Prof. Daffonchio's research interests are in the microbial ecology of complex ecosystems in conventional and extreme aquatic and terrestrial habitats. His research is spanning from basic aspects of microbial ecology through the application of synthetic ecology approaches to applied aspects for the environmental protection and sustainability of agriculture.

Professor Daffonchio has developed research on the exploration and characterization of extreme marine and terrestrial environments, both pristine and polluted. He is actually dealing with the study and exploitation of extremophile microorganisms along the water stress continuity from the Arabian Desert to the depth of the brine pools in the Red Sea. A particular focus is on the bacteria-host symbiosis with plants and animals in relation to the water and salinity stresses.