Marine Microbial Ecology MEES498/684 Course is taught at the Institute of Marine and Environmental Technology, or the Horns Point Laboratory. Course will also be broadcasted via the Interactive Video Network. Course Instructors: Dr. Feng Chen, IMET, Room 4047. Ph: 410 234 8866. E-mail [email protected] Dr. Sairah Malkin, HPL, AREL Room 134. Ph: 410 221 8418. E-mail: [email protected] Course Description: To become familiar with the diversity, ecology, and biogeochemical roles of Bacteria, Archaea, microbial Eukaryotes, viruses, and fungi in the marine environment. The course will also cover the latest discoveries in molecular microbial ecology. Each main topic will begin with a lecture and will be followed by a paper discussion. For the paper discussions, each student will present selected papers specified in the syllabus (or by consensus with the course instructors). Students will also participate in class discussions. Class Schedule: Classes are taught over IVN and are held at 10-11:30 Tuesday and Thursday in IMET 2041 or HPL Coastal Classroom. Dates for student presentations and assignments are given in the syllabus Expected Learning Outcomes: 1. Students will become familiar with marine microorganisms, their biogeochemical activities and energetic constraints, and their ecological roles in marine environments through lectures and from reading and discussion of primary scientific literature and published reviews. 2. Students will be introduced to widely used techniques in marine microbiology through 2 hands-on laboratory sessions focusing on (1) visualizing marine microbial communities and (2) using gene sequence data to infer microbial phylogeny and ecophysiology. 3. Students will demonstrate mastery of course material by leading class discussions of primary literature, participation in class discussions, through preparation of a formal synthesis paper in which a single topic is covered in depth, and two exams. Every opportunity will be provided for all students to actively participate in the discussion and students are strongly encouraged to comment on strengths and weaknesses of the papers discussed in this class. 1 Grading: Class participation 10% Paper presentations 20% Term paper 30% Exam I 20% Exam II 20% Paper Presentation: Each week, a student will present a seminar on one or two papers on a related topic. Paper assignments will be determined in the first week of class (papers are listed in course reading material below). The presentation will include a general introduction to the topic covered, a detailed explanation of the methods employed in the paper, detailed examination of the results described in the papers, discussion of the significance of the work, and a critique of the strengths and weaknesses of the papers. The presenting student should cover background material and additional details of methods by doing supplementary reading as necessary. All students are expected to read all discussion papers and to participate in class discussion on the topic. Term paper: Identify and review an open debate or controversy relevant to marine microbiology (maximum 1500 words, excluding references). The topic should be chosen by the student in discussion with a course instructor. (e.g., (1) What is the source of the surface ocean methane maximum? (2) Is the marine nitrogen cycle in balance?) At least 5 papers related to the topic (in addition to the two papers already covered in the class) should be carefully read and synthesized. Students should consider what is exciting and novel about the research and make clear how the papers advance our understanding of the topic. We are looking for an integrated understanding of the topic, rather than a summary of five individual papers. Your review should also identify what important questions still need to be answered. There will be three steps in the development of your term paper. The topic should be identified during the first month of class, by Mar 1, 2018, in discussion with a course instructor. By Mar 15, 2018, an annotated bibliography will be submitted to the course instructor. The bibliography will present 5 key references, and a short paragraph (4-5 sentences) describing the content of the reference. The final paper is due 19 April, 2018. The term paper is mandatory, and must be completed at the scheduled time, subject to standard university guidelines. Makeup assignments as allowed by the University must be requested (in writing) within one week of the missed assignment. Course Evaluation At the end of the course, students are strongly encouraged to complete the on-line process facilitated by the MEES Graduate Program to provide anonymous feedback to the instructors on our course. This feedback is extremely valuable for planning and preparing future classes. Time will be allocated at the end of the course for a general discussion led by students for improving the course in future years. 