CONTICOMIC - Assessment of the scientific challenges to better understand the role of the soil-water continuum in maintaining functional microbial biodiversity in agroecosystems

Agroecosystems, which carry high socio-economic stakes, are ecosystems that illustrate the importance of the soil-aquatic continuum, due to the close links between watersheds and adjacent aquatic environments, particularly in headwater sections. While these links are relatively well studied in terms of chemical transfers (e.g. nitrates, phosphates and pesticides), little attention is paid to biological exchanges between soil and aquatic environments. In agroecosystems, microbial communities are present in all environmental compartments, where they contribute to various ecological processes that contribute to a wide range of ecosystem functions and services. 
Thus, these are study models that seem particularly well suited to addressing this type of issue, drawing in particular on the emerging concept of ‘coalescence’.

In this context, the ContiComiC consortium project aimed to conduct a collective reflection on the concepts of ‘coalescence’ and ‘functional continuum’ in agroecosystems and the approaches/methods to be developed to explore these concepts based on the study of microbial biodiversity and certain services it supports.

Approaches

A working seminar held on 24 and 25 November 2021 brought together eight participants representing four INRAE research units/joint research units (RiverLy, Agréocologie, CARRTEL, EMMAH) and one non-INRAE joint research unit (LECA).

The seminar was divided into four working sessions, which respectively enabled participants to:

• Define the scientific framework and place the concept of microbial coalescence in the context of the soil-aquatic environment continuum.
• Identify the main scientific issues surrounding this concept.
• Take stock of the existing literature on the subject and conduct a critical analysis.
• Define the main conceptual and methodological needs and list the skills/disciplines to be mobilised.

Results

In addition to the importance of considering the various interface zones between environmental compartments, one of the main challenges identified concerns the need to better understand how coalescence processes in interface zones influence the ability of newly formed microbial communities to fulfil their ecological role, based on the functions to which they contribute.

The parallel literature review showed that few studies take into account coalescence processes along the soil-aquatic environment continuum. Furthermore, all the studies reviewed have methodological limitations (choice of spatial and temporal sampling strategy, failure to take the functional dimension into account), which make it difficult to assess the influence of this continuum on the structural and, above all, functional characteristics of microbial communities. On the other hand, recent methodological developments, particularly in the fields of “omics”, bioinformatics and biostatistics, make it possible to envisage the implementation of new approaches that are particularly suited to the study of microbial coalescence processes at different environmental interfaces in agrosystems, addressing this from a taxonomic, structural and functional perspective.

Discussions and collective reflections also clearly highlight the need to mobilise a wide range of interdisciplinary skills in order to truly understand the role of the soil-aquatic environment continuum in maintaining functional microbial biodiversity in agroecosystems. The disciplines to be mobilised (apart from microbial ecology) include, but are not limited to, hydrology, pedology, modelling (of flows), bioinformatics, biostatistics and functional ecology.

Participants

INRAE units involved

• UMR Agroécologie
• UMR EMMAH - Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes - Avignon University
• UR RiverLy
• UMR CARRTEL - Centre Alpin de Recherche sur les Réseaux Trophiques et les Ecosystèmes Limniques - University of Savoie Mont Blanc

Partners

• LECA - Laboratoire d'écologie alpine - CNRS