227.4006 – Marine Microbiology

Semester A

Time: Tuesday- 10-12

Instructor: Dr. Daniel Sher

Office Hours: by appointment

Teaching Assistants & Office Hours: None

Course Type: Lecture & Seminar

Course Level: M.Sc, open to 3rd year B.Sc

Pre-Requisites: Courses in molecular biology, biochemistry, genetics, basic microbiology

Course Overview:
Every milliliter of seawater in the surface ocean contains on the order of one million microorganisms, including the tiny photosynthetic algae that collectively perform about half of the photosynthesis on Earth and form the base of the marine food chain. Understanding the dynamics of how these microbes live and die, and the fluxes of energy and nutrients within the community, is necessary in order to develop predictive models of marine ecosystems, their relationship to global nutrient and carbon cycles, and how they may respond to environmental and climate change. The “marine microbiology” course will discuss major themes in marine microbiology and microbial oceanography through lectures, seminars and discussions. Informed discussion is a key aspect of the course, and the students are required to read a paper or review for every lesson. The papers will be available on the course Moodle website. In addition, every student will present a 45-minutes seminar on a hot topic in marine microbiology during a full “marine microbes day”.

Topics:
1. The weird physics of microbial life in the ocean

2. Phytoplankton I: the tiny primary producers that drive ocean ecosystems

3. The oligotrophic heterotrophs – how do they survive with so little food?

4. Phytoplankton II: Prochlorococcus – connecting genes, physiology and global dynamics

5. Heterotrophic bacteria and how they interact with DOM and POM

6. Is everything everywhere? Temporal and Spatial distributions of microbes in the ocean

7. The nitrogen and sulfur cycles and how they mediate

8. microbial interactions

9. Microbe-Microbe interactions in the Sea

10. Viruses and phage in the oceans: agents of change

11. Summary – putting everything together and a view to the future

 
At the end of the course students will be able to: [Learning Outcomes]
1. Students will gain a broad understanding of the roles of microorganisms in marine

2. Ecosystems, the physiology of these microorganisms and their effect on global biogeochemical cycles.

Requirements:
Attendance in lectures, seminar

Grading:
Seminar – 70%
Participation in discussions – 30%

Website:
None

Reading List:
1. Falkowski, 2012. Nature 483, S17

2. Giovannoni, Annu. Rev. Mar. Sci. 2017. 9:12.1–12.25

3. Biller et al, Nat Rev Micro 2014, doi:10.1038/nrmicro3378

4. Azam and Malfatti, 2007, doi:10.1038/nrmicro1747

5. Omalley, Nature Reviews Microbiology 5, 647–651, 2007

6. Zehr and Kudela, Annu. Rev. Mar. Sci. 2011. 3:197–225

7. Amin, Parker and Armbrust, Microbiol. Mol. Biol. Rev. 2012, 76(3):667.

8. Rodriguez-Valera et al, Nat Rev Micro 7, 828-836, 2009

 

Marine Biology Policy and Management Seminar (227.5002)

Semester B

The course will deal with policy and management related to marine biology. The discussed topics will be selected by the students in the first meeting. Then, each student will find a review paper related to her or his chosen topic and, after my approval, the review will be sent to the class. The lecturer will prepare a 45 min presentation using the review article and additional other papers. In addition, the lecturer will suggest specific subtopics (hats), which will be given to the class in advance. Each student will prepare one subtopic for the discussion using scientific papers or official reports. The success of the seminars will rely on teamwork and student participation in preparing the subtopics and in the discussions.

Requirements: Attendance, discussion preparation, presentation

Grading:
Discussion participation 40%
Presentation 60%
Website: The course program and all review papers will be posted on Moodle

Departmental Seminar – 227.4002
Semester A & B

Time: Thursday 10:00-12:00

Course Type: Seminar

Course Level: M.Sc. Ph.D

Course Overview:

The departmental seminar is a graduate level seminar course which aims to increase the exposure of graduate students to cutting edge research in biology.

Topics:

1. Cell and Molecular Biology
2. Developmental biology
3. Regulation of gene expression
4. Genomic and genetic research
5. Evolution
6. Ecology and ecosystems
7. Coral physiology
8. Biomineralization
9. Photosynthesis
10. Marine Oceanography

At the end of the course students will be able to: [Learning Outcomes]

1. Have an up to date advanced knowledge in the various field in the marine environment
2. Gain the ability to understand the main issues that scientists worldwide are tackling in marine biology.
3. Will have a very wide view of the different aspects of marine biology and ecology,
4. will have the ability to understand all current literature with critical reading.

Requirements: 80% attendance

Website: Moodle

 Instructors: Dr Laura Steindler & Professor Michael D. Krom

Teaching Assistants & Office Hours:  None

Course Type: Lectures

Course Level : Postgraduate

Pre-Requisites: None

Course Overview:

The course is taught by LS and MDK and various members of the Marine Biology staff and outside speakers each teaching their particular expertise. The first part of the course identifies key biogeochemical processes in the global ocean. Where appropriate examples from the Eastern Mediterranean are presented and discussed. The second part of the course is focused on the biology that lies behind the biogeochemistry and provides insights on some of the key players, from micro (photosynthetic bacteria, (photo)heterotrophic bacteria) to macro (tunicates, planktonic cnidarians, ctenophores). The course ends with a lesson on numerical models and their application in biological oceanography.

Topics:

1. Acidification of the global ocean

2. Nutrient cycling in the global system concentrating on the marine system

3. Nutrient limitation in the global ocean

4. Particulate matter in the ocean

5. Use of stable and radioactive isotopes in Marine Biogeochemical systems

6. Physical control on primary production and metabolism

7. Photoheterotrophy in the Sea

8. Selective feeding by benthic and pelagic tunicates (Prof. G. Yahel)

9. Gelatinous zooplankton

10. Numerical models in biological oceanography

At the end of the course students will be able to: [Learning Outcomes]

To understand the key biogeochemical processes which control marine primary and secondary productivity in the global ocean in general and in the eastern Mediterranean in particular. To know who are the key players involved in these processes, from micro to macro.

Requirements : Attendance at course and Exam

Grading: The exam results will be graded from 0-100% with a pass mark of 60%

Website: None

Reading List:

There is no course book or specific reading list. Each lecturer identifies relevant reading (papers, books etc.) during their lecture. This changes from year to year as the course material in updated.