Bioremediation

A.Y. 2024/2025
15
Max ECTS
168
Overall hours
SSD
AGR/13 AGR/16 CHIM/06
Language
English
Learning objectives
The course aims to provide the students with the elements to know, understand, measure and remediate, using plants and microorganisms, organic and inorganic contamination in different environmental compartments (water, air, soil, plants).
The course is organised as an interdisciplinary laboratory, in which professors from different disciplines (environmental chemistry, environmental microbiology, and plant physiology) guide students in carrying out a project based on a real case study by integrating lectures, fieldwork, laboratory work, and data analysis.
This laboratory gives students the possibility, while learning specific concepts and skills related to bioremediation, to acquire transversal skills, such as working in a group, discussing results, communicating concepts, and critically evaluating and using literature sources.
Expected learning outcomes
At the end of the course, the student should:
· know and understand the causes of environmental contamination;
· know, understand and use the main methods to determine the distribution of organic and inorganic contaminations in different environmental compartments (water, air, soil, plants);
· know, understand and utilize analytical techniques for environmental monitoring;
· know and understand the role of plants and microorganisms in environmental processes and bioremediation, and the main bioremediation techniques;
· be able to propose a bioremediation plan;
· be able to apply statistical analysis of environmental data.
· be able to frame the contamination cases in terms of the environmental legislation in force.
Students will acquire practical skills in the use of analytical instruments for the quantification of: organic and inorganic compounds, microflora connected to environmental processes, physiological state of plants.
Students will also be able to independently evaluate methods to monitor and analyse contamination problems, and to evaluate the remediation interventions needed.
They will also be able to independently find and evaluate literature sources about bioremediation to update their knowledge.
Students will develop soft skills such as public speech, teamwork, and critical discussion of scientific data.
The skills acquired in environmental remediation, waste treatment and material recovery technologies will allow students to interact with professionals working in the environmental restoration sector.
The students will come into contact with external stakeholders thanks to the organization of seminars with environmental management experts, and they will develop communication skills thanks to the application of flipped learning methods.
Single course

This course can be attended as a single course.

Course syllabus and organization

Single session

Responsible
Lesson period
First semester
Prerequisites for admission
Basic knowledge of chemistry and biology.
Assessment methods and Criteria
Verification method: final discussion of the environmental bioremediation project considered, via power point presentation of the group work.
Evaluation criteria: i) knowledge of the basic notions provided during lectures; ii) ability to discuss the experimental results obtained; iii) communicate the information present in the scientific literature; iv) knowing how to work in a team.
Students with SLD or disability certifications are kindly requested to contact the teacher at least 15 days before the date of the exam session to agree on individual exam requirements. In the email please make sure to add in cc the competent offices: [email protected] (for students with SLD) o [email protected] (for students with disability).
Environmental microbiology and phytoremediation
Course syllabus
ENVIRONMENTAL MICROBIOLOGY
- Frontal lectures (2.75 CFU):
1. Course overview. Notes on environmental legislation. Microbiological sampling. Characterization and monitoring of microbial communities in soil and water: cell count methods on specific pollutants, enrichment cultures, microcosms. Environmental genomics: polymerase chain reaction (PCR), quantitative Real Time PCR, clone libraries, Sanger sequencing, Illumina sequencing. (6 hours)
2. Biodegradation of organic pollutants and genetics: monoaromatic hydrocarbons, polycyclic aromatic hydrocarbons (PAH), aliphatic compounds. Reductive dehalogenation of chlorinated solvents in groundwater. Bacterial resistance and metabolism of heavy metals and Arsenic. Microbial life in extreme environments: the acid mine drainage. (8 hours)
3. Bioremediation approaches of contaminated soil and water. Real-cases of biorestoration interventions. Rhizosphere and endosphere microbiology: plant growth promoting bacteria useful in phytoremediation processes (rhizo-degradation, metal translocation). Microbial electrochemical systems: electroactive bacteria, microbial fuel cells. (8 hours)
- Flipped learning classes (0.25 CFU): levering basic microbiology knowledge.
- Practical activities (2 CFU):
1. Educational trips: overview of the contaminated site under investigation and environmental contest, microbiological sampling, registration and conservation of samples. (0.5 CFU)
2. Microbiology laboratory: safety rules in microbiology laboratories. Preparation and conservation of samples for microbiological and molecular analysis. Total aerobic, anaerobic bacterial plate count, MPN count of pollutant degrading bacteria. Phenotypic characterization of bacterial isolates: resistance to heavy metals and arsenic, mineralization of organic pollutants, plant growth promotion (siderophores, IAA, EPS, phosphate solubilisation, ACC deaminase, mobility). DNA extraction from environmental samples. Preparation of polymerase chain reaction (PCR) and quantitative PCR (qPCR): 16S rRNA and functional genes. Electrophoresis run on agarose gel. (1.125 CFU)
3. Bioinformatic laboratories and team working: scientific literature search and preparation of scientific reports also by using AI chatbot tools. Calculations and statistical data processing. Experimental data analysis and discussion. Analysis of nucleotide sequences. (0.25 CFU)
4. Seminars: seminars are held by private companies involved in bioremediation activities, by public bodies involved in environmental monitoring and managing and by scientists working on environmental microbiology. (0.125 CFU)


