Dynamique des communautés bactériennes et effet du glyphosate lors du compostage de biomasse lignocellulosique

Composting is an anthropic process based on the natural decay of biomass that exploits the enzymatic activity of microorganisms under the control of several environmental factors. Due to their composition and low moisture content, lignocellulosic residues are particularly suitable for composting and serve as a structuring element, which confers them an important role in the process. Although mostly of plant origin, the organic matter (OM) directed towards composting sites is highly diversified, as are the types of contaminants it can contain. The impact of these contaminants, such as glyphosate, on the biodegradation process and their persistence in the environment remain to be investigated. The objective of this thesis is thus to report on the effect of the composition of the lignocellulosic biomass and the presence of glyphosate on the evolution of the physicochemical parameters and the recruitment of bacteria during composting, while ensuring the follow-up of the transformation of the vegetable organic matter and the degradation of glyphosate during the process.  Two field studies were conducted to measure the effect of stem age and winter storage on the transformation of wood chips, and to study the dynamics of bacterial succession involved in the carbon and nitrogen cycle during the composting of plant residues. The results obtained revealed a difference in the composition of 2-year-old and 3-year-old stems from shrub willow (Salix sp.), with the younger ones containing more extractable compounds and the more mature ones richer in structural sugars. These differences were reflected in a higher and faster temperature rise in the younger chip pile. A decrease in extractives, retention of structural sugars, and an increase in the proportion of lignin demonstrate the importance of the soluble carbon source for the initiation of wood decomposition and recalcitrance of lignocellulosic elements. The second experiment revealed a very high diversity of bacteria responsible for the decomposition of cellulose, hemicelluloses and lignin during the thermophilic phase of composting. This phase, during which intense activity took place, had fewer species, but they were very abundant, a trend that reversed as the organic matter matured. The observed dynamics reflect a functional redundancy of the communities, which seems to evolve according to the temperature, oxygen level and nature of the available substrate.  A third experiment conducted in a controlled environment demonstrated the negligible impact of glyphosate on microbial activity and the evolution of physicochemical parameters during composting. Glyphosate was almost or completely degraded after composting, while the main product of degradation, aminoethylphosphonic acid (AMPA), was not detected. The impact of glyphosate on bacterial communities was also negligible, while species richness at different sampling times was the same when comparing the control treatment and the treatment containing "pure" glyphosate. The beta-diversity analysis found no significant difference between the communities present in the control and glyphosate treatments, while a few bacteria were differentially abundant between the two treatments, the vast majority being less abundant in the glyphosate treatment.  This thesis has thus highlighted the importance of the initial nature of the organic matter on microbial activity as well as on the recruitment and dynamics of bacterial communities during composting, while the presence of glyphosate was shown to be a weak determinant of decomposition processes and species abundance. This information should help to optimize the treatment of organic matter by composting and to better assess the potential risks associated with composting contaminated biomass.

Keyphrases: Glyphosate, Composting, Willow, Bacteria, Metagenomic