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Toward sustainable agriculture

Where roots meet partners.

Plants don’t live alone. Beneath every healthy crop is a community of bacteria and fungi that decide what gets in, what gets defended, and what gets fed. We study those conversations and learn how to shape them.

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Recent work · Nature Plants · 2026

Spatial signatures of host immune restriction govern rhizobial strain selection in Lotus japonicus root nodules

Iyer A, Lehtonen H, Moreau L, Aurelia M

Not every compatible rhizobial strain ends up inside a root nodule. By mapping host immune outputs at single-cell resolution across the Lotus japonicus root cortex, we show that nodule occupancy is decided long before bacterial entry — in a narrow window of locally relaxed immunity that only some strains can read. The work reframes strain selection as a spatial negotiation, not a binary compatibility switch, and suggests new levers for designing inoculants that survive the host’s first hour of scrutiny.

link doi.org/10.1038/s41477-026-01734-9
What we work on

Research Overview

Our work centres on the rhizosphere — the millimetre of soil around a plant root — where bacteria, fungi, and host immune cells negotiate access in real time. We combine field surveys of agricultural soils with controlled gnotobiotic plant systems to ask how mutualistic communities assemble, persist, and collapse.

A second program focuses on legume–rhizobia nitrogen fixation. Using genetic tools in Medicago truncatula and Lotus japonicus, we map the signalling networks that allow a host to admit a microbial partner into its cells without triggering full immune rejection. The same logic may apply to engineered symbioses in non-legume crops.

The plant–microbe interface from soil to symbiosome.
The plant–microbe interface from soil to symbiosome.

Across both programs we are translating findings into microbiome-informed agronomic strategies — inoculants, cover-crop sequences, and host-genotype matching — that reduce synthetic nitrogen and phosphorus inputs without sacrificing yield. Our long-term aim is a soil-microbiome toolkit usable by smallholder and industrial growers alike.

In the lab

What's new

  1. article

    Aishwarya’s paper on rhizobial strain selection is out in Nature Plants.

  2. mic

    Marisol speaks at the Gordon Conference on Plant-Microbe Interactions (June 2026).

  3. grass

    Spring sampling season opens at the three partner cereal field sites. Tomas leads field logistics.

  4. person_add

    Welcome Daniyar Aitkhozhin, joining as a PhD candidate.

  5. trophy

    Marisol named an international young investigator (cohort 2025).

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We are growing. Three openings are currently active — write to Marisol with a one-page note about what you want to grow.