Soil Microbiology and Plant-microbe interactions (2017/2018)

Course code
Name of lecturer
Giovanni Vallini
Giovanni Vallini
Number of ECTS credits allocated
Academic sector
Language of instruction
II sem. dal Mar 1, 2018 al Jun 15, 2018.

Lesson timetable

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Learning outcomes

This course aims at elucidating the influence of the soil environment on settlement and activity of the microbial cenoses (microbiomes) in different pedological contexts. Within the completion of this course, students will have acquired a comprehensive overview of both the major phyla of microorganisms found in soil and the methods (including the new molecular high-throughput sequencing technologies) for their quantitative estimation as well as for the characterization of their physiological properties either in bulk soil or in the rhizosphere. Particular emphasis will be given to plant-microbe interactions, with a special attention to the multiple cross signaling mechanisms among plants and PGPR (Plant Growth Promoting Rhizobacteria) at the rhizosphere level. Symbiotic nitrogen fixation and different mycorrhizal associations will be discussed in deep details. Transformations of organic and inorganic pollutants mediated by soil microorganisms will be treated. Eventually, the understanding of soil microbial ecology principles will allow the students to correctly interpret environment-friendly strategies for improvement of crop productivity, biological control of plant pathogens and biodegradation/bioremediation of contaminated sites.


Part I – The soil medium
Inert component: Solid mineral fraction, Organic matter, Liquid phase, Gaseous phase, Soil structure. Living components: microbiota and macrobiota with particular emphasis to bacteria and fungi. The Rhizosphere concept. Root exudates.

Part II – The soil microbiome
Microbial biodiversity in bulk soil and rhizosphere: copiotrophs and oligotrophs. Methods for quantitative and qualitative (taxonomical) estimation of soil microbial populations. Measurement of biological activity in the soil: Microbial biomass, Metabolic reactions. Effects of physico-chemical and edaphic factors on soil microbial cenoses: Water content and availability, Soil pH, Oxygen concentration in soil atmosphere and redox potential, Concentration of nutrients, Xenobiotic compounds and heavy metals. Significance of soil microbial biodiversity to biogeochemical cycling.

Part III – Soil microbial interactions
Microbe-microbe interactions. Effects of microorganisms on plants. Effects of plants on microorganisms. Plant Growth Promoting Rhizobacteria (PGPR). Symbiotic diazotrophs: Rhizobia and association with legumes. Mycorrhizal associations: Ectomycorrhizae, Endomycorrhizae with particular emphasis to AM fungi, Ectendomycorrhizae.

Part IV – Managing rhizosphere microbiome
Perspectives for the development of novel strategies for sustainable crop production, biological control of plant pathogens and environmental bioremediation through rhizosphere microbiome exploitation.


Principles of Plant-Microbe Interactions - Microbes for Sustainable Agriculture
Ben Lugtenberg (Ed.)
Springer (Heidelberg - New York - Dordrecht - London), 2015
ISBN 978-3-319-08574-6

Soil Microbiology and Sustainable Crop Production
Geoffrey R. Dixon • Emma L. Tilston (Eds.)
Springer (Dordrecht - Heidelberg - London - New York), 2010
ISBN 978-90-481-9478-0

Advanced Techniques in Soil Microbiology
Ajit Varma • Ralf Oelmüller (Eds.)
Springer-Verlag (Berlin – Heidelberg – New York), 2007

Reference books
Author Title Publisher Year ISBN Note
K. Bouarab, N. Brisson, F. Daayf Molecular plant-microbe interactions (Edizione 1) CAB International 2009 9781845935740
Eldor A. Paul Soil Microbiology, Ecology and Biochemistry - 4th Edition (Edizione 4) Elsevier 2014 9780124159556

Assessment methods and criteria

Final profit verification by written examination. The test consists of submitting to the student a multi-page form containing a number of questions ranging from 20 to 25, structured as single-textbox questions, multiple-choice questions, calculation exercises, request of short comments and descriptions. Each question is given a different weight in points. The rating is in thirtieths, based on the percentage of points matched with the correct answers.