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Home , Marine prokaryotes

Marine 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 , , microbial , , 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 , 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 through 2 hands-on laboratory sessions focusing on (1) visualizing marine microbial communities and (2) using 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.

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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 maximum? (2) Is the marine 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.

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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 , and Tu Feb 6 Background 3 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 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 (, 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 , 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

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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; . Required background reading: Kirchman 2008. Introduction and overview (Chapter 1, Microbial Ecology of the , 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 and Ecology. 366: 99–103 2nd class, hands-on practice, meet in person at IMET Sample collection, filtration, of microbes, epifluorescent microscopy, visualization and enumeration of microbes, image processing

Week 3: Protists, dinoflagellates and phytoplankton Topics: grazing, phytoplankton, harmful algal blooms, Required background reading: Jurgens and Massana 2008. Protisan grazing on marine (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 . UMESCO. Discussion papers: (1) Caron et al. 2017. Probing the , ecology and physiology of 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 . Harmful Algae 55: 163–171

Week 4: Photosynthetic and phototrophic bacteria Topics: , picocyanobacteria, AAnP and proteorhodopsin-containing . Required background reading: Beja and Suzuki, 2008. Photoheterotrophic (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)

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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 in the oceans. Annu. Rev. Mar. Sci. 9:231–55 (long paper)

Week 6: Marine viruses and their ecological role Topics: virioplankton, , algal viruses, giant viruses Required background reading: Marine viruses: community dynamics, diversity and impact on microbial processes (Chapter 12, Microbial Ecology of the Oceans, ed. David Kirchman 2008). Wommack and Colwell. 2000. Virioplankton: Viruses in aquatic . Microbiol. Mol. Biol. Rev. 64:69-114 Discussion papers: (1) Wilson et al. 2017. Genomic exploration of individual giant ocean viruses. ISME Journal. doi:10.1038/ismej.2017.61 (2) Philosof et al. 2017. Novel abundant oceanic viruses of uncultured marine group II . Current Biology 27: 1362–1368

Week 7: Diversity and function of microbes, molecular tools Topics: PCR, sequencing, phylogenetic analysis, single cell technology, basic bioinformatics Required background reading: Fuhrman and Hagstrom 2008. Bacterial and archaeal community structure and its patterns; Worden and Not. 2008. Ecology and diversity of picoeukaryotes (Chapter 3 and 6, Microbial Ecology of the Oceans, ed. David Kirchman 2008). Hands-on practice: sequence blast search and multiple sequence alignment, and phylogenetic analysis

Week 8: Genomics and environmental genomics Topics: genomics, transcriptomics, proteomics, meta- Required background reading: Moran 2008. Genomics and of marine prokaryotes (Chapter 4, Microbial Ecology of the Oceans, ed. David Kirchman 2008). Haroon 2013. In-solution fluorescence in situ hybridization and fluorescence activated cell sorting for single cell and population genome recovery, pp. 3- 19. In Microbial Metagenomics, Metatranscriptomics, and Metaproteomics DeLong, E. F (ed). Methods in Enzymology Volume 531, Pages 2-598 Discussion papers: (1) Stec et al. 2017. Modelling plankton ecosystems in the meta-omics era. Are we ready? Marine Genomics 32:1-7. (2) Haggerty and Dinsdale 2017. Distinct biogeographical patterns of marine bacterial and functional . Global Ecology and Biogeography 26: 177–190. 5

Week 9: Spring break Week 10: Marine N cycle – aerobic processes (N-fixation, nitrification) Topics: distribution of nitrogen phases in the ocean; bioenergetics of N-fixation; diversity and ecology of N- fixing bacteria, pathways and bioenergetics of chemoautotrophic nitrification Required background reading: Zehr and Pearl. 2008. Molecular ecological aspects of N-fixation in the marine environment (Chapter 13 in Kirchman, ed). Discussion Papers (2 of these will be chosen by class): (1) Grosskopf et al. 2012. Doubling of marine dinitrogen–fixation rates based on direct measurements. 488:361; (2) Farnelid et al. 2016. New insights into the ecology of the globally significant uncultured nitrogen-fixing symbiont UCYN-A. Aquatic Microbial Ecology. 77: 125-138. (3) Daims et al. 2015. Complete nitrification by Nitrospira bacteria. Nature 528: 524-

