Environmental biochemistry and microbiology

A.Y. 2020/2021
Overall hours
BIO/10 BIO/19
Learning objectives
The course aims to train the student on the structure, function and interaction of biomolecules, with particular reference to: i) metabolic processes and their regulation mechanisms; ii) information translation mechanisms, from informational molecules to cellular functions; iii) modalities of degradation of complex molecules and energy generation.
Expected learning outcomes
At the end of the course the student will know: i) the general bases of bacterial biochemistry that will be used to understand concepts related to higher cellular mechanisms, ii) the principles relating to the engineering of microorganisms for industrial or bioremediation purposes, ii) the principles related to symbioses and interactions between organisms.
The course will allow the student to acquire competences related to various methodologies and basic instrumentations for biochemical analysis relating to biochemical techniques for monitoring environmental pollutants, energy production and bioremediation.
Course syllabus and organization

Single session

Lesson period
Second semester
The course will be delivered both in presence and in remote.
Lectures will be held both in the classroom (in person) and via videoconference (Teams platform) at the scheduled lecture time.
Students who cannot attend in person may follow lectures online in order to develop the same skills acquired through the activities proposed in the classroom.
Lecture times and all other details will be published on the study program website (https://spa.cdl.unimi.it/it) by the start of the first lecture.
All updates will be communicated directly to students (frequently consult mail@studenti.unimi.it).
It is also important to regularly consult the ARIEL teaching site for all communications relating to the course.
The modality to reserve a place in the classroom will be communicated on the course website.
Course syllabus
-The four molecule classes in the cell (nucleic acids, proteins, carbohydrates and lipids)
-Acid base concept and interactions in organic molecules.
-Proteins: the four structural levels, roles in the cell, enzymes and inhibition, enzyme of interest in environmental research and application
- Glucides and their metabolism, fermentations.
-Lipids and lipid metabolism.
-Nitrogen metabolism
-Biochemical techniques for studying DNA and proteins

Environmental Microbiology
-Short description of the bacterial cell and genome"
---Classification and molecular taxonomy, introduction to Next generation Sequencing
---Cellular functions, metabolic and gene regulatory networks
---DNA replication
---Basic structure of the promoter
---Cell division
---Cell wall, functions and major constituents
---Horizontal gene transfer, plasmids
---small RNAs, with RyhB example on iron omeostasis
---Quorum sensing in Vibrio, Bacillus and Streptococcus species
-Metagenomics an introduction
-Biogeochemical cycles and microorganisms
-Symbiosis Sinorhizobium meliloti/Medicago
-Paper: "Urban metagenomics uncover antibiotic
resistance reservoirs in coastal beach and sewage waters"
-Paper: Bio-augmentation e Bio-remediation "Prospects for harnessing biocide resistance for bioremediation and detoxification"
-Paper: Chromium bio-remediation "Successive use of microorganisms to remove chromium from wastewater"
-Paper: Bioremediation di idrocarburi "Enhanced bioremediation of oil spills in the sea"

the parts preceded by Paper are commented readings of published papers. The indicated title has to be considered a suggestion and could change meanwhile, but not the topic.

All topics will be treated, whenever possible, in an environmental perspective.
Prerequisites for admission
Suggested, Biology
Teaching methods
Lessons supported by projected material. Students will be stimulated to participate actively to the lesson/discussion to improve their skills by analysing the cited literature. We strongly suggest to attend all the lessons.
In case the emergency will last, consider the information written in field "Didattica Fase Emergenziale"
Teaching Resources
Biochemistry: Molecole e metabolismo (Editore Pearson). Autori: Dean R. Appling, Spencer J. Anthony-Cahill and Christopher K. Matthews
- Introduzione alla biochimica di Lehninger (Editore Zanichelli). Autori: Davide L. Nelson, Michael M. Cox.

The preparation of the exam concerning Environmental microbiology can be done without a specific text, in the following I list papers that can help the interested student to go more in deep on some topic.

(Genetica dei procarioti, meccanismi generali) Biologia dei microrganismi (a cura di Dehò-Galli), Casa Editrice Ambrosiana

The following papers will allow the interested student to explore in more detail the themes discussed by the teacher

1. Des Marais DJ. Biogeochemistry of hypersaline microbial mats illustrates the dynamics of modern microbial ecosystems and the early evolution of the biosphere. Biol Bull. 2003;204(2):160-167.
2. Chiu HC, Levy R, Borenstein E. Emergent Biosynthetic Capacity in Simple Microbial Communities. PLoS Comput Biol. 2014;10(7). doi:10.1371/journal.pcbi.1003695.

