Microbial Ecology for Successful Inoculation

Objective

The potential of microbiome solutions in sustainable agriculture and soil health improvement has resulted in accelerated efforts to identify and isolate microbes for novel inoculants; however, inoculation outcome is still variable, especially in the diverse and heterogeneous soil environment. Integrating an ecological perspective into the development of microbial inoculants can greatly improve their success. The MESI project (Microbial Ecology for Successful Inoculation) will study how ecological processes (i.e., priority effects, predation) affect the bioaugmentation of pesticide-contaminated soils in the face of common environmental disturbances (e.g., high temperatures). A two-strain pesticide-degrading consortium will be used as a model. Firstly, the fitness of the consortium members and their response to a gradient of heat disturbance intensities and protist predation will be characterised by analysing pesticide degradation efficiency, growth rates, respiration and metaproteomes. Then, by replicating the inoculation 100 times in identical pesticide-contaminated soil microcosms, the frequency of priority effects after inoculation and the role of microbial predation on variability in establishment will be characterised through metabarcoding. Finally, by exposing contaminated and inoculated soil microcosms to repeated heat disturbances and reinoculation, the effects of these events on intra-consortium and consortium-microbiota trophic interactions and bioaugmentation success will be determined using DNA-SIP coupled with metagenomic analysis. The MESI project will use an integrative approach to systematically assess the expected success rate of inoculation, considering the ecology of the soil/inoculum system and examine how climatic fluctuations influence reinoculation success, with the goal of developing more targeted bioaugmentation practices that improve both sustainability and outcomes.