Week 11: Marine N cycle – anaerobic processes (denitrification, anammox, DNRA) Topics: pathways of N loss from anaerobic and low O2 environments (i.e,. minimum zones and sediments) Required background reading: Thamdrup and Dalsgaard 2008. N cycling in Sediments (Chapter 14 in Kirchman, ed); pp 527 Discussion Papers (1 and 2 paired): (1) Canion et al. 2014. Temperature response of denitrification and anammox reveals the adaptation of microbial communities to in situ temperatures in permeable marine sediments that span 50◦ in latitude. Biogeosciences 11: 309-320 (2) Brin et al. 2016. Similar temperature responses suggest future climate warming will not alter partitioning between denitrification and anammox in temperate marine sediments. Glob. Change Biol. 23: 331-340 (3) Ulloa et al. 2012. Microbial oceanography of anoxic oxygen minimum zones. PNAS 109: 15996–16003

Week 12: Metal oxide respiration (Fe, Mn, electrodes) and Iron Cycling Topics: respiring solid phase metals (Fe, Mn); mechanisms of external electron transport (nanowires); and biotechnology applications; iron (II) reoxidation Required background reading: Lovley 2012. Electromicrobiology. Ann. Rev. Microbiol. 66: 391-409 Optional background reading: Nealson and Rowe 2016. Electromicrobiology: realities, grand challenges, goals and predictions. Microbial. Biotech. 9: 595-560. – and – Richter et al. Dissimilatory Reduction of Extracellular Electron Acceptors in Anaerobic Respiration 2012. Appl. Environ. Microbiol. 78: 913-921 Discussion Papers: (1) Summers et al. 2010. Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria. Science 330: 1413-1415 (*plus supplemental material) (2) McBeth, Fleming, and Emerson 2013. The transition from freshwater to marine iron-oxidizing bacterial lineages along a salinity gradient on the Sheepscot River, Maine, USA. Enviro. Microbiol Rep. 5: 453–463

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Week 13: Marine S cycle – Sulfate reduction, S oxidation, disproportionation Topics: sulfate reducing bacteria (euxenic basins and sediment); oxidizing bacteria, disproportionation; Required background reading: Wasmund et al. 2017. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. Enviro. Microbiol. Rep. doi:10.1111/1758-2229.12538 Discussion Papers: (1) Canfield et al. 2010, A Cryptic in Oxygen-Minimum–Zone Waters off the Chilean Coast. Science, 330: 1375-1378; (2) Pfeffer et al. 2012, Filamentous bacteria transport electrons over centimetre distances. Nature 491: 218‐ 221.

Week 14: Marine CH4 cycle – methanogenesis, aerobic and anaerobic oxidation of methane Topics: Archaeal methanogenesis; aerobic bacterial methane oxidation; anaerobic methane oxidation coupled with sulfide (bacterial-Archaeal consortia) Required background reading: Conrad 2009. The global methane cycle: recent advances in understanding the microbial processes involved. Enviro. Microbiol. Rep. 1: 285-292 Optional background reading: Reeburgh 2007. Oceanic Methane Biogeochemistry. Chem. Rev. 107: 486−513 Discussion Papers: (1) Ettwig et al. 2010. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature. 464: 543- 548 + supplemental material (2) Ettwig et al. 2012. Archaea catalyze iron-dependent anaerobic oxidation of methane. PNAS. 113: 12792– 12796

Week 15: Biofilms, Life on particles, phytoplankton-bacterial interactions Topics: evolution of biofilms, Role of particles in a low- open ocean, bacteria-algal interactions during Required background reading: Buchan et al. 2014. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. 12: 686-698 Discussion Papers: (1) Gardes, Iversen, Grossart, Passow and Ullrich. 2011. -associated bacteria are required for aggregation of Thalassiosira weissflogii. ISME J. 5: 436–445 (2) Orsi et al. 2016. Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. ISME J. 9:1747-1763.

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Week 16: Hydrocarbon oxidation (aerobic and anaerobic) Topics: natural and anthropogenic sources of hydrocarbons to the environment; microbial degradation of hydrocarbons in aerobic and anaerobic marine environments Required Background Reading: Head et al. 2006. make a meal of oil. Nat. Rev. Microbiol. 4: 173-182. Discussion Papers: (1) Jaekel et al. 2013. Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps. ISME J. 7: 885–895 (2) Gutierrez et al. 2013 Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP. ISME J. 7: 2091-2104

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