Daniele Daffonchio, Ph.D.


​Professor of Bioscience

Research Interests

Prof. Daffonchio is a professor of Bioscience in the KAUST Red Sea Research Center. The Italian native joined KAUST in 2014 as an environmental microbiologist. Daffonchio's research interests at KAUST focus on the microbial ecology of complex ecosystems in conventional and extreme aquatic and terrestrial habitats. His research moves through the basic aspects of microbial ecology up to the application of synthetic ecology approaches to applied aspects for the environmental protection and sustainability of agriculture.

Over a lengthy career, Daffonchio has developed research on the exploration and characterization of extreme marine and terrestrial environments, both pristine and polluted. In Italy, his original research was in the agro-food sector where he focused on microbes, especially wastewater treatment systems and anaerobic systems in particular. Before moving more in the direction of soil systems and the study of the agricultural system, including research devoted to the anaerobic digestion and methane production from agro-food wastewaters.

"Indeed, if I have to make a retrospective analysis of my work, most of the systems I have used were indeed extreme, even the experimental reactors I used in the lab," he said

It was a conference on the snout beetle Rhynchophorus ferrugineus, more commonly known as the red palm weevil, that first brought Daffonchio to KAUST. Upon arriving on campus, he was instantly appreciative of the campus's beauty and facilities. "I was invited here to a conference on the red palm weevil. Then I learned that there was a position opening here and I successfully applied."

It is the unique environment that surrounds the university and campus that he feels contributes to KAUST acting as "an open laboratory" for his type of research. "I can work on extreme marine systems, extreme land systems and I have the desert on one side where I can go easily. We also have this coastal ecosystem that is incredible, extremely beautiful."

"At KAUST  you can see unique phenomena, you can see plants surviving where there is nothing, really nothing. You can find traces of animals, you can find unique and beautiful flora and fauna in the sea. Before KAUST, very few researchers had explored the Arabian desert and the Red Sea, but now we have this opportunity for research, and it is very exciting,"

Daffonchio believes that the central thrust of his research is understanding the forces that determine the assembly of the microbial communities. His goal is to understand why, in any given place, in any given drop of water, in any given gram of soil, do we have a specific unique assembly of microbes. This research goal is Daffonchio's attempt to help answer the central question in microbiology.

"It is commonly said that we [as humans] are an organism in a nation of microbes. The world is made of microbes, and microbiology is essential for understanding  the functioning of our planet, because microbes are regulating the global ecosystem. My approach to responding to this general question is, 'okay I diversified the communities, I go to look to communities in the arid soil in the deep sea, in anaerobic reactors in, whatever is the source.'"

"Then by paralleling all these observations and coupling these with reconstructive experiments through the synthetic ecology. I can have a better view on what is the real diversity. So, in a few words, from the observational works in the field, in the different environments, I can then establish a collection of microbes in a culture that can then be assembled in a synthetic community to respond to a specific question. This is essentially what I am doing at KAUST," he concluded.

Daffonchio believes that his research, and that of his colleagues, can be of  benefit to Saudi Arabia and its future.

"Considering how delicate the environment and the ecosystem is here in Saudi Arabia, due to the extreme conditions,  the desert ecosystem, the lack of water, the salinity of the seas, the continued high temperature for all these years, understanding these topics is, I think, extremely important."

"The problem of Saudi Arabia is that the green color is lacking, except in the flag. But if you move inland, it is yellow, brownish. There is no green color. If you go to the coast and you look at Google Earth or these kinds of systems you can see that there is a strip of green color along the coast and this is the mangrove system. This strip of green is providing essential services to preserve the coastal fish stocks, for instance.

"For example, to determine the rate of coastal erosion is extremely important and so is studying how the microbes contribute to the functioning of the mangrove ecosystem. With our research, we want to contribute to the Kingdom's future sustainable ecological protection drives for the Red Sea and the country's ecosystem at large."

Selected Publications

  • Ensuring safety in artisanal food microbiology 
    L. Cocolin, M. Gobbetti, E. Neviani, D. Daffonchio
    Nature Microbiology, 1:16171 , (2016)
  • Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteog... 
    H. Sghaier, 4 other Authors, D. Daffonchio, 6 other Authors
    ISME Journal, 10:21-29, (2016)
  • Environmental conditions and community evenness determine the outcome of biological invasion 
    K. De Roy, 6 other Authors, D. Daffonchio, N. Boon
    Nature Communications, 4:1383 , (2013)
  • A drought resistance-promoting microbiome is selected by root system under desert farming 
    R. Marasco, 9 other Authors, D. Daffonchio
    PLoS One, 7:e48479, (2012)
  • Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersa... 
    S. Borin, 17 other Authors, D. Daffonchio
    PNAS, 106:9151-9156, (2009)
  • Initial community evenness favours functionality under selective stress 
    L. Wittebolle, 3 other Authors, D. Daffonchio, 4 other Authors
    Nature, 458:623-626, (2009)
  • Paternal transmission of symbiotic bacteria in malaria vectors 
    C. Damiani C, 7 other Authors, D. Daffonchio, G. Favia
    Current Biology, 18:R1087-R1088, (2008)
  • Bacteria of the genus Asaia stably associate with Anopheles stephensi, an Asian malarial mosquito vector 
    Favia G, 22 AA, D. Daffonchio
    PNAS, 104:9047-9051, (2007)
  • Stratified prokaryote network in the oxic-anoxic transition of a deep sea halocline 
    D. Daffonchio, 23 other Authors
    Nature, 440:203-207 , (2006)
  • The enigma of prokaryotic life in deep hypersaline anoxic basins 
    P.W.J.J. Van der Wielen, 2 other Authors, Daffonchio D, 11 other Authors
    Science, 307:121-123, (2005)


  • ​​​​Post Doctoral Scientist, LabMet, University of Gent, Gent, Belgium, 1994
  • Ph.D., Chemistry Biochemistry and Ecology of Pesticides and Xenobiotics, University of Milan, Milan, Italy, 1993
  • M.Sc, University of Milan, Milan, Italy, 1988

Professional Profile

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

Scientific and Professional Membership

  • ​Editorial Board member of the scientific journals
  • Annals of Microbiology (2006-present)
  • BioMed Research International (2008-present)
  • Environmental Microbiology (2014-present) 
  • Journal of Microbiological Methods (2011-present)
  • Microbiological Research (2013-present)
  • Plos One (2014-present)
  • Research in Microbiology (2012- present)
  • Scientific Reports (2016-present) 


  • ​President of the Italian Society of Agriculture, Environmental and Food Microbiology, SIMTREA 

KAUST Affiliations

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

Research Interests Keywords

Microbial ecology Extreme environments Deep sea brine pools Mangrove ecosystem microbiology