Bio 371, Restoration of Aquatic Ecosystems, Fall Course Syllabus, Course Overview, Learning Objectives, and More Provisional Schedule

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1 Bio 371, Restoration of Aquatic Ecosystems, Fall 2018 Course Syllabus, Course Overview, Learning Objectives, and More Provisional Schedule Course Instructor: Jeffrey Levinton (office Room 680, tel ), Field and Lab Instructor: Brooke Arena (office Room 625, office hours Wed 11-1) Overview of Course Our objective is to take a team and collaborative learning approach to studying the components of the environment that are needed to understand the means and potential of restoring the eastern oyster Crassostrea virginica, and other bivalves to a large bay, Jamaica Bay, New York. In the process we will learn about the concept of ecological restoration, the functioning of estuaries, the ecology of oysters and oyster beds, and the interactions between oysters and the seabed and water column. Website for Course: These are our main objectives: Overall Objectives: (a) To collect data and evaluate information on three important aspects of the environment of Jamaica Bay and nearby Stony Brook Harbor and the potential for bivalves to affect water quality, mainly algal density; (b) To give progress reports in class and eventually write group reports on these three components. Specifically: (1) Monitor water quality along an environmental-water quality gradient in Jamaica Bay and Stony Brook Harbor; (2) Study by experimentation the response of water from polluted and clean water to nutrient additions that may or may not be limiting to the important algal food for bivalves; (3) Measure the performance of oysters (respiration and feeding rate) within polluted Jamaica Bay and compare this to a cleaner site in Stony Brook; Lectures will cover a range of topics, including (a) Oyster ecology and estuarine structure; (b) pollution history of Jamaica Bay, the site we will study; (c) studies of bivalves, oysters, and the biology of suspension feeding; (d) studies of the role of nutrient input into polluted estuaries; (e) topics relating to data analysis and statistical analysis. You will join, BY NEXT FRIDAY September 7, one of three teams.

2 1. Water Quality measurements 2. Experimental nutrient studies 3. Oyster performance respiration and feeding rate It is crucial that you not only become part of an interactive team, including having your own suggestions for studies, but also be willing to occasionally help out another team to fill in when someone on another team cannot do some task. Field work will include (a) 1 required field trip to the site for the whole class on Friday September 7, a second field trip to Jamaica Bay on October 5, plus at least 2 other required field trips for each of three teams. Times of departure and return will vary but you have to have the morning available for departure. We will be taking water samples, monitoring oysters, and doing measurements of water quality. Lab work will include (a) Preparation of water for studies of nutrient addition and analysis of responses; (b)studies of oyster feeding and oxygen consumption; (c) shucking oysters and measurement of dry weight; (d) measurement of chlorophyll and other water parameters. The work will be done by students with instructor help and demonstrations. Requirements for the course: 1. Mandatory attendance of class and field trips (if you cannot spare the time for trips you must decide NOW whether to continue in this course). 2. Participation with your team in data collection, laboratory work. 3. Participation with your team in two progress reports during the semester (oral plus powerpoint). 4. Participation with your team in production of a polished report and oral presentation on November 30, and a completed paper by December Self-evaluation paper of your own participation in your team, with report on your work, writing, data analysis and other participation (more details to come). 6. Readings of assigned background material. Resources for the course: 1. Laboratory, with microscopes, hood, various preparatory materials, desktop computers 2. Readings, downloaded from course web site 3. Access to a variety of instruments and environmental chamber. This course will be challenging, require cooperation, but will be very rewarding and fun. Jamaica Bay is a very interesting place and much more than an urban site. Field and Laboratory Exercises and Sampling Program It is difficult to learn how to study a field site without a comprehensive introduction into field sampling and experimentation. The exercises outlines below are just some suggestions for work that could be accomplished by a few intensive field trips with a class of 15 or so, followed by laboratory investigations and measurements. The field work can be done by all students, but, for the exercises below, we suggest dividing students into the three teams mentioned above.

3 A Pep Talk Before Starting Field trip days will be very busy and require preparation. The instructors will not be able to be at every work site and we need you to be as independent as possible, while paying attention to safety considerations. Everyone should read through these methods and try their best to understand what will be going on in the field and the laboratory. It goes without saying that everything should be done with extