Daniele Daffonchio

Professor, Bioscience ​

Office Location: Ibn Al Haytham (Building 2) · Level 3 · Room 3236​
Email: daniele.daffonchio@kaust.edu.sa


Research Keywords
Microbial Ecology; Environmental Microbiology; Microbial Biotechnology; Bioremediation; Host-microbe interactions


Research Interests
Research interests are in the microbial ecology of complex ecosystems in conventional and extreme aquatic and terrestrial habitats. Daffonchio’s 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. He 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. 


Main Techniques
The Daffonchio’s laboratory uses the state of the art techniques of molecular microbial ecology including PCR-fingerprinting for community characterization, Quantitative PCR and genomic and metagenomic techniques. Different cultivation strategies are developed to establish new microbial cultures of previously non-cultivated microorganisms. One major effort is the transformation of wild bacteria from different environments for the generation of mutants as well as for the labeling with marker proteins like fluorescent proteins. A multidisciplinary technical approach is applied to study the symbiosis between microorganisms with plants and animals in particular arthropods.


Members of the Lab
Dr. Stelios Fodelianakis: Post Doctoral scientists focusing on the use of Synthetic Microbial Ecology approaches for shaping microbial ecology theories including the effect of diversity parameters on horizontal gene transfer and microbial biofilms. Dr. Fodelianakis obtained his PhD from the University of Heraklion, Greece.

Dr. Marco Fusi: Post Doctoral scientist focusing on the microbial symbiosis and the biology of mangrove crabs and their contribute to the functioning of the mangrove ecosystem. Dr. Fusi obtained his PhD from the University of Milan, Italy.

Dr. Ramona Marasco: Post Doctoral scientist focusing on microbial diversity associated to plants in arid and desert soils and the contribution of such microorganisms to plant resistance to drought and water stress. Dr. Marasco obtained his PhD from the University of Milan, Italy.

Dr. Giuseppe Merlino: Post Doctoral scientist focusing on the ecology and biotechnology of marine microorganisms capable of degradation of oil hydrocarbons and chlorinated compounds with particular reference to the effect of pressure on their physiology. Dr. Merlino obtained his PhD from the University of Milan, Italy.

Jenny Booth: First year PhD student focusing on the microbial diversity in the mangrove sediment and rhizosphere and its role in maintaining mangrove functional homeostasis.

Patrick Bianchi: First year PhD student focusing on the physiological response of hydrocarbonoclastic marine microorganisms to salinity, oligotrophy and pressure.

Asma Soussi: First year PhD student focusing on the interactions between microorganisms and plant roots with particular reference to date palm.


Selected Publications
Daffonchio D., Borin S., Brusa T., Brusetti L., Van der Wielen P.W.J.J., Bolhuis H., Yakimov M.M., D’Auria G., Giuliano L., Marty D., Tamburini C., McGenity T.J., Hallsworth J.E, Sass A.M., Timmis K.N., Tselepides A., de Lange G.J., Huebner A., Thomson J., Varnavas S.P., Gasparoni F., Gerber H. W., Malinverno E., Corselli C., BioDeep Scientific Party. 2006. Stratified prokaryote network in the oxic-anoxic transition of a deep sea halocline. Nature, 440:203-207.

Favia G., Ricci I., Damiani C., Raddadi N., Crotti E., Marzorati M., Rizzi A., Urso R., Brusetti L., Borin S., Mora D., Scuppa P., Pasqualini L., Clementi E., Genchi M., Corona S., Negri I., Grandi G., Alma A., Kramer L., Esposito F., Bandi C., Sacchi L., Daffonchio D. 2007. Bacteria of the genus Asaia stably associate with Anopheles stephensi, an Asian malarial mosquito vector. Proceedings of National Academy of Science of USA, 104:9047-9051.

Wittebolle L., Marzorati M., Clement L., Balloi A., Daffonchio D., Heylen K., De Vos P., Verstraete W., Boon N. 2009. Initial community evenness favours functionality under selective stress. Nature 458:623-626.

Marasco R., Rolli E., Ettoumi B., Vigani G., Mapelli F., Borin S., El-Behiri U., Sorlini C., Cherif A., Zocchi G., Daffonchio D. 2012. A drought resistance-promoting microbiome is selected by root system under desert farming. PLoS One 7:e48479.1-e48479.14.

De Roy K., Marzorati M., Negroni A., Thas O., Balloi A., Fava F., Verstraete W., Daffonchio D., Boon N. 2013. Environmental conditions and community evenness determine the outcome of biological invasion. Nature Communications 4:1383.