In recent decades, the use of fertilizers and pesticides has doubled global food production but has also led to significant environmental problems, including eutrophication, reduced biodiversity, and a substantial contribution to global warming. These rapid changes are pushing agriculture towards a fundamental transformation, necessitating sustainable alternatives to reduce the carbon footprint of agricultural practices and enhance plant adaptation to environmental stresses. Exploiting soil microbial communities offers great potential to improve the efficiency of agricultural production, increase resilience to environmental stresses, and promote the agroecological transition of food systems. Soil microbiota influence plant growth, health, and stress resistance by facilitating the uptake of essential nutrients such as nitrogen and phosphorus, and by helping plants resist drought, high salinity, and pathogen attacks.
The impact of microorganisms on plant growth
Research is focusing on optimizing soil microbial communities for beneficial interactions with plants by selecting plant varieties that respond well to these microbes. New tools now allow us to explore plant-microbiome interactions in unprecedented detail, revealing insights into resistance mechanisms against simultaneous pathogen attacks and interactions with beneficial microbes. A new conceptual framework for improving microbial inoculation success is emerging.
The impact of microorganisms on plant growth and health has led to the integration of the microbiome into the basic model that determines a plant’s phenotype (Y) through the relationship between genotype (G) , epigenetic (eG) and environment (E), resulting in the model Y ∼ G x eG x E x M. Microbial inoculation only enhances the ability to cope with stress when all factors are aligned: the plant genotype must respond to the inoculated microorganism, the inoculant must adapt to the soil’s physical-chemical environment, and it must establish itself in the local microbiome.
While the role of plant-associated microbes in plant health is clear, a comprehensive understanding of how plants influence their microbiome, both in harmful and beneficial ways, is still under development. There is growing evidence of genetic variation in the regulation of plant-microbe interactions, which plant breeders can exploit. This new breeding strategy proposes incorporating the entire plant holobiome into resistance selection strategies to discover complex defense mechanisms.
Reducing the use of agrochemicals
Microbiome-assisted plant production aims to maintain yields while reducing the use of agrochemicals. Instead of relying on fertilizers and pesticides, beneficial microbes are added to the soil or plants, with specific plant species enriching these microorganisms and soil management practices creating favorable conditions. Many microorganisms improve plant nutrition or increase resistance to stresses, offering promising opportunities to ensure crop productivity and stability.
However, large-scale adoption of these technologies faces challenges, such as “context dependency,” where the benefits of microbes can vary significantly depending on environmental factors such as soil type, climate, and crop species. This variability complicates the prediction of outcomes in different agricultural contexts. Inoculation of selected microorganisms is promising but faces obstacles related to regulation, registration, consumer acceptance, and market dynamics.
A sustainable and reliable agricultural practice
Progress has been made with microbial consortia for biocontrol and biofertilization, where the synergy between fungal and bacterial strains promotes plant growth and suppresses pathogens. However, improving application technologies and formulations to achieve high cell counts and shelf life remains essential.
To advance microbiome-assisted plant breeding, a thorough understanding of genotype-microbiome interactions and the ecology of the inoculating strains or consortia is crucial. Efficient screening tools are needed to select suitable plant genotypes and consider the variability of the soil microbiome in different environments. With an integrated, science-based strategy, microbiome-assisted crop production could become a sustainable and reliable agricultural practice, ensuring food security in a changing world.
In this context, agroecology provides a fundamental framework. This approach combines scientific knowledge and local experience to promote sustainable, resilient, and diverse agricultural systems. Agroecological transformation enhances plant-microbe interactions, reduces dependence on chemical inputs, and improves soil health. The adoption of agroecological breeding strategies promotes agriculture that mitigates climate change, conserves biodiversity, and ensures food security
