Engineering multi-degrading bacterial communities to bioremediate soils contaminated with pesticides residues

Parallel to the important use of pesticides in conventional agriculture there is a growing interest forgreen technologies to clear contaminated soil from pesticides and their degradation products. One spe-cific technique, the inoculation of degrading micro-organisms in polluted soil, known as bioaugmenta-tion, is a promising method still in needs of further developments. Specifically, improvements in theunderstanding of how degrading microorganisms must overcome abiotic filters and interact with the au-tochtonous microbial communities are needed in order to efficiently design bioremediation strategies.Here we designed a protocol aiming at studying the degradation of two herbicides, glyphosate (GLY)and isoproturon (IPU), via experimental modifications of two source bacterial communities. We usedstatistical methods stemming from genomic prediction to link community composition to herbicidesdegradation potentials. Our approach proved to be efficient with correlation estimates over 0.8 - betweenmodel predictions and measured pesticide degradation values. OTUs significantly associated with thedegradation ability, and therefore identified as relevant by the models were confronted to the literature.Next, multi-degrading bacterial communities were obtained by coalescing bacterial communities withhigh GLY or IPU degradation ability based on their community-level properties. Finally, we evaluatedthe efficiency of constructed multi-degrading communities to remove pesticide contamination in a differ-ent soil. While results are less clear in the case of GLY, we showed an efficient transfer of degrading ca-pacities towards the receiving soil even at relatively low inoculation levels in the case of IPU. Altogether,we developed an innovative protocol for building multi-degrading simplified bacterial communities withthe help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil.