Programme

Introduction to Microorganisms and Fundamental Concepts of Microbial Ecology
Structure and function of the prokaryotic cell; metabolic diversity and adaptation in natural ecosystems. Microbial communities, microbiota, and microbiome. Biogeochemical cycles of carbon, nitrogen, phosphorus, and sulfur. Role of microorganisms in terrestrial and aquatic ecosystems. Interactions between microorganisms, plants, and animals; symbiosis and microbiomes. Effects of environmental disturbances and xenobiotics on microbial communities; ecosystem resilience and resistance. Regulated and emerging environmental contaminants (pesticides, pharmaceuticals, antibiotics, PFAS, microplastics). Processes of biodegradation, biotransformation, bioaugmentation, biostimulation, and plant-assisted bioremediation (phytoremediation). Microbial ecology applied to environmental quality assessment. Principles of ecotoxicology and the use of bioindicator organisms. Reference environmental legislation (Water Framework Directive, Legislative Decree 152/2006, European Watch List). Role of microorganisms in wastewater treatment plants and nature-based solutions (constructed wetlands). Antibiotic resistance in ecosystems and the One Health approach. Electroactive bacteria, microbial fuel cells, and innovative biotechnological applications. Methods for studying microbial communities: cultivation techniques and enrichment cultures. Optical microscopy, epifluorescence, and cell staining. Microbial counting and cell viability assessment. Fluorescence In Situ Hybridization (FISH). PCR, RT-PCR, and qPCR. 16S rRNA gene sequencing, metagenomics, metatranscriptomics, and metaproteomics. Analysis of functional and antibiotic resistance genes. Practical activities: Laboratory exercises regarding the isolation and cultivation of microorganisms from environmental samples, microscopy, assessment of microbial abundance and activity, DNA extraction, and application of microbial ecology methods. A visit to the IRSA-CNR laboratories in Montelibretti is also planned.

Prerequisiti

For a fruitful understanding of the topics covered in the course, it is recommended that students have already assimilated the general concepts of Cell Biology, Genetics, Chemistry, and Biochemistry. In particular, a basic knowledge of prokaryotic cell structure, biological macromolecules (DNA, RNA, proteins), main metabolic pathways, and the core principles of general microbiology is useful. The necessary key concepts will nonetheless be reviewed and recalled during lectures to align the students' foundational knowledge. With reference to the different study pathways, these baseline concepts will allow students to: • Master’s Degree in Molecular, cellular and health biology: more easily follow the in-depth studies on advanced molecular mechanisms and modern culture-independent techniques. • Master’s Degree in Biodiversity and Environmental Protection: better understand the integration of microorganisms into ecological networks and their role in global biogeochemical cycles. • Master’s Degree in Natural and Environmental Sciences: connect general microbiology to the study of ecosystem responses to perturbations and the use of microorganisms as bioindicators.

Core Documentation

Brock, Biology of Microorganisms;
Prescott's Principles of Microbiology (2009), McGraw-Hill

Attendance

Attendance at theoretical lectures is optional, although highly recommended for optimal learning of the subjects' course. On the contrary, given the applied and methodological characteristics of the discipline, attendance at the 3-4 practical sessions, including the one held at the IRSA-CNR laboratories in Montelibretti (RM1 Research Area), is mandatory. • Attendance tracking: In accordance with the Teaching Regulations of the Department of Sciences, attendance will be verified by collecting signatures at the beginning of each session. To obtain validation for the practical component and the right to take the final exam, students must attend at least 2/3 of the practical sessions (equivalent to a minimum of 75% of the total laboratory hours).

Type of evaluation

Assessment of student performance is carried out via an oral exam aimed at verifying knowledge and understanding of the course content, the ability to correlate the different processes regulating microbial ecology and biogeochemical cycles, and autonomy in interpreting scientific evidence. The exam consists of two integrated parts. Individual In-Depth Study: The student will give a short slide-supported presentation focusing on the critical analysis of an international scientific article previously agreed upon with the professor. This first part aims to assess communication skills, the use of appropriate terminology, and the ability to convey advanced knowledge in the field. It can also be taken as an in-course assessment (in itinere) to stimulate active debate and constructive discussion with other students. The presentation is designed to verify the student's ability to independently investigate a scientific topic, select and organize relevant information, link the chosen topic to the contents covered during the course, and communicate it in a clear, concise, and scientifically appropriate manner. Oral Examination on Course Content The presentation is followed by an in-depth oral exam, during which the student answers questions related to the topics covered during theoretical lectures and practical exercises. The oral examination aims to verify knowledge and understanding of the fundamental role played by microorganisms in the evolution and reshaping of natural and anthropogenic environments, the impact of biotic and abiotic factors on microbial communities, and the genomic plasticity of bacteria and archaea. Furthermore, the ability to critically analyze microbial ecology methodologies to estimate the presence and metabolic activity of microorganisms within different environmental matrices (water, soil, sediment) will be assessed. Evaluation Criteria and Final Grade Determination The final grade is expressed out of thirty (up to a maximum of 30/30) and is derived from the combination of the scores from both parts, according to the following percentage weights: • Scientific Article Presentation (PPT): Accounts for 30% of the overall evaluation and allows for a maximum of 9 points. In-depth questions will be asked during the presentation; an outstanding performance, accompanied by relevant answers and an effective visual and conceptual synthesis of the slides, will grant a bonus valid towards achieving honors (lode). • Oral Examination: Focused on verifying the content covered in lectures and exercises, it accounts for the remaining 70% and allows for a maximum of 21 points. Precise and rigorous answers, demonstrating a solid and thorough understanding of the subject, will allow students to aspire to honors (lode). The overall evaluation will take into account: • The correctness and completeness of microbiological and ecological knowledge; • The ability to understand and correlate metabolic biodiversity and global biogeochemical cycles; • The ability to use scientific evidence and microbiological data to formulate reasoned interpretations regarding ecosystem resilience; • The autonomy demonstrated in individual study and critical discussion of international literature, avoiding a purely memorized approach; • The ability to integrate traditional cultivation approaches with modern cultivation-independent molecular and metagenomic techniques; • Clarity of expression, logical rigor, and appropriateness of scientific terminology. To achieve a passing grade, students must demonstrate adequate knowledge of the fundamental concepts of the course and the ability to correctly describe the role of microorganisms as bioindicators and key players in environmental processes. Higher grades will progressively require greater completeness of knowledge, the ability to independently connect different topics, critical interpretation of data, and the ability to clearly and autonomously discuss complex problems related to environmental microbiology. Taken together, the two parts of the examination verify knowledge and understanding, applying knowledge and understanding, making judgments (autonomy of judgment), communication skills, and learning skills.