While the microbiome is commonly associated with our guts, it is important to recognise that microorganisms are everywhere, and they play a critical role in our everyday life. An interesting case is the soil microbiome, the community of microorganisms (including viruses, bacteria, archae, and fungi) that live in the soil and are essential for its health, fertility, as well as nutrient cycling and plant growth. However, the soil microbiome doesn’t only play a crucial role in ensuring a sustainable food supply for our growing population, but also, somewhat unexpectedly, impacts our health.

Studies conducted in a joint project of the University of Helsinki and the Natural Resources Institute of Finland have recently explored the relationship between the microbial quality of our environment, specifically soil, and the incidence of inflammatory disorders in children, such as allergies, asthma, and type 1 diabetes (1). The biodiversity hypothesis (2) postulates that such disorders may result from weak interactions with environmental microbes, causing an imbalance in immune regulation. To explore this hypothesis, researchers conducted a 2-year intervention comparing standard urban day-care centers with playgrounds amended with a biodiverse forest floor vegetation and soil. The study found that intervention strategies can enrich commensal (beneficial) microbiota and suppress potentially pathogenic bacteria on the skin, ultimately reducing the incidence of immune-mediated diseases in children.

These findings underscore the importance of protecting and restoring the health of our soil to ensure the long-term health of both humans and the environment. In CIRCLES, an EU-funded project, we explore food production systems from two important angles. First, we investigate microbiome interactions and circulation within six food chains: spinach, tomatoes, poultry, swine, farmed and wild salmon and seabream. Secondly, we study the potential of manipulating the soil microbiomes. (3)

Over 95% of our food, including fruits, vegetables, grains, meat, and dairy, is directly or indirectly reliant on soil (FAOSTATs 2022). However, intensive farming practices and poor soil management have led to one-third of the world’s soil becoming degraded, resulting in a loss of fertility and an inability to support plant growth. These practices can cause essential nutrient leaching and physical damage to soil structure, disturbing the complex ecosystem of microorganisms that live in soil.

Soil microbiomes play a crucial role in maintaining ecosystem balance. They have multiple functions, including purification of forming groundwater, decomposition, formation of clumps of soil called aggregates, cycling of nitrogen, pathogen control, and uptake of nutrients and water for plants in natural ecosystems. Soil microbiomes also aid in carbon sequestration, making them important in reducing carbon loss. Recent estimates suggest that up to half of persistent carbon in soil comes from dead microbes (4). Bacteria and fungi help to transform photosynthesized carbon into more stable forms in the soil by breaking down organic matter and creating new substances that hold the soil together. Fungi are particularly important for soil health because they help to keep the soil carbon stable and form aggregates that hold water and prevent soil erosion and nutrient loss. The greater the variety of microbes in the soil, the better the soil’s ability to hold water and nutrients.

The work of CIRCLES comprises studies on the microbiomes of both food chains and soil. A pronged methodological approach is performed to elucidate the impact of the crop and other food chain microbiomes on sustainable agriculture.

The "observation phase" involves researchers working with crop growers on "lab-in-the-field" sites to perform a "census" of the microbiome associated with both more and less productive plants. This approach is known as comparative metagenomics and uses state-of-the-art DNA sequencing technologies. Then follows an "Intervention phase", where researchers use bioinformatics tools to mine the comparative metagenomics results and identify what is missing or imbalanced in the microbiome of less productive plants. Researchers then attempt to restore a healthy microbiome with a targeted application on the farm of natural microbes and/or products. They assess the intervention by measuring crop performance, as well as the impacts on the environment and people participating in the crop production process.