PHYTOREMEDIATION
Frontal lectures (2.75 CFU):
1. Course overview, plant physiology recap. (4 hours)
2. Introduction to Phytoremediation, advantages and limitations, types and processes. Natural hyperaccumulator plants for metals and their limitations. (2 hours)
3. Phytoremediation of organic pollutants: chlorinated solvents and/or pesticides, etc. Toxicity of organic pollutants and environmental impact; plant processes (physiological and biochemical mechanisms) involved in phytoremediation of various organic pollutants. (2 hours)
4. Phytoremediation of Inorganic pollutants, i.e., heavy metals, metalloids, etc. Toxicity of inorganic pollutants and environmental impact; plant processes (physiological and biochemical mechanisms) involved in phytoremediation of various Organic pollutants. (2 hours)
5. Case studies: discussion and an overview. (2 hours)
6. Phytoremediation strategies: i.e., site assessment, plant species for phytoremediation, soil amendments, etc. (2 hours)
7. Phytomining: using plants to mine precious metals like gold and silver and stabilize abandoned gold mine sites. (2 hours)
8. Metabolomics techniques for studying plant stress: from sample extraction to data analysis. (8 hours)
Practical activities (2 CFU):
- Educational trip: overview of the contaminated site under investigation and environmental contest, soil, water and plant sampling, registration and conservation of samples. (0.25 CFU)
- Phytoremediation laboratory: 1) Plant growth and treatment; 2) Monitoring of Chlorophyll a fluorescence and other physiological parameters; 3) Metabolome extraction and derivatization; 4) GC-MS-driven metabolomic analysis. (1.375 CFU)
- Bioinformatic laboratories and team working: scientific literature search and preparation of scientific reports also by using AI chatbot tools. Calculations and statistical data processing. Experimental data analysis and discussion. (0.25 CFU)
-Seminars: seminars are held by scientists working on phytoremediation. (0.125 CFU)
Teaching methods
Attending students:
- Frontal lectures (5.5 CFU)
- Flipped learning classes (0.5 CFU)
- Educational trips (0.75 CFU)
- Microbiology and phytoremediation practical activities (2.5 CFU)
- Bioinformatic laboratories and team working (0.5 CFU)
- Seminars (0.25 CFU).

NOT attending students:
- Independent study of the topics covered in frontal lessons (5.5 CFU)
- Flipped learning on topics chosen in accordance with the professors (0.5 CFU)
- Analysis of real cases of contamination and bioremediation approaches related to field activities (2 CFU)
- Independent study of methods used in microbiology and phytoremediation laboratories (1.25 CFU)
- Bioinformatic laboratories and considerations of real cases of bioremediation interventions via Microsoft Teams (0.5 CFU)
- Seminars via Microsoft Teams or recordered (0.25 CFU).

Attendance is encouraged, but not compulsory.
At the beginning of the course, NOT attending students MUST fix an appointment with Prof. Lucia Cavalca (Environmental Microbiology) and Prof. Fabrizio Araniti (Phytoremediation) to assess independent study and practical activities.
Teaching Resources
- Slides of lectures on the MyAriel site of the course
- Scientific papers and review articles uploaded on the MyAriel site of the course and provided by professors
- Practical classes notes
- Links to useful online resources.

TEXT BOOKS
Some of the information given during the course can be found in the following textbooks available in the UNIMI Library link https://unimi.primo.exlibrisgroup.com/discovery/search?vid=39UMI_INST:VU1&lang=en.

Environmental Microbiology:
- M.T. Madigan, J.M. Martinko, K.S. Bender, D.H. Buckley, D.A. Stahl. Brock - Biology of microorganisms, 2016, Ed. Pearson.
- M.T. Madigan, J.M. Martinko, K.S. Bender, D.H. Buckley, D.A. Stahl. Brock - Biologia dei Microrganismi, 2022, Ed. Pearson.
- B. Biavati e C. Sorlini. Microbiologia Agroambientale, Casa Editrice Ambrosiana.
- B. Biavati e C. Sorlini. Microbiologia Generale e Agraria, Casa Editrice Ambrosiana.

