Learning outcomes of the course unit
Students will understand the most important aspects of microbial metabolism for the purification and remediation of contaminated sites, along with the bioremediation technologies and how they are applied. They will be able to understand a technical report and a remediation project. They will be able to critically read a scientific article that deals with the role of microorganisms in remediation processes and evaluate the applicability of the proposed technologies to solve pollution problems.
Microbiology and microbial metabolism.
Course contents summary
“Bioremediation” is a technology increasingly used for the remediation of contaminated sites. This teaching deals with the role that microorganisms play in managing environmental pollution problems. In the first part of the course, students will be introduced to the different metabolic capacities of microorganisms compared to the major environmental pollutants and how these capacities can be used to solve water and soil contamination problems. They will also be introduced to the consultation of specific databases that collect information on all the catabolic pathways characterized to date relating to different microorganisms and different contaminants. In the second part, the main bioremediation technologies will be illustrated, case studies will be discussed and applications of the theoretical knowledge acquired will be illustrated. In the last part of the course, the taxonomic and functional investigation methodologies of microbial populations will be explored.
The bacterial cell: main cellular structures and interaction of the cell with the environment, microbial metabolism, the role of the metabolic diversity of microorganisms in bioremediation, the regulation of metabolism in response to environmental stimuli.
Environmental microbiology: Microbial ecology and dynamics of microbial communities, microorganism-microorganism and microorganism-environment interactions, the biosphere and sampling methods for the study of environmental microbial communities.
Bioremediation: Introduction to Bioremediation and concepts of recalcitrant compounds, xenobiotic, biomagnification, bioaccumulation, biodegradation, mineralization, biotransformation, types of contamination. Phenomenon of natural attenuation, monitoring of natural attenuation, bioremediation. Biodegradation of organic contaminants: Aerobic biodegradation of alkanes, aerobic biodegradation of aromatic hydrocarbons, anaerobic biodegradation of aliphatic and aromatic hydrocarbons, biodegradation of halogenated compounds. Heavy metals bioremediation, radionuclide bioremediation, anammox bacteria and their applications, Enhanced biological phosphorus removal (EPBR). DL152-2006 and sites of national interest, introduction to in situ and ex situ bioremediation techniques and their microbiological monitoring.
Methods of analysis: Methods of sampling and classical microbiological analysis of environmental samples, molecular methods of characterization of microbial communities. DNA sequencing, next-generation DNA sequencers based on short and long reads, in situ sequencing. Microbial bioinformatics, sequence databases, functional / metabolic databases, culturomics associated with genomics for the functional characterization of microorganisms. Comparative genomics as an investigation tool for identifying common or unique characteristics of a phylogenetic clade, phylogenetic investigations. Metagenomic analyzes based on the use of amplicon-based and shotgun-based approaches for the study of the taxonomic composition of complex populations. Shotgun-based metagenomic approaches for the metabolic-functional characterization of complex populations, transcriptomics and metatranscriptomics, metabolomics.
Computer lab: How to operationally work with genomes and sequence databases, phylogenomics, the search for metabolic characteristics in bacterial genomes. How to operationally work with metagenomic data: amplicon-based profiling, shotgun metagenomics data for taxonomic and functional investigations, basic statistics.
Group work: Discussion of case studies related to applications of bioremediation technologies with evaluation of the microbial populations using classical and molecular methods. Discussion of case studies related to applications of bioremediation technologies with evaluation of the microbial populations through metagenomic methods. Meta-analysis and integration of data from metagenomic investigations of different studies.
Barbieri, Bestetti, Galli e Zannoni, "Microbiologia ambientale ed elementi di ecologia microbica"(2008) Casa Editrice Ambrosiana Martin Alexander “Biodegradation and Bioremediation” (1999) 2nd Ed. Academic Press. Some chapters of these texts were a source of information to elaborate the didactic material (slides) shown in class. This material is updated every year in the light of new knowledge, while the basic notions remain substantially unchanged. The updated slides will be made available on the Elly platform after the lessons. For non-attending students, the study of the slides must be integrated with the study of the suggested texts because the information they contain is quite schematic and is developed during the lessons and with the discussion of case studies. The articles discussed will be made available on the Elly platform. Students, in particular non-attending students, are reminded to check the didactic material available and the information provided by the teacher through the Elly platform.
Lectures will alternate with collective discussions of specific problems. Students will be asked to prepare seminars on articles chosen from the bibliographic databases (among the most recent). Practical data analysis lessons will also be performed.
Assessment methods and criteria
The exam will be oral and will verify that the students knows the topics covered in the program, knows how to explain and discuss them and knows how to connect the various, biochemical-molecular, technological, regulatory aspects related to the different types of pollution. Learning of data analysis methodologies will also be verified.