Description du sujet de thèse

Biological inhibition of denitrification by plants: a new strategy for micromanagement of the nitrogen cycle in ecosystems

Director: Florence PIOLA, UMR 5023 CNRS UCBL LEHNA - Lyon, florence.piola@univ-lyon1.fr
Co-supervision: Amélie CANTAREL, UMR 5557 CNRS 1418 INRAE UCBL LEM - Lyon, amelie.cantarel@univ-lyon1.fr
Co-supervision: Marie SIMONIN, UMR 1345 IRHS - Angers, marie.simonin@inrae.fr

Context: The ANR PRC Plant-Mana project, in which this thesis is included, proposes a new paradigm for the micro-management of the nitrogen cycle in ecosystems, based on plant biodiversity and the BDI strategy as a new solution for managing plant nitrogen nutrition. Indeed, plants can control the microorganisms associated with the nitrogen cycle in the soil and thus develop strategies to improve their nitrogen nutrition. Biological denitrification inhibition (BDI) is one such strategy, based on the production of specialized metabolites (procyanidins) that inhibit soil microbial denitrification activity (Bardon et al., 2014, 2018). First described by our teams in Japanese knotweed (Angiosperms - Polygonaceae, Fallopia spp.) (Bardon et al. 2014, 2018; Cantarel et al. 2020, 2024), this strategy has also been demonstrated in two other species (Bardon et al., 2018): common fern (Monilophytes) and ash heather (Angiosperms - Ericaceae). These results suggest that root procyanidin production and BDI could be a widespread and conserved ancestral trait in angiosperm phylogeny that could be exploited on a wide panel of plant species.
To develop this new nature-based solution for nitrogen micromanagement in agroecosystems, the Plant-MaNA project has two main objectives:
(1) explore plant biodiversity and the procyanidin-driven BDI strategy as a new approach to sustainable plant nitrogen nutrition,
(2) provide a new way of designing ecosystems (in particular crop ecosystems) on the scientific basis of agroecology and nature-based solutions for selecting plant genotypes capable of controlling and managing the soil nitrogen microbiome.

The thesis project will evaluate the capacity for root procyanidin production, BDI strategy development and soil microbiota management for some 50 plant species previously selected for their root procyanidin production. The first axis will validate the existence of a BDI strategy among procyanidin-producing species, and measure the microbial activities and diversity of the N cycle microbiota. The second axis will evaluate (1) the intraspecific variability of the BDI strategy for each of the plant species identified, through a greenhouse experiment, and (2) validate its efficacy in the field. Field missions in France are planned.

Host teams
The thesis will be carried out in Lyon in the following teams:
- Equipe EVZH (Ecologie Végétale et Zones Humides), UMR 5023 LEHNA, UCBL
- Equipe Dive-N (Diversité fonctionnelle et cycle de l'azote), UMR 5557 LEM, UCBL
The person recruited may be required to carry out occasional assignments in the co-supervisor's laboratory.
- EmerSys team (Emergence, systematics and ecology of plant-associated bacteria), UMR 1345 IRHS, Angers

Scientific and technical skills required
- Plant ecology and physiology: analysis and study of plant physiology, measurement of plant traits, botany
- Microbial ecology, measurement of potential soil microbial activities
- Molecular biology analysis and microbial diversity
- Analytical chemistry
- Statistics: uni- and multi-variate analyses

Contexte de travail

The thesis will be based in Lyon in the following teams:
- Equipe EVZH (Ecologie Végétale et Zones Humides), UMR 5023 LEHNA, UCBL
- Equipe Dive-N (Diversité fonctionnelle et cycle de l'azote), UMR 5557 LEM, UCBL
The person recruited may be required to carry out occasional assignments in the co-supervisor's laboratory.
- EmerSys team (Emergence, systematics and ecology of plant-associated bacteria), UMR 1345 IRHS, Angers