Environmental biochemistry and microbiology

A.Y. 2019/2020
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
Course syllabus
- Molecules in the cell. Structural and functional aspects.
-Nucleic acids: synthesis and structure.
-Proteins: structure, roles in the cell, enzymes and proteosynthesis.
-Glucides and their metabolism, fermentation processes.
- Lipids and their metabolism.
-Nitrogen metabolism.

Environmental microbiology
-Horizontal gene transfer and plasmids: "sharing genes in the bacterial cloud".
-Interactions among organisms: the Sinorhizobium/Medicago symbiosis and nitrogen fization.
-Communication and jamming: "sensing and quenching the quorum signal".
-Antibiotic resistances and environment.
-Energy production with microbial fuel cells, concepts, progress, potential.
- Microorganisms as sensors.
-Microorganisms for the recovery of polluted environments.
-Rational engineering of microorganisms for the production of compounds of interest.
Prerequisites for admission
Suggested, General 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.

Also in this case, the situation imposes that we make changes. Therefore we will erogate the course through video or audio recorded lessons that will then be uploaded on locations accessibile by the student through the Ariel page.
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 part concerning environmental microbiology will mostly refer to the following publications.

(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
First choice was for a written examination, with open questions and multiple choice. However, as it is quite complicated to manage written examination in remote, we communicate that we will perform ORAL examination up to the moment when mobility restrictions will cease. We will advertise examination dates through the standard channels, and we will agree a modality for the examination with the candidates (skype, teams, zoom).
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