In the face of global change, one of the major challenges for contemporary societies will be the preservation of biodiversity. In this context, it is necessary to identify the most vulnerable areas, especially within drainage basins and their river networks, very sensitive to these pressures. In order to inform public policy and help prioritize decision-making, it has become essential to better understand the consequences of management decisions and climate change scenarios on future biodiversity, which necessitates the study of projections (i.e. simulations) based on species models.

Lakes and ponds of the Aquitaine Atlantic coast are unique natural ecosystems, not only at the national but also at the European scale. These systems host a high taxonomic diversity, especially for aquatic plants. Indeed, isoetid communities represent a set of species with high conservation value, also including one endemic species. These communities are however highly threatened, especially by anthropogenic activities, and most of the coastal Aquitaine’s lakes have already experienced their extinction. Knowledge on these species is still however scarce, particularly concerning their genetic diversity. While conservation and restoration actions are emerging with the redaction of a National Plan for preserving these communities, understanding their genetic diversity, their relationships with taxonomic and functional diversity appear as a major issue.

Some of the agricultural contaminants (pesticides, nitrogen) spread on cultivated soils reach the hydrosphere through agricultural drainage (1) with proven consequences on aquatic ecosystems and their functions. Constructed wetlands are designed to break down nitrates and certain pesticides through natural purification features. Nevertheless, they constitute potential reservoirs of contaminants likely to impact the wild species they shelter by acting as ecological traps.

Climate change is altering the way living beings function and pushing ecosystems towards their ecological limits, beyond which they will no longer be able to maintain their functioning and provide ecosystem services at current levels. Our current knowledge suggests that this will have dramatic consequences for life on Earth (erosion of biodiversity) and for human societies (living conditions). One of the challenges of this thesis is to analyse and evaluate how biodiversity, from both an ecological and functional perspective, can be a major lever for adapting livestock farming systems to climate change and supporting their transition. We will focus on managed agro-ecosystems that are rich in biodiversity, such as permanent grasslands. In particular, we will be seeking to better characterise and understand the spatio-temporal dynamics of plant communities in a context of climate change and their impact on ecosystem functioning and its capacity to deliver ecosystem services, in relation to a diversity of management practices.

Permanent grasslands play an essential role in maintaining grass-fed livestock and providing key ecosystem services for the agro-ecological transition (pollination, pest control, soil fertility) and society (carbon storage, water purification, aesthetic value). In France, permanent grasslands are one of the most diversified ecosystems but also one of the most threatened at the national scale. Indeed, their surface has considerably decreased over the last decades, which hinders the functioning of agricultural landscapes as well as the conservation of a unique heritage biodiversity. Moreover, global changes are likely to influence the characteristics of the remaining grasslands. However, we lack knowledge on the temporal dynamics of biodiversity and ecosystem services of permanent grasslands at the French national scale, as well as on the underlying causes and consequences of these dynamics.

The project aims to understand the way in which the biological activity of agroforestry systems is structured, in time and space, in relation to the soil multifunctionality in Mediterranean and semi-arid tropical environments. The project will be divided into three lines of research. The first will focus on community structures and soil interaction networks according to different spatial and temporal heterogeneity gradients. The aim is to identify patterns of community assembly and interaction networks at different scales (i) spatial and (ii) temporal.

The Camargue (Rhône delta) is a complex social-ecosystem with important issues regarding biodiversity conservation and economic and cultural activities. In a context of global change, anthropogenic (water management in agricultural and natural areas, agricultural practices) and climatic (rainfall, evapotranspiration) drivers affect the hydro-saline balance. This hydro-saline functioning is a central element in the dynamics of the Camargue's habitats and species, and the associated networks of activities and services.

The increasing use of various kinds of plastics leads to the accumulation and long-term storage of microplastics (MP) in soils. There is a growing scientific literature linking the presence of MP and the consequences for soil organisms that perform essential ecological functions. However, for the most part, these are ecotoxicological approaches through effects on certain organisms studied separately (microorganisms, micro-, macrofauna and plants), without addressing ecotoxicity issues. Moreover, in agricultural soils, the presence of MP may be due to inputs via amendments with organic matrices and their impact on the biological functioning of soils is then little documented.

Mixing species is an agroecological practice central to increasing the ecological functioning of agroecosystems (resilience to hazards, stability of performance, efficient use of resources, regulation of pests and diseases) in a context of global change (reduction of inputs, climate change). However, this practice comes with a complexity in the choice and management of crops and requires farmers to have knowledge and tools to help them implement it.