How crops shape their microbial communities

Finger millet (Eleusine coracana) is a grain that has been feeding communities for thousands of years. Grown mostly in Africa and Asia, it is a staple in many developing countries and is packed with nutrients like proteins, minerals, and antioxidants. Finger millet has the ability to thrive where other crops cannot, growing well in dry, salty, and nutrient-poor soils. This makes it a lifeline in regions where farming is tough.

However, this cereal does not manage this on its own—it has help from an invisible world beneath the soil. Its roots, stems, and seeds host a wide variety of microbes that help the plant grow, stay healthy, and cope with stress. Different parts of the plant attract different microbes, creating tiny ecosystems that boost the plant's strength and resilience.

Microbial communities Vary Around the Plant

In a new study, researchers from SLU, together with colleagues from Ethiopia, investigated how different types of finger millet plants (wild and domesticated), as well as their growth stages, affect the types of microbes living in and around their roots.

Only 8% of the core microbiota was shared between the soil and root compartments, while over 90% varied dynamically with plant genotype and developmental stage. Domesticated varieties of finger millet had less microbial diversity compared to the wild type, particularly during flowering.

– Domestication has led to a narrowing of microbial diversity, especially in the interior of the roots. This might have trade-offs in terms of resilience and stress tolerance, but it also offers opportunities to reintroduce beneficial microbes through targeted microbiome management, says Saraladevi Muthusamy.

Plants engineer their own microbiomes

The biggest changes occurred in the soil around the roots during the flowering stage, especially involving a group of bacteria called Pseudomonas.

– Plants are not just passive; they play an active role in choosing which microbes live in and around them. It is remarkable that plants engineer their own microbiomes by attracting different microbes at different growth stages and in different root parts to help them grow better and stay healthy, says Fantaye Ayele Dadi.

Improving future food production

This research could open the door to using helpful microbes in plant breeding, making crops naturally stronger and healthier.

– By tapping into these plant-microbe partnerships, we could grow food with less need for chemical fertilizers and pesticides, says Rodomiro Ortiz.

– Our next step is to explore how we can harness the knowledge from this study and our previous research to improve crop resilience under stress, concludes Ramesh Vetukuri.

The study was supported by SIDA and the SLU Centre for Biological Control.