Caring for the microbiota in the soil: the agriculture of the future

Despite being treaded, trampled, and plowed, the soil is nevertheless a source of life. Soil is a living environment in which many essential organisms evolve, whose importance has long been overlooked and underestimated. Although it is the guardian of plant health and growth, this microbiota has been sidelined and underestimated in the intensive agricultural model. Today, at a time when soil fertility is degraded and threatened, it is back at the center of a regenerative and revitalizing culture, progressive and vital, which considers the flora’s growth ecosystem. 


Like the intestine, the soil contains a rich, diverse microbiota that is an integral part of the “One Health” concept. It is a reservoir of biodiversity, containing 26% of the world’s known species, and 60% to 90% of the planet’s living and dead biomass. It is essential to the Earth’s organic matter cycle. Soil nourishes plants, contributes to carbon storage and retains rainwater and runoff. The soil microbiota is therefore an essential factor in meeting the environmental and health challenges we face today.  

The holy grail of fertile soil 

As Marc-André Selosse, professor at the National Museum of Natural History in Paris, puts it so well: “The soil is the beginning of everything. It is a nourishing layer that regulates the rest of life”. Starting with plants. One gram of soil contains 1 billion bacteria, and 100,000 to 1 million different species of fungi, amoebae, springtails, mites and viruses, united in a vast network that extracts and transfers minerals and essential nutrients to the plant and animal world. 

Fertile soil protects plants, ensures their nutrition and serves as a support for crops, but also for biodiversity, which itself contributes to the degradation and transformation of organic matter into plant-assimilable nutrients. Microbiota also contributes to soil structuring. By producing organic molecules, bacteria help to form aggregates, encouraging soil aeration and the passage of water, making it more favourable to plant development. 

The richness of the terrestrial microbiota has become an indicator of plant health(1) (Saleem et al 2019). Imbalances caused by changes in the abundance of microbial species can lead to disease and proliferation of pathogenic species(2) (Adam et al 2016). A healthy, thriving soil microbiota is, so to speak, indispensable to plants, yet it is no less fragile.  

As infinite, inexhaustible and deep as the soil may seem, it is far from immutable. This rich, fertile source, home to the microbial, animal and plant biodiversity vital to life above ground, is now being depleted beneath our feet. Soils are bearing the full brunt of climate change and intensive farming.  

The loss of brown gold 

In reality, soil is only a few meters thick, so it is subject to erosion,  

a natural phenomenon that results from the reduction of the soil’s surface layers and the displacement of its constituent materials by the action of water, wind, rivers, glaciers or man. Certain agricultural practices deployed since the agricultural revolution have triggered and/or reinforced soil erosion. For example, frequent ploughing, particularly deep ploughing, disturbs soil organisms, reduces the stock of organic matter (the main source of energy for the soil’s inhabitants) and disrupts the soil’s structure, aeration, compactness, texture, pH or composition, thereby modifying its functioning. 

 Synthetic petrochemical fertilizers and pesticides used in excessive quantities can contaminate the environment and be toxic to soil flora and fauna. Their application can cause significant changes in the biological composition and functions of soils, leading, for example, to the disappearance of certain sensitive species and the proliferation of other adapted organisms. In France, despite dedicated policies, the level of pesticide use has not fallen over the past 10 years. In a pilot study(3), researchers demonstrated the widespread presence in arable land of some sixty active substances derived from pesticides, including on land that had never been treated (Froger et al, 2023). 

Europe’s land and soil are subject to a variety of pressures, including urban expansion, contamination by agriculture and industry, soil sealing, landscape fragmentation, low crop diversity, soil erosion and extreme weather events linked to climate change(4) (European Environment Agency, 2019). 

Today, 70% of soils in Europe, and a third of soils worldwide, are considered degraded and/or in poor health. In agricultural areas, 80% of this degradation is due to intensive farming practices (5) (Richelle and Brauman, 2022).  

Losing soil is irreversible,” says Selosse. “A country that destroys its soil destroys itself. We’re in an emergency situation. We need to regain awareness of its richness, of the importance of protecting it for our food autonomy. Just because we can still grow geraniums doesn’t mean we can feed humanity”.  

Soil revitalization and regenerative agriculture  

The key to life, organic matter, is sorely lacking in our cultivated soils, but it can be promoted and/or reintroduced over the long term. Today, this can be achieved in two ways: by feeding plants directly with alternatives to synthetic fertilizers; or by using 5 categories of micro-organisms (bacteria, fungi, archaea, protists, viruses). Plants and animals are consumed and decomposed by soil micro-organisms, then transformed into nutrients available to plants. In fact, once organic matter has been decomposed and transformed into assimilable nutrients, it can be used to feed plants and promote their growth.  

All too often, approaches to soil regeneration have focused on the first method, concentrating on the nutrient needs and deficits of plants. They have long ignored the ecosystems involved and the important role played by the microorganisms that support their development. Today, the productivity of microbial communities plays an integral role in revitalization strategies(6). (Soong et al 2020).  

In recent years, there has been a strong interest in the use of agricultural practices that consider the functioning of the holobiont(7)plant, or even the ecosystem, and not just the cultivated plant. These agroecological practices aim to take advantage of the interactions between organisms in a field, by maintaining a functional microbiota for crops. By modulating the composition of plant and soil microbiota, it is possible to improve the functions essential to plant survival, to treat and even prevent disease, and thus to improve both plant health and soil quality.  

A healthy soil microbiota plays a major role in maintaining soil health by contributing to soil structuring – promoting soil aeration and water passage, and by enabling the release of mineral elements into the soil, making them available to plants.  

Rediversifying and revitalizing soils is a long and difficult process. 

It’s a long and difficult transformation, but with the right support, farmers will reap major benefits. Adjustment is possible, but a global and progressive vision is essential. 

Sources : 

(1) More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health – Annual Review of Ecology, Evolution, and Systematics Vol. 50:145-168  
(2) Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human GutAdam & al. – Front Microbiol. 2016 Jul 13;7:1079 
(3) Pesticide Residues in French Soils: Occurrence, Risks, and Persistence Froger& al. – Environ. Sci. Technol. 2023, 57, 7818−7827  
(4) Vers une gestion durables des terres et des sols – European Environnement Agency 
(5) La santé des sols : une approche holistique et transdisciplinaire – Brauman & al., UMR Eco &Sol, Montpellier – Science & Durabilité – Fiche n°72 
(6) Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling Soong & al. – Global Change Biologie Vol. 26, Issue4 -April 2020 – Pages 1953-1961 
(7) holobionte : The holobiont concept considers the functional unit made up of plants and these microorganisms. It promotes a holistic approach to crop management and, more generally, to the vision of living things.