groundwater clean-up and to a lesser extent for soil from pesticide handling and storage areas. In India the pesticide is manufactured and widely used and hence there is a more urgent need for soil cleanup methods. The development of atrazine remediation strategies will also be of value for other countries with similar problems in both climate regions.


This project aims at using genomic tools in the development of a bioremediation strategy for pesticide contaminated soil and groundwater using atrazine as a model pesticide. The project is a Finnish-Indian collaboration between the Finnish Environment Institute and the National Environmental Engineering Research Institute (NEERI), Nagpur, India.

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Closed groundwater intake plant.

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Indian sugar cane field.


Drilling in winter.


Jørgensen, K.S. 2008. Advances in monitoring of catabolic genes during bioremediation. Indian J. Microbiol. 48: 152-155.

Jørgensen, K.S., Nousiainen, A., Björklöf, K., Purohit, H., and Kapley, A. 2010. Biodegradation of atrazine in Finnish and Indian soil samples. Proceedings of 3rd Joint Nordic Meeting on Remediation of Contaminated Sites - NORDROCS, Copenhagen, Denmark, 15.-16.9.2010, pages 83-86.

Jørgensen, K.S., Salminen, J., and Björklöf, K. 2010. Monitored natural attenuation. In (ed.) S.P. Cummings. Bioremediation. Methods for Molecular Biology 599:217-233. Humana press.

Nousiainen, A.O., Björklöf, K., Kapley, A., Purohit, H.J., and Jørgensen, K.S. 2010. Assessment of quantitative detection of atrazine degradation genes in boreal and tropical soils. Abstract no PS07.083. 13th International Symposium on Microbial Ecology ISME -13, Seattle, WA, USA, 22-27 August 2010.

Jørgensen, K.S. 2011. In situ bioremediation.  Chap 6.07, Vol 6: Environmental Biotechnology and Biosafety (ed. S.N. Agathos). Pages 59-67. In: Comprehensive Biotechnology. 2nd ed. Elsevier BV.

A. O. Nousiainen, K. Björklöf, H. Purohit, A. Kapley and K. S. Jørgensen. 2011. Validation of quantitative PCR for atrazine degradation genes in two different soils. Ecology of Soil Microorganisms. 27.4.-1.5.2011, Prague, Czech Republic.

Jørgensen, K.S., Nousiainen, A., Björklöf, K., Sagarkar, S., Mukherjee, S., Purohit, H.J., and Kapley, A. 2011. The use of genomic tools in bioremediation of atrazine contaminated soil and groundwater. Abstract: Finnish-Indo Workshop on Genomic tools in Bioremediation. Nagpur, India, 29.-30.11.2011.

Sagarkar, S., Mukherjee, S., Nousiainen, A., Björklöf, K., Purohit , H.J., Jørgensen, K.S., Kapley, A. 2013. Monitoring bioremediation of atrazine in soil microcosms using molecular tools. Environ. Pollut. 172: 108-115.

Nousiainen, A., Björklöf, K., Sagarkar, S., Mukherjee, S., Purohit, H.J., Kapley, A., and Jørgensen, K.S. . Atrazine degradation in boreal nonagricultural subsoil and tropical agricultural soil. J. Soil Sediments.

Sagarkar, S., Nousiainen, A., Shaligram, S., Björklöf, K., Lindström, K., Jørgensen, K.S., and Kapley, A. 2014. Soil mesocosm studies on atrazine bioremediation. J. Environ. Managem. 139:208-216.


Nousiainen, A., Björklöf, K., Sagarkar, S., Nielsen, J.L., Kapley, A., and Jørgensen, K.S. 2014.  Bioremediation strategies for trace amounts of atrazine in boreal soil. 15th International Symposium on Microbial Ecology ISME 15, August 24-29, Seoul, Korea. Abstract.


Nousiainen, A.O., Björklöf, K., Sagarkar, S., Nielsen, J.L., Kapley, A., and Jørgensen, K.S. Bioremediation strategies for removal of residual atrazine in the boreal groundwater zone. Submitted manuscript.


Nousiainen, A. 2015. Application of genomic tools in bioremediation of atrazine contaminated soil and groundwater. Doctoral dissertation, 2/2015. University of Helsinki, Finland

Furher Information

Leading Researcher Kirsten Jørgensen, Finnish Environment Institute SYKE






Published 2014-02-27 at 16:55, updated 2016-07-25 at 10:01