Antibiotic resistance and the environment
3. Davies J. Are antibiotics naturally antibiotics? J Ind Microbiol Biotechnol. 2006;33(7):496-499.
4. Sengupta S, Chattopadhyay MK, Grossart H-P. The multifaceted roles of antibiotics and antibiotic resistance in nature. Front Microbiol. 2013;4:1-13.
5. Walsh F. Investigating antibiotic resistance in non-clinical environments. Front Microbiol. 2013;4(February):19.

6. Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv. 2017;35(7):845-866.
7. Bilal M, Adeel M, Rasheed T, Zhao Y, Iqbal HMN. Emerging contaminants of high concern and their enzyme-assisted biodegradation - A review. Environ Int. 2019;124:336-353.

8. Thouand G, Durand MJ. Microbial Biosensors for Environmental Applications. In: Chemical Sensors and Biosensors. Hoboken, NJ, USA: John Wiley & Sons, Inc.; 2013:373-407.
9. Van Ginkel SW, Oh S-E, Hassan SHA, Hussein MAM, Abskharon R. Toxicity assessment using different bioassays and microbial biosensors. Environ Int. 2016;92-93:106-118.

Plasmids and Horizontal Gene Transfer
10. Smillie C, Garcillan-Barcia MP, Francia M V., Rocha EPC, de la Cruz F. Mobility of Plasmids. Microbiol Mol Biol Rev. 2010;74(3):434-452.
11. Zhang T, Zhang X-X, Ye L. Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS One. 2011;6(10):e26041.

Metabolic Engineering
12. Gowen C. Model-Guided Systems Metabolic Engineering of Clostridium thermocellum. 2011.
13. Dong X, Quinn PJ, Wang X. Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for the production of l-threonine. Biotechnol Adv. 2011;29(1):11-23.
14. Vogt M, Haas S, Klaffl S, et al. Pushing product formation to its limit: Metabolic engineering of Corynebacterium glutamicum for l-leucine overproduction. Metab Eng. 2014;22:40-52.

Microbial Fuel Cells
15. Trapero JR, Horcajada L, Linares JJ, Lobato J. Is microbial fuel cell technology ready? An economic answer towards industrial commercialization. Appl Energy. 2017;185:698-707.
16. Santoro C, Arbizzani C, Erable B, Ieropoulos I. Microbial fuel cells: From fundamentals to applications. A review. J Power Sources. 2017;356:225-244.

Sensing the environment
17. Keller L, Surette MG. Communication in bacteria: an ecological and evolutionary perspective. Nat Rev. 2006;4:249-258.
18. Marijuán PC, Navarro J, del Moral R. On prokaryotic intelligence: strategies for sensing the environment. Biosystems. 2010;99(2):94-103.
19. Maeda T, García-Contreras R, Pu M, et al. Quorum quenching quandary: resistance to antivirulence compounds. ISME J. 2011;6(3):1-9.
20. Basavaraju M, Sisnity VS, Palaparthy R, Addanki PK. Quorum quenching: Signal jamming in dental plaque biofilms. J Dent Sci. 2016;11(4):349-352. doi:10.1016/j.jds.2016.02.002.

21. Christian N, Masakapalli SK, Pfau T, Ebenhöh O, Sweetlove LJ, Poolman MG. The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. Sci Rep. 2018;8(1):1-11.
22. Bever JD, Platt TG, Morton ER. Microbial Population and Community Dynamics on Plant Roots and Their Feedbacks on Plant Communities. Annu Rev Microbiol. June 2012:265-285.
Assessment methods and Criteria
If the covid-19 emergency will last up to the second semester, examinations will be in written form, online, by using the Moodle platform. As a guide, there will be two partial exams, one for Biochemistry and one for Environmental Microbiology, each structured with a multiple choice test and open questions.
In case the situation will allow exams in presence, the exams will still be written.
Environmental biochemistry
BIO/10 - BIOCHEMISTRY - University credits: 0
BIO/19 - MICROBIOLOGY - University credits: 0
Lessons: 24 hours
Environmental microbioloy
BIO/10 - BIOCHEMISTRY - University credits: 0
BIO/19 - MICROBIOLOGY - University credits: 0
Lessons: 24 hours
Professor: Brilli Matteo