​Pesticide contamination: what can microbiologists do?

Each year over $30 billion is spent on the several millions of tonnes of pesticides used worldwide. A side effect of such crop protection can be contamination of the wider environment, which impacts the health of humans, other animals and ecosystems. Responsible governments thus have tight regulatory frameworks to monitor and control pesticide contamination, in the interests of maintaining both food and water security. In the EU, this translates to tight regulatory limits on contamination of drinking water sources with pesticides.

What has any of this got to do with microbiology? Traditionally, very little. Preparation of raw (reservoir or river) water for drinking is treated as a physico-chemical rather than biological process. Regulatory analyses of pesticide fate in the environment do not take into account biological processes such as evolutionary adaptation, despite well-established evidence that accelerated biodegradation of pesticides arises in response to their historic or recent use.

Technology does not exist in a vacuum, and to inform and influence the development of technological solutions, microbiologists need to engage with stakeholders to understand the problems and consider the space in which solutions might exist. With respect to pesticides, these stakeholders include: the water companies who are given responsibility for the provision of clean water; the farmers who use pesticides on their land; regulatory authorities who set out the policies for pesticide use; engineers who design water treatment plants; and consumers who want clean water. The physical/chemical design and infrastructure of water treatment plants is just one element within a wider context of ‘catchment management’ in which water companies liaise with agricultural and industrial contributors to mitigate contamination risk.

Drinking water is not sterile, and soil is the most microbiologically diverse structure known. Specialist soil bacteria that can degrade problematic pesticides can be readily isolated and studied in the laboratory. It must be possible to harness the power of biological catalysis in this context to develop technological solutions to limit pesticide contamination. Three broad areas in which microbiologists might be able to use such natural resources to make an impact are:

Treatment

We have been working recently on the pesticide metaldehyde, a cyclic ether that is not degraded by standard water treatment methods (such as granular activated carbon). Bacteria that can degrade metaldehyde however, can be isolated and there is potential to use these in water treatment. There are considerable challenges with bioaugmentation of such organisms into water treatment plants, as the bacteria may not be retained or may not degrade the pesticide in the presence of other potential carbon substrates present in the water. Feasibility of biological treatment needs testing at a variety of scales and using a variety of treatment settings, from municipal water treatment plants to the farm-scale field-side ditch. Knowledge and understanding of the underlying biological mechanisms will allow us to have smarter biological diagnostic tests of the degradation potential in a given setting. Imagine a quantitative PCR test for pesticide-degrading genes, which will add a new level of biological analytical richness to the water treatment process.

Diagnostics

Current monitoring methods involve sophisticated logistics and laboratory-based high-end chromatography methods, which may not be translatable to field testing, or suitable for roll out to, say, developing countries with fragile institutional structures. Biological sensitivity and specificity offer the potential for the design of new biosensor-based diagnostics that can detect and quantify pesticide residues. Without completely presupposing the needs of stakeholders, microbiologists can set out a range of possible pathways to new diagnostics that might rely on microfluidics coupled to biophysical analysis methods, antibody-based sensors or strategies based on intact microbial cell live bioassays. A range of approaches for diagnostic development will enable us to develop tools that work in different settings, whether this is governed by cost, speed, robustness or other specifications that could be established by liaison with end users.

Regulation and policy

The persistence of pesticides in environments depends on physio-chemical factors in soils but also on biological processes in the soil microbiome. Taking into account the spatiotemporal variation in microbial activity will require collection of more data on the metagenomic predisposition for pesticide degradation and how this changes over time and across landscapes. This will also involve a paradigm shift for regulatory authorities, taking into account biological variables that have to date been sidelined in favour of the chemical/physical properties that have been easier to measure. Knowledge of degradation potential will also have the potential to impact on farmers’ use of pesticides, to ensure best dosage and the most effective and sustainable use.

Ultimately, human chemical interventions in agriculture will continue to be required to achieve the increases in yield necessary to feed the world’s population. Application of microbiological research has the potential to enable sustainable use of pesticides and other agrochemicals, and to deal with the downstream contamination issues that arise.