Phytoremediation:
1) Lee Newman, Abid Ali Ansari, Sarvajeet Singh Gill, M. Naeem, Ritu Gill - Phytoremediation Management of Environmental Contaminants, Volume 7
ISBN : 3-031-17988-9
ISBN : 9783031179877
2) Norman Terry, Gary S. Banuelos - Phytoremediation of Contaminated Soil and Water
DOI: https://doi.org/10.1201/9780367803148
ISBN: 9780367803148
3) Cuypers, Ann, editor.; Vangronsveld, Jaco, editor. - Phytoremediation - ISBN: 978-0-12-802853-7
4) Steven C. McCutcheon, Jerald L. Schnoor - Phytoremediation: Transformation and Control of Contaminants
ISBN:9780471273042
DOI:10.1002/047127304X
Environmental chemistry
Course syllabus
Frontal lessons (3 CFU):
1. Course overview. Units of measurement, equivalences used in the environmental field. Heavy metals: chemistry and notes on toxicology. Sampling: planning of sampling depending on the environmental sector and the aims of the investigation. Sample collection methods, storage and average life of the samples. (8 hours)
2. Hydrocarbons. The four categories of hydrocarbon pollutants: alkanes, alkenes, alkynes and aromatic hydrocarbons. (8 hours)
3. Spectroscopic methods of analysis: UV-Vis, theory, applications, calibration line. Nuclear Magnetic Resonance (NMR): theory, chemical shift, quadrupolar nuclei, coupling constants. NMR of nuclei other than H and C. (4 hours)
4. Mass spectrometry: theory, instrumentation, applicability. Quadrupole and ICP-MS. Chromatography: theory of chromatographic separation, use of GC and HPLC in the environmental field. (4 hours)
Practical activities (2 CFU):
- Educational trip: Sampling at the study site. (0.25 CFU)
- Practical laboratory: Safety in the Chemistry Laboratory. Sample treatment, extraction, separation and quantification via UV-Vis, HPLC, GC and GC-MS of organic pollutants. Analysis of the results. Mineralization of samples and analysis via ICP-MS for the determination of heavy metals and other elements of environmental interest. Analysis of the results. Use of NMR in the environmental field, acquisition of spectra of organic pollutants. (1.375 CFU)
- Team working: Data analysis and discussion. Drafting of the final report. (0.25 CFU)
- Seminars: seminars are held by scientists working on phytoremediation. (0.125 CFU)
Teaching methods
Attending students:
- Frontal lectures (2.75 CFU)
- Flipped learning classes (0.25 CFU)
- Educational trips (0.25 CFU)
- Chemistry laboratory (1.375 CFU)
- Data analysis and team working (0.25 CFU)
- Seminars (0.125 CFU).

NOT attending students:
- Independent study of the topics covered in frontal lessons (2.75 CFU)
- Flipped learning on topics chosen in accordance with the professor (0.25 CFU)
- Analysis of real cases of chemical contamination related to field activities (1 CFU)
- Independent study of methods used in analytical laboratory (0.625 CFU)
- Considerations of real cases of bioremediation interventions via Microsoft Teams (0.25 CFU)
- Seminars via Microsoft Teams or recorded (0.125 CFU).

Attendance is encouraged, but not compulsory.
At the beginning of the course, NOT attending students MUST fix an appointment with Prof. Michail Christodoulou to assess independent study and practical activities.
Teaching Resources
- Slides of lectures on the MyAriel site of the course
- Scientific papers and review articles uploaded on the MyAriel site of the course and provided by the professor
- Practical classes notes
- Links to useful online resources.

TEXT BOOKS:
Some of the information given during the course can be found in the following textbooks available in the UNIMI Library link https://unimi.primo.exlibrisgroup.com/discovery/search?vid=39UMI_INST:VU1&lang=en.
· Introduction to Organic Chemistry, Brown and Poon
· Essential Organic Chemistry, Bruice
· Fundamentals of Analytical Chemistry, Scoog and West
· Spectroscopic methods in organic chemistry, Hesse, Meier and Zeeh.
Environmental chemistry
CHIM/06 - ORGANIC CHEMISTRY - University credits: 5
Field activity: 4 hours
Practicals: 6 hours
Laboratories: 22 hours
Lessons: 24 hours
Shifts:
Turno
Professor: Christodoulou Michail
Environmental microbiology and phytoremediation
AGR/13 - AGRICULTURAL CHEMISTRY - University credits: 5
AGR/16 - AGRICULTURAL MICROBIOLOGY - University credits: 5
Field activity: 8 hours
Practicals: 12 hours
Laboratories: 44 hours
Lessons: 48 hours
Shifts:
Turno
Professors: Araniti Fabrizio, Cavalca Lucia
Educational website(s)
Professor(s)
Reception:
Every day by appointment via phone or email
Office (building 21090) at the "Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia"
Reception:
By appointment
DEFENS-Environmental Microbiology, Via Mangiagalli 25, 3rd floor