85862 - Microbiology In Plant Nutrition

Learning outcomes

At the end of the course, students are able to scientifically and technically develop field interventions based on the use of microorganisms to improve soil fertility and to transfer the information acquired to operators in the agricultural sector. The profound knowledge of the microbiological processes of the rhizosphere and of the microorganism-plant interaction represents an indispensable scientific basis for the efficient management of plant nutrition in the agricultural sector.

Course contents

Part 1: MICROBIOLOGICAL ASPECTS OF NUTRITION held by Diana Di Gioia (30 hours)

• Recall of some basic concepts of general microbiology: this aspect will be managed according to the general microbiology knowledge of the student cohort.

• Activity of microorganisms in the soil and role in biogeochemical cycles: Soil as a resource to be protected; role of microorganisms in the carbon cycle in soil; degradation of complex polymers in soil (starch, hemicellulose, pectin, chitin, cellulose, lignin); humus formation; role of microorganisms in the nitrogen cycle in the biosphere (proteolysis and ammonization, ammonium assimilation, nitrification, assimilative or dissimilatory reduction of nitrate, denitrification, nitrogen fixation); sulfur cycle; phosphorus cycle.

• The rhizosphere and plant microorganism associations: The rhizosphere and its microbial communities; Positive and negative associations between soil microorganisms; methods for studying microbial diversity in soil; Mycorrhizae; Actinorrhize.

• Nitrogen fixation: Free (non-symbiotic) non-photosynthesizing nitrogen-fixing bacteria; nitrogen-fixing bacteria and biocoenosis relationships; free photosynthesizing nitrogen-fixing bacteria; chemolithotrophic nitrogen-fixing bacteria; symbiotic nitrogen-fixing bacteria; nitrogenase; oxygen protection mechanisms implemented by different microorganisms.

• Bacteria that promote plant growth: Definition of PGPR and their role in soil fertility; action of PGPRs in promoting plant growth.

• The composting process: Definition of compost and usable substrates; microbial successions in the composting process; microbiological and chemical-physical parameters involved in the composting process; stability of the compost. Microbiological safety requirements for compost.

Skills acquired in module 1: Structure and function of the main soil microbial groups and role of microorganisms in the cycle of organic matter in the soil.

 

Part 2: RHIZOSPHERE-PLANT INTERACTION AND ENDOPHYTES held by Daniele Alberoni (30 0RE)

Prerequisites
The student enrolling in this course should hold a solid foundation in the fundamentals of biochemistry and microbiology acquired during a Bachelor’s degree in one of the following (or a closely related) programs L‑25 R – Agricultural and Forestry Sciences and Technologies, L‑13 R – Biological Sciences or similar Bachelor's courses. 

Specifically, the student should be familiar with:

- Protein structure and function
- Enzymatic activities: cofactors and catalytic mechanisms
- DNA/RNA structure and extraction principles
- Basic molecular techniques: end‑point PCR and gel electrophoresis
- Morphology and physiology of bacteria and fungi
- Familiarity with scientific software (e.g., Excel, R, or similar)

Module 2 Content: Biotechnologies Applied to Plant Nutrition

• Review of Basic Microbial Biotechnology Concepts (~ 1 hour): Tailored to the cohort’s existing knowledge of core biotechnology principles.
  

• Soil Microorganism–Plant Associations and Interactions (~ 3 hours): Biofilms, Quorum sensing: overview, chemical mediators, examples in both Gram‑positive and Gram‑negative bacteria.
  

Molecular Biology Applied to Plant Nutrition:

•  qPCR or Real‑Time PCR (∼6 hours): study of qPCR applied to the total quantification of specific microbial genera present in soil or in the root system; analysis of gene expression in soil microorganisms involved in nitrogen fixation.
• Primer design (∼3 hours – theoretical/practical): design of primers to detect specific functions or traits of microorganisms in plant nutrition.
• Next Generation Sequencing (NGS) (∼3 hours): second‑ and third‑generation DNA and RNA sequencing techniques (Illumina and Oxford Nanopore); application of these methods to characterize soil microbial communities.

• Experimental activities (∼6 hours – laboratory): laboratory work focused on extracting microbial DNA from the root system (legume root nodules) and applying qPCR/Real‑Time PCR to the extracted DNA to quantify the microbial communities present.

• Endophytes and seed microbiota (∼1 hour): what endophytic microorganisms are; types of endophytes and their role in growth promotion; notes on endophytic fungi; diversity, phylogeny, and colonization mechanisms of seed endophytes; functions of the seed microbiota.

• Microbial inoculants (∼2 hours): overview of the various types of commercially available microbial inoculants for agricultural and nursery use; basic procedures for their preparation and application. 

• General review for the exam (∼2 hours): comprehensive recap of all topics in preparation for the exam.

Skills acquired in part 2: Understanding of the mechanisms of microorganism-plant interaction and biochemical-molecular techniques for the characterization of microorganisms useful in agriculture.

Activities common to Module 1 and Module 2:

• Seminar on SWEET and RELEAF projects (∼3 hours): applied example of the effect of plant nutrition on attractiveness to pollinating insects (SWEET) and an applied example of circular‑economy approaches to biofertilizer production (RELEAF).

• FOMET seminar (∼3 hours): presentation by a company producing microbial biofertilizers.

• Seminar on biocompost in plant nutrition (∼3 hours): overview of field trials designed to evaluate plant nutrition using biocompost.

The course (Part 1 + Part 2) also includes a visit to a company that produces microbial inoculants and/or biofertilizers.

Readings/Bibliography

V. M. Sellitto, I microrganismi utili in agricoltura. 2020 EDAGRICOLE

G.R. Dixon, E.L. Triston Editors Soil Microbiology and Sustainable Crop Production (2010) Springer

M.T. Madigan, JM Martinko, KS Bender, DH Buckley, DA Stahl BROCK Biologia dei Microrganismi Microbiologia generale. ambientale, industriale.14a Edizione,2016 Casa Editrice Pearson.

Papers provided during classes.

Teaching slides available on Virtuale.

Teaching methods

he course is based on 2 teaching units. Moreover practical activities are provided.

Theoretical teaching units. The student will acquire knowledge on microbiological aspect of plant nutrition.

Practical activities. It will refer to the recent research and applications, in addition an excursion to a company working on the field will be performed. The activities will be conducted in respect to anticovid regulations.

As concerns the teaching methods of this course unit, all students (including all the international incoming exchange students, i.e. ERASMUS) must attend Module 1, 2 online [https://www.unibo.it/it/servizi-e-opportunita/salute-e-assistenza/salute-e-sicurezza/sicurezza-e-salute-nei-luoghi-di-studio-e-tirocinio ], while Module 3 on health and safety is to be attended in class. Information about Module 3 attendance schedule is available on the website of your degree programme ("studiare"--"formazione obbligatoria su sicurezza e salute").

Assessment methods

The learning test for this course is made through a final written examination, carried out together with the module of Microbiology of Nutrition of the integrated course. The written exam is made of 24 multiple choice questions (1 point for each correct answer) and two open answer questions about the two modules of the integrated course (maximum 3 points for each correct answer). You can, on request, sustain the final exam in English.

Teaching tools

The class rooms are equipped with video and overhead projectors, PC and Wi-Fi connection. The teacher will use the slides available with the text book. The practical parts will be performed in laboratories dedicated to this activities.

Office hours

See the website of Diana Di Gioia

See the website of Daniele Alberoni