2 Course Schedule (at a glance) Week Topic Date Reading Activities/Due Dates 1 Course Introduction Th Jan 25 Introduction to marine microbial Tu Jan 30 Background 2 ecology Th Feb 1 Lab activities at IMET Protists, dinoflagellates and Tu Feb 6 Background 3 phytoplankton Th Feb 8 Discussion papers Photosynthetic and phototrophic Tu Feb 13 Background 4 bacteria Th Feb 15 Discussion papers Heterotrophic bacteria, archaea, and Tu Feb 20 Background 5 important groups of bacteria Tu Feb 22 Discussion papers Marine viruses and their ecological Tu Feb 27 Background 6 role Th Mar 1 Discussion papers Term Paper topics selected Tu Mar 6 Background Diversity and function of microbes, 7 Hands on lab (IMET); molecular tools Th Mar 8 Annotated bibliography due Genomics and environmental Tu Mar 13 Background reading First exam; take-home 8 genomics Th Mar 15 Discussion papers 9 spring break – Mar 18-25 Marine N cycle – aerobic processes Tu Mar 27 Background 10 (N-fixation, nitrification) Th Mar 29 Discussion papers Marine N cycle – anaerobic processes Tu Apr 3 Background 11 (denitrification, anammox, DNRA) Th Apr 5 Discussion papers Metal oxide respiration (Fe, Mn, Tu Apr 10 Background 12 electrodes) and Iron Cycling Th Apr 12 Discussion papers Marine S cycle – Sulfate reduction, S Tu Apr 17 Background reading 13 oxidation, disproportionation Th Apr 19 Discussion papers Term Papers due Marine CH cycle – methanogenesis, Tu Apr 24 Background reading 14 4 aerobic and anaerobic oxidation Th Apr 26 Discussion papers Biofilms, Life on particles, Tu May 1 Background reading 15 phytoplankton-bacterial interactions Th May 3 Discussion papers Final exam (non- Hydrocarbon oxidation (aerobic Tu May 8 Background reading 16 cumulative; take home) and anaerobic) Th May 10 Discussion papers 3 Topics and Reading List Course 1st half (Chen) Weeks 1 and 2: Introduction to marine microbial ecology Topics: history of microbial ecology, great plate count anomaly, types of microbes; microbial loop. Required background reading: Kirchman 2008. Introduction and overview (Chapter 1, Microbial Ecology of the Oceans, ed. David Kirchman 2008). Sherr and Sherr 2008. Understanding roles of microbes in marine pelagic food webs: a brief history (Chapter 2, Microbial Ecology of the Oceans, ed. David Kirchman 2008); Fenchel T (2008); The microbial loop – 25 years later. Journal of Experimental Marine Biology and Ecology. 366: 99–103 2nd class, hands-on practice, meet in person at IMET Sample collection, filtration, nucleic acid staining of microbes, epifluorescent microscopy, visualization and enumeration of microbes, image processing Week 3: Protists, dinoflagellates and phytoplankton Topics: Protist grazing, phytoplankton, harmful algal blooms, picoeukaryotes Required background reading: Jurgens and Massana 2008. Protisan grazing on marine bacterioplankton (Chapter 11, Microbial Ecology of the Oceans, ed. David Kirchman 2008). Worden and Not. 2008. Ecology and diversity of picoeukaryotes (Chapter 6, Microbial Ecology of the Oceans, ed. David Kirchman 2008). Hallegraeff 2003. Harmful algal blooms: a global overview, pp. 25–49. In: Hallegraeff, G. M., Anderson, D. M., Cembella, A. D.; Enevoldsen, H.O. (ed.) Manual on Harmful Marine Microalgae. UMESCO. Discussion papers: (1) Caron et al. 2017. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat. Rev. Microbiol. 15:6-20. (long paper) (2) Banguera-Hinestroza et al. 2016. Seasonality and toxin production of Pyrodinium bahamense in a Red Sea lagoon. Harmful Algae 55: 163–171 Week 4: Photosynthetic and phototrophic bacteria Topics: cyanobacteria, picocyanobacteria, AAnP and proteorhodopsin-containing prokaryotes. Required background reading: Beja and Suzuki, 2008. Photoheterotrophic marine prokaryotes (Chapter 5, Microbial Ecology of the Oceans, ed. David Kirchman 2008). Discussion papers: (1) Yelton et al. 2016. Global genetic capacity for mixotrophy in marine picocyanobacteria. ISME Journal 10: 2946-2957 (2) Ferrera. et al. 2017. Light enhances the growth rates of natural populations of aerobic anoxygenic phototrophic bacteria. ISME Journal doi: 10.1038/ismej.2017.79 (Short communication) 4 Week 5: Heterotrophic bacteria, archaea, and important groups of bacteria Topics: Classically culturable bacteria, sea water culturable bacteria, not yet culturable bacteria, marine archaea. Required background reading: Fuhrman and Hagstrom 2008. Bacterial and archaeal community structure and its patterns (Chapter 3, Microbial Ecology of the Oceans, ed. David Kirchman 2008) Discussion paper: (1) Gionannoni et al. 2017. SAR11 bacteria: the most abundant plankton