Thèse Vers une Compréhension des Facteurs Multi-Échelle Contrôlant la Diversité et le Cycle de l'Azote dans les Microbiomes Associés aux Bryophytes H/F - 31

Établissement : Université de Toulouse
École doctorale : SDU2E - Sciences de l'Univers, de l'Environnement et de l'Espace
Laboratoire de recherche : CRBE - Centre de Recherche sur la Biodiversité et l'Environnement
Direction de la thèse : Antoine LECERF ORCID 0000000278029773
Début de la thèse : 2026-10-01
Date limite de candidature : 2026-06-01T23:59:59

Les activités humaines affectent l'environnement d'une manière sans précédent, avec des effets négatifs démontrés tant sur la biodiversité que sur le fonctionnement des écosystèmes. Cependant, une compréhension mécanistique du lien entre biodiversité et fonction- nécessaire pour prédire la manière dont les écosystèmes s'adapteront à des conditions environnementales fluctuantes - demeure difficile à atteindre, en raison de la forte redondance fonctionnelle caractéristique des microbiomes, ainsi que de notre manque de connaissances sur la régulation microbienne dans un contexte environnemental complexe.
Ce projet vise à mieux comprendre le lien causal entre la structure et l'activité des microbiomes environnementaux dans un contexte de changements globaux (climatiques, pollution). Plus précisément, le doctorant utilisera des échantillons de bryophytes modèle, facile à manipuler, en conditions naturelles et dans le cadre d'expériences de perturbation, afin d'étudier le couplage entre les modifications des dépôts atmosphériques (métaux, composés azotés) dues à la proximité d'activités humaines (routes, terres agricoles, zones urbaines) et des activités microbiennes biogéochimiques clés du cycle de l'azote (N). Nous nous intéressons en particulier à la production et à la consommation de protoxyde d'azote (NO), un puissant gaz à effet de serre, ainsi qu'à la fixation biologique de l'azote, qui permet la fertilisation naturelle des écosystèmes en azote et qui est connue pour contraindre la production primaire dans une large fraction des écosystèmes terrestres.
En adoptant une approche multi-échelle afin d'intégrer l'hétérogénéité spatiale aux niveaux intra-site, inter-sites, types d'écosystèmes et biomes, ainsi que la proximité des activités humaines, cette recherche renseignera sur la réponse et la résilience des microbiomes et de leurs activités face aux impacts humains.

Environmental microbiomes are driving the cycling of most important chemical elements on the planet since the origin of Earth. In terrestrial ecosystems, their contribution to the cycling of nitrogen is vital to ecosystems function. Indeed, N is known to limit primary production (Du et al., 2020; LeBauer & Treseder, 2008), particularly in pristine or cold ecosystems where N deposition rate from natural or human origin is low and soil N cycling is slower due to energy limitation and recalcitrant organic matter. This N limitation and the uncertainty associated with N input at the global scale has drastic consequences for our ability to predict the direction and magnitude of the carbon sink in the next decades (Wang & Houlton, 2009; W. Wieder et al., 2015; Zaehle, 2013). Biological nitrogen fixation (BNF) is the only pathway that regulates the entry of new N into ecosystems (Zhang et al., 2020), yet large uncertainties remain on the small-scale spatial distribution of N entry fluxes and on its responses to change in environmental conditions that influence the outcome of our current land surface models (Davies-Barnard et al., 2022; W. R. Wieder et al., 2015). Opposite to this, N is highly abundant in more anthropized area where agrochemical N fertilizer input and fossil fuel combustion introduce large excess of nitrogen to the ecosystems, causing decrease in biodiversity, strong modification of N biogeochemical cycle, and increase GHG emissions (Fowler et al., 2013; Galloway et al., 2004).
The enzymes responsible for the cycling of nitrogen in microbes themselves require trace amount of several metals, most often molybdenum, copper, iron (Glass & Orphan, 2012; Zhang et al., 2020). The availability of these metals to micro-organisms can ultimately limits their N cycling activity and their response to changes in environmental conditions (Barron et al., 2008; Darnajoux et al., 2022). Similarly to nitrogen, the cycling of these metals is accelerated by human activity (Schlesinger et al., 2017; Wong et al., 2021) and it can have both positive fertilizing effect (Darnajoux et al., 2019) or negative adverse effect (Gaetke & Chow, 2003; Hauck et al., 2006) on organisms depending on the rate of input and on the demands.
In between these two extrema could lie a sweet spot where low-paced human activities would contribute to natural fertility with a low and constant flux of essential trace metal and nitrogen, which could enhance ecosystem function and growth without much of the adverse effect found in high deposition area. Ultimately, this would represent the boundary of what an ecosystem can buffered in term of N and metal pollution, and would represent an ideal of human impact on nature, albeit limited to the coarse nitrogen cycle.
One of the key gatekeepers of atmospheric deposition in natural ecosystems are the vegetation and ground cryptogamic covers, such as mosses, lichens, and biocrust (Garty, 2001; Wolterbeek, 2002). The physiology and biochemistry of these organisms are strongly constrained by the chemical and physical environment, and they adapted to respond quickly to changes in environmental conditions (Nash, 2008). They are also large contributors to the nitrogen natural fertilization by BNF, particularly in high latitude forests where their associated cyanobacterial partners can contribute as much a 50% of measured N input to ecosystems (DeLuca et al., 2002; Elbert et al., 2012; Rousk et al., 2017). Their associated microbiomes are also known to be able to produce substantial amount of N2O (Lenhart et al., 2015; Machacova et al., 2017), although the exact pathway is not well understood. As N fixers and N2O producer, cryptogamic covers represents ideal models to understand the link between atmospheric deposition of nitrogen and metal and the response of environmental microbiomes in fast changing ecosystems.
Using bryophytes as a well-defined micro-ecosystem, this project aims to decipher how metal and nitrogen influence environmental microbiomes diversity and function across various spatial and temporal scales, from plot-level heterogeneity to biome-scale and from days to years. Within this project, the student will have the opportunity to focus its investigation on one or more questions in relation to the adaptation and resilience of the nitrogen cycling function in contrasting environment condition, the drivers of spatial and temporal heterogeneity over microbiomes diversity and activity and their correlation at different scales, and/or how nitrogen cycling capacity can influence mosses fitness and ecological success, in relation to moss invasiveness.

This thesis will build an extensive dataset to address specific questions related to microbial ecology and biogeochemistry. It will notably aim to
- Understand how the diversity and activity of microbiomes associated with keystone bryophytes species is controlled by natural and perturbated environmental conditions across biomes (boreal, temperate, tropical).
- Investigate causal relationships between functional diversity and biogeochemical activity.
- Identify early predictors of human impact on biogeochemical activity in cryptogamic microbiomes.

This research will investigate primarily N cycle biogeochemistry, with a focus on nitrogen enzyme functional genes relating to the input and output of N (nif, nir, nos), and N cycling activities (N fixation with ARA and 15N tracer experiment, and N2O production using IR-spectrophotometry). We are going to use the emblematic forest pleurocarps Pleurozium schreberi and the wetland genera Sphagnum sp. as model organisms for this study. Both mosses are found across climate zone (from arctic, boreal, temperate, Alpine, and Tropical) and are implicated in the cycling of nitrogen. We are first going to establish baselines microbial composition, functional genes diversity, and biogeochemical activity for both organisms in ecosystems with contrasting environmental conditions (temperature, humidity) and human impact (proximity to road, crop fields, or urban center). In a second set of experiments, transplant experiment will be conducted to create a network of samples along a continuous of gradient of human impact from the Landes forest (lowland, warm climate) to the Pyrenean Mountain areas (cold climate). Environmental conditions (temperature, light, humidity) will be recorded using field sensors (Hobot technology inc.), and chemical environmental composition will be analyses using in-house methods. Finally, all data will be processed using numerical ecology methods such as clustering, mixed-effect linear models, gradient analyses, and structural equation models in order to address specific hypotheses related to the microbial ecology of bryophytes.
A preliminary dataset from a transplantation experiment conducted in North America, including chemical information (metal content, %C, %N, d15N, d13C), biogeochemical fluxes (CO2, CH4 , N2O, and N fixation) and rRNA16S DNA diversity for two temperate moss species, is also available to start with the project.