Professor 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.

• Direct quantification of ecological drift at the population level in synthetic bacterial communities. Fodelianakis, S., Valenzuela-Cuevas, A., Barozzi, A., Daffonchio, D. ISME Journal, (2020).
• Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity. Fodelianakis, S., Lorz, A., Valenzuela-Cuevas, A., Barozzi, A., Booth, J.M., Daffonchio, D. Nature Communications, 10(1), (2019).
• Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions. Booth, J.M., Fusi, M., Marasco, R., Mbobo, T., Daffonchio, D. Scientific Reports, 9(1), (2019).
• Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+-pumping pyrophosphatase in pepper plants. Vigani, G., Rolli, E., Marasco, R., Dell'Orto, M., Michoud, G., Soussi, ...Daffonchio, D. Environmental Microbiology, 21(9), 3212-3228, (2019).
• Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems. Mosqueira, M.J., Marasco, R., Fusi, M., Michoud, G., Merlino, G., Cherif, A., Daffonchio, D. Scientific Reports, 9(1), (2019).
• Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco, R., Rolli, E., Fusi, M., Michoud, G., Daffonchio, D. Microbiome, 6(1), (2018).
• Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host 06 Biological Sciences 0605 Microbiology 06 Biological Sciences 0602 Ecology 06 Biological Sciences 0607 Plant Biology. Marasco, R., Mosqueira, M.J., Fusi, M., Ramond, J.-B., Merlino, G., Booth, J.M.,...Daffonchio, D. Microbiome, 6(1), (2018).

• 2014-Present: Professor of Bioscience, BESE, KAUST, Kingdom of Saudi Arabia
• 2010-2014: Full Professor, DeFENS, University of Milan, Italy (now, leave of absence until March 2019).
• 2002-2010: Associate Professor, DiSTAM, University of Milan, Italy.
• 1998-1999: Adjunct Professor of Industrial Microbiology, University of Urbino, Italy.
• 1995-2002: Assistant Professor (permanent position), DiSTAM, University of Milan, Italy.
• 1994-1995: Post-Doctoral Fellow, DiSTAM, University of Milan, Italy.
• 1994: Post-Doctoral Scientist, Laboratory of Microbial Ecology, Gent University, Belgium.
• 1992-1993: Post-Doctoral Fellow, Department of Food Science and Microbiology (DiSTAM), University of Milan, Italy. 

• Red Sea Research Center(RSRC)
  
• Biological and Environmental Science and Engineering Division (BESE)
• Marine Science Program