Microbial functional diversity as an indicator of sustainable farming practices

Farmers examing dirt while tractor is plowing field
© iStock/fotokostic

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 Dr Nasmille L. Larke-Mejía, who is a Postdoctoral Researcher at the Earlham Institute, UK 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.

What are the challenges that this research addresses?

Soils are living systems that provide multiple ecosystem services, including nutrients, water and anchorage for crops. Healthy soil contains a diverse and abundant number of micro-organisms that interact with each other and mediate functions such as carbon transformations, nutrient cycles, and energy flow on which soil fertility depends. In farming, healthy soils are essential for the stability, yield and resilience of crops. 

Soils and their biota are being threatened by global and anthropogenic changes such as climate change, land use, farming practices and chemical pollution. These alter the complex interactions between soil physical and chemical factors, and the ability to resist and recover from perturbations. Loss of soil functional diversity can reduce ecosystem functions and impairs crop sustainability over time. 

What findings and solutions were provided by this research?

Researchers at the Earlham Institute are using metagenomics to investigate: 1) How soil microbial communities respond to the long-term use of agrochemicals; 2) How soil microbial communities react to shifts in agronomic treatment regimes (e.g. what happens when we stop using agrochemicals in a field?); and 3) What effects do particular agronomic treatments have in soil micro-organisms' activity?

Metagenomics is the study of microbial organisms using high-throughput sequencing (NGS) applied directly to soil samples collected from fields. It goes much further than assessing the abundance of species in the soil. Metagenomics can answer what soil micro-organisms are doing (functional diversity) and how different datasets compare.

Using metagenomics, we are sampling adjacent arable fields under different farming conditions. In an international study, we are studying neighbouring perennial plantations that use conventional agrochemicals or have switched to using only organic fertilisers for a different number of years. In a separate study, we are comparing various combinations of chemical and biological nematicides in annual crops. 

How can this research support the transition to a more sustainable future?

Understanding the effect of agricultural practices on soil health is essential in the search of sustainable practices that would encourage healthy, productive and reliable crops. Furthermore, the growing demands from consumers and impacts from climate change are pushing the food production sector to explore new ways to satisfy the needs for environmental sustainability. Soil microbiome diversity is used as a soil quality indicator (SQI) in agricultural ecosystems.

What is the future for research and innovation in this area?

We can improve the management of soils if we can measure the impacts on farming functioning from different farming practices. 

Nasmille L. Larke-Mejía
© Nasmille L. Larke-Mejía
About the author

Dr Nasmille L. Larke-Mejía is a Postdoctoral Scientist on the GROW Colombia project, working in the Agricultural Diversity Programme at the Earlham Institute. More information about her work is available here.