Using the Soil Microbiome for Sustainable Agriculture

At Mohammed VI Polytechnic University (UM6P), our research focuses on understanding how soils, plants, and microorganisms interact to sustain agricultural productivity. We study soil composition, microbial communities, nutrient cycling, and the biological processes that allow plants to access essential nutrients in a sustainable way.

A central goal of our work is to understand how beneficial bacteria support plant nutrition, particularly for phosphorus, which is often present in soils in forms that plants cannot readily absorb. While nitrogen fixation has been extensively studied, many questions remain about how nitrogen and phosphorus availability are regulated under real field conditions. Addressing these questions is essential for developing efficient and environmentally responsible agricultural solutions.

Some microorganisms live in close association with plants, including within plant tissues. Certain specialised endophytic bacteria are capable of fixing atmospheric nitrogen and supplying it directly to the plant. This nitrogen contributes to vital plant processes such as the synthesis of chlorophyll, amino acids, and proteins. Our objective is to understand how these interactions can be optimised to promote plant growth without excessive chemical fertiliser use, even under stressful environmental conditions. Ultimately, this research aims to support the development of targeted biofertilisers adapted to local ecosystems.

A key challenge in agriculture is nutrient availability. Although soils may contain large amounts of nitrogen and phosphorus, much of it is not immediately accessible to plants. We investigate how microorganisms help mobilise these nutrients and how plants efficiently use them once they become available.

Molecular Insights into Plant–Microbe Interactions

Beyond observing these interactions at the organism level, our work focuses on what happens at the molecular scale. We study genes, regulatory proteins, and molecular signals that control nutrient exchange between plants and microbes. Understanding these regulatory mechanisms allows us to explain why certain plant–microbe partnerships succeed under stress while others fail.

Plants rely on nitrogen for growth, but the process of uptake, transport, and utilisation is highly regulated. Our research examines plant-derived signals, the ways microorganisms influence nutrient uptake at the root level, how nitrogen is transported from roots to shoots, and how these processes are coordinated within the plant. We study these mechanisms across different environmental conditions, with a particular emphasis on water and heat stress.

Stress conditions such as drought and high temperatures are major constraints on agriculture, especially in semi-arid regions of Africa. We investigate how plants adapt to these stresses and how beneficial microorganisms contribute to stress tolerance. This includes analysing stress-related molecules and the pathways that regulate their production.

For example, we have studied how plants accumulate proline under heat stress. Proline is a key molecule that helps protect cells by stabilising proteins and membranes, maintaining redox balance, and supporting water retention. We also examine how microbes produce plant hormones such as auxins, which play an important role in regulating plant growth. Importantly, the effects of these hormones depend on their concentration, timing, and the plant species involved.

The Importance of Local Conditions

Environmental context matters greatly in agriculture. The same bacterial group may exist in different parts of the world, but its interaction with plants can vary depending on climate, soil type, and farming practices. For this reason, our work prioritises the use of locally adapted microorganisms.
Rather than transferring microbes from one continent to another, which is often ineffective or suboptimal, we isolate bacteria from local soils and study how they interact with crops under regional conditions. We analyse how these microorganisms colonise plants, communicate with their hosts, and contribute to nutrient acquisition and stress tolerance.
Although many of these bacteria can be grown in the laboratory, the greatest challenge is understanding how they behave in natural environments. What signals do they exchange with plants? Which molecules do they produce? How do these interactions contribute to long-term soil health? Addressing these questions allows us to design solutions that serve local farming communities.

Research Focus

My research is structured around two main pillars:

1. Soil-microbe-plant interactions: Understanding how microorganisms facilitate the acquisition of nutrients such as nitrogen and phosphorus, improving crop productivity while reducing reliance on chemical fertilisers.
2. Mitigation of abiotic stress: Using plant growth-promoting bacteria to help crops tolerate heat, drought, and salinity.

This approach goes beyond observation. By applying molecular biology tools, we aim to decode the biological “language” between plant roots and microorganisms, enabling the development of tailored biofertilisers that help crops anticipate and cope with environmental stress.

A Holistic Approach to Crop Performance

Our work combines field trials and controlled greenhouse experiments. In recent studies, we tested a biostimulant on wheat over multiple growing seasons. While this product showed strong performance in temperate regions, results were more variable in tropical and semi-arid environments. This motivated us to investigate how local conditions influence its effectiveness.

We initiated trials in Benguerir, Morocco, and the results have been very encouraging, with clear improvements in yield and plant vigour. To understand why these benefits occur, we are now conducting biochemical and molecular analyses, including transcriptomic analysis and detailed studies of plant–microbe interactions from the earliest stages of development.

Additional experiments on crops such as tomatoes, canola, onions, and soybeans have confirmed positive effects on early growth, robustness, and productivity. This life-cycle approach from seed germination to final yield provides a comprehensive view of how biostimulants and beneficial microbes influence plant performance.

Beyond microbial products, we have also tested plant based biostimulants. These compounds tend to be effective across a wide range of crops and are readily assimilated by both plants and soil microorganisms, making them a complementary tool for sustainable agriculture.

Biostimulants, Environment, and Detoxification

A central aim of our research is to reduce the environmental footprint of agriculture. Soil nutrient profiles vary widely across regions. In some areas, nitrogen is abundant but phosphorus is limiting, while in others both nutrients are scarce and poorly absorbed by plants.

By introducing beneficial microorganisms, we seek to improve nutrient uptake efficiency, reduce fertiliser losses, and minimise harmful residues in soils. Plant-based biostimulants are also designed to be easily assimilated, ensuring that nutrients are recycled rather than lost to the environment.