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

These data and scripts are related to the article entitled "Engineering multi-degrading bacterial
communities to bioremediate soils contaminated with pesticides residues".   The objective of this study is to broaden our understanding 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.
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 used
statistical methods stemming from genomic prediction to link community composition to herbicides
degradation potentials. Then OTUs significantly associated with the degradation 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 with
high GLY or IPU degradation ability based on their community-level properties. Finally, we evaluated
the 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 with
the help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil. 

Data and codes needed to reproduce the statistical analyses presented in the manuscript are provided.