Special Topics in Environmental Microbiology

Sylllabus

1. Microbial consortia and their role in the environment. How we study them and what we know about them.
2. Plasmids and horizontal gene transfer: their role in the functioning of natural and artificial ecosystems. What metagenomics teaches us.
3. Natural microbial toxins: Which microbes they produce them and why? Biosynthetic pathways and biotechnological exploitation.
4. Cyanobacteria and Microcystins: genetic background and environmental impact.
5. Protozoa: their ecological role and interactions with other microorganisms microorganisms in the food chain.
6. The microbiome of insects, plants and animals: their role, interactions with the environment and biotechnological exploitation.
7. Microbial antibiotics resistance: Mechanisms, environmental dispersal and mitigation measures
8. Microbial degradation of antibiotics and other pharmaceutical substances – environmental implications and biotechnological exploitation.
9. Omic methods in the study of the function and ecological role of microorganisms in the environment.

Student performance evaluation

Student evaluation focuses on the evaluation of the theoretical knowledge acquired by students in the context of the lectures. Thus, the performance in the course is evaluated by written exams at the end of the semester (50%) and by submission and presentation of work upon completion of the course deliveries (50%). Assignments are assigned only to students who have attended more than 70% of the lectures. Students are notified online (eclass platform) of the list of project topics, four weeks before the end of the semester. Students are then asked to choose one of the proposed topics which they present both in writing and orally. The presentations take place in the context of the last lecture of the course and the students at the end of the presentation are asked to answer questions from the instructor in order to evaluate the degree of understanding and deepening by the students. The assignments are individual and the grading criteria are a) quality of presentation (30%), b) understanding of the problem and the theoretical background (40%), c) response to questions and in-depth analysis (30%). Students who do not attend the course lectures or have attended and participated in less than 70% of the lectures are examined only through written exams (100%) at the end of the semester.

Suggested bibliography

The exact content of the course is not fully covered by any of the currently available Greek textbooks and for this reason textbooks are listed that partially cover the material of the course.

Manuscripts:

• Madigan M.T., Martinko J.M., Parker J. 2005. Brock: Biology of microorganisms. Volume II,
  Crete University Press

Indicative journal articles:

• Luo et al. (2016) Diverse gene functions in a soil mobilome. Soil Biology and Biochemistry 101: 175-183
• Kikuchi et al., (2016) Symbiont-mediated insecticide resistance. PNAS 109 (22): 8618-8622
• Cavaliere et al., (2018) Cooperation in microbial communities and their biotechnological applications. Environmental Microbiology doi:10.1111/1462-2920.13767
• Albers et al., (2018) Catabolic task division between two near-isogenic subpopulations co-existing in a herbicide-degrading bacterial consortium: consequences for the interspecies consortium metabolic model. Environmental Microbiology 20:85-96
• Aleklett et al., (2018) Build your own soil: exploring microfluidics to create microbial habitat structures. The ISME Journal 12: 312-319
• Allison SD and Martiny JBH (2008) Resistance, resilience and redundancy in microbial communities. PNAS 105: 11512-11519

Teaching Material / E-class

https://eclass.uth.gr/courses/BIO_U_130/