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Microbial indicators to evaluate the impact of pesticides

Innovative microbial ecotoxicity technologies have been developed and tested to evaluate the impact of pesticides on the functions of soils and sediments. Completion of this work has led to the design of three new methodologies that have been, or could be, standardised with the International Standards Organization (ISO).

indicateurs microbiens pour évaluer l’impact des pesticides © Fabrice MARTIN –LAURENT
Updated on 06/06/2018
Published on 03/28/2018

New tools to evaluate the ecosystem functions fulfilled by soils and sediments

The microbial populations present in soils assure different activities that support ecosystem functions, such as regulation of the climate (carbon storage, water retention, etc.), the primary production of biomass and water filtration and purification, etc. Numerous studies have shown that the agricultural use of pesticides constitutes a threat to the diversity and activity of soil micro-organisms, causing a deterioration of the biological and/or chemical quality of environmental compartments connected to agricultural plots, such as water courses.  Actors and managers in the farming world are unable to estimate the impact of these inputs on soil functions, notably when introducing new cultivation practices that prefer the use of low-dose products.
Work carried out by scientists from INRA and IRSTEA* belonging to the Ecotox (see insert) and EcotoxicoMic (see insert) networks have been focusing on this situation. Their aim is to propose a series of innovative methods that can be transferred to a broad range of actors in order to evaluate the impact of pesticides on the microbial component in soils and sediments and on the ecosystem services they provide.
The European Food Safety Agency (EFSA) is closely following the development of such methods. It recently proposed that they should be included in the environmental evaluation of pesticides during the qualification process for new plant health products.

From a methodology…

The scientists used the TYPOL method developed by INRA to choose pesticides representative of their diversity and degradation products. This method is based on both the behaviour of these substances in the environment (persistence and mobility) and their molecular properties. A total of 68 pesticides were selected and tested, and three of them were chosen to conduct ecotoxicological studies on soil micro-organisms.  
Two of the principal services rendered by micro-organisms were studied. One was linked to their role in satisfactory completion of the biogeochemical cycles of carbon, phosphorus and nitrogen. The other concerned an evaluation of the purification capacities of soil micro-organisms via their activity on pesticide mineralisation.
Furthermore, the abundance and composition of the microbial community were evaluated using molecular techniques based on extracting nucleic acids (DNA) from soil and sediment samples and their amplification using polymerase chain reactions (PCR).
The impact of the three model pesticides (applied alone or in a mixture) was determined by conducting laboratory experiments. An impact study was also performed on two types of plot (vineyard and arable) by collecting samples at different times of the year.

… to the introduction of new international standards

This work made it possible to propose three new methods. Two of them have already been standardised and the third is under development (see insert). In the future, they could constitute references when evaluating the ecotoxicological risk of pesticides, both before and after they are approved. These studies also demonstrated that microbial activities in the nitrogen cycle (e.g. nitrification) are sensitive to pesticides, as had been suggested by the EFSA in a scientific opinion published in 2016.
More generally, they could be of use to professionals responsible for monitoring and managing the environment, so that they can:

  • Characterise contaminations alongside more conventional analytical chemistry techniques,
  • Evaluate more or less long-lasting or reversible disturbances to the structure of microbial populations,
  • Monitor the treatments used to rehabilitate polluted sites.

*the following also participated in this work: Stéphane Pesce (IRSTEA – Lyon), Pierre Benoit, Laure Mamy and Olivier Crouzet (INRA & AgroParisTech - Grignon)

Scientific contact(s):

  • Fabrice MARTIN–LAURENT Joint Research Unit for Agroecology (UMR 1347) under the joint management of INRA, AgroSup Dijon and Université de Bourgogne et Franche-Comté, 17 rue Sully, BP 86510, 21065 Dijon

The ECOTOX network

Ecotox. © INRA

Set up in 2009 and supported since then by INRA, the terrestrial and aquatic ecotoxicology ECOTOX network groups a community of 260 members from research institutes and organisations, universities, advanced schools, agricultural technical institutes and industry.
Its aims are to:

  • Contribute to scientific thinking with respect to research in ecotoxicology,
  • Contribute to exploiting and disseminating research findings,  
  • Enhance the visibility of ecotoxicology and those active in this field.

The EcotoxicoMic network

EcotoxoMic is a multidisciplinary thematic network focused on microbial ecotoxicology supported by the CNRS Institute of Ecology and Environment (INEE) and National Institute for Earth Sciences and Astronomy (INSU), IRSTEA and the Fondation de Coopération Scientifique Rovaltain. It was set up in 2015, based on the French-speaking network on microbial ecotoxicology created in 2013 by Stéphane Pesce (IRSTEA) and Fabrice Martin-Laurent (INRA). Comprising 131 members from 50 research laboratories and eight private companies, its aim is to federate and enhance the visibility of the community of microbial ecotoxicologists in order to encourage transversal actions between the ecosystems studied and scientists belonging to different research organisations. To ensure the international development of this network, in November 2017 EcotoxicoMic organised its first international symposium in Lyon, which attracted 170 scientists from 25 different countries.

ISO standards

  • ISO 17601:2016 - Estimation of abundance of selected microbial gene sequences by quantitative PCR from DNA directly extracted from soil.
  • ISO/FDIS 20130 – Measurement of enzyme activity patterns in soil samples using colorimetric substrates in micro-well plates.
  • ISO 14239:2017 - Laboratory incubation systems for measuring the mineralisation of organic chemicals in soil under aerobic conditions.