Using evolution to understand the impact of human-induced stressors on the future of sustainable agriculture.

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The Microbiology Society is undertaking a project entitled A Sustainable Future as part of our 75th Anniversary, which aims to highlight the Sustainable Development Goals (SDGs) to our members and empower them to use their research to evidence and impact the goals. Earlier this year, we put a call out to our members to submit case studies in the following three areas: antimicrobial resistance, soil health and the circular economy.

This case study is written by Matthew Kelbrick, who is a PhD researcher at the University of Liverpool and a member of the Microbiology Society. It focuses on Soil Health; maintaining the health of our soils has gained increasing prominence in recent years. Soils are essential for the global food system and regulate water, carbon and nitrogen cycles but are put under pressure from population growth and climate change.

Agricultural Innovation

The innovation of agriculture was a pivotal moment in human civilisation leading to urbanisation and setting us down a path towards the modern society we know today. However, we did not accomplish our current agricultural prowess alone; beneath the soil surface reside complex microbial communities which underpin our whole agricultural infrastructure.

Microbial Communities Under Threat

Microbial communities are fundamentally important in agriculture as they fix nitrogen, recycle nutrients, and protect crops from infections. These features allow microbial communities to maintain soil fertility and health, increasing crop yields while reducing the risk of crop failure. However, microbial communities are under threat due to anthropogenic influences. For example, elevated soil salinity and increasingly frequent heatwaves associated with climate change are killing some microbial species, leading to decreases in microbial biomass and community function. Communities are under further stress due to the overuse of chemical and antimicrobial pesticides through direct application and via run-off from animal agriculture. These compounds can be lethal to microbes, causing alterations in community structure and selecting for antimicrobial resistance (AMR). These human-driven changes may decrease the presence and abundance of microbes essential for sustainable agriculture. Will the microbial communities be able to adapt to these stressors? Or will the changes we, as humans, are enforcing mean that microbial communities will no longer be able to support our growing demand for sustainable agriculture?

When microbial communities are exposed to stresses, they are forced to either migrate, adapt, or go extinct. If the agriculturally beneficial microbes are unable to adapt, and are forced to use one of the two alternative options, this will lead to increased crop disease and infertile soils. Much experimental research to date has focused on adaptation to individual stressors within ‘petri dish’ environments, limiting the impact of external stressors on community structure. However, in natural soil environments microbes do not have the luxury of adapting to a single stressor at a time. Instead microbes are often overwhelmed by a combination of antimicrobial compounds, pesticides, high salinity, heat waves, and many other stressors. The impact of multiple anthropogenic stressors on soil microbial community evolution is important for developing sustainable agriculture, but this has gone mostly unexplored.

Harnessing Microbial Evolution to Protect the Future of Agriculture

My PhD research aims to understand the impact of multiple anthropogenic stressors on complex communities of agriculturally beneficial microbes. To investigate this, I am using experimental evolution to examine microbial adaptability to both biotic and abiotic factors within natural soil communities. This will allow us to simulate how microbial communities might adapt to combinations of stressors and identify changes in community structure.

My project will provide a clearer idea about the ability of these communities to adapt to the challenges of their constantly changing environment. This will be essential for developing sustainable agriculture practises in a microbe-dominated world. In addition, these findings may inform policy on the sustainable use of antimicrobial compounds and pesticides in agriculture, allowing us to protect the complex microbial communities and reduce the spread of AMR in natural environments. Not only will this aid in achieving our goal of a sustainable future, but it allows us to advance our knowledge on the fundamental mechanics of evolution and the innerworkings of microbial ecosystems, which will have far-reaching impacts for future evolutionary and microbiological research.

About the Author

Matthew Kelbrick is a PhD researcher at the University of Liverpool, and a member of the Microbiology Society. More information on his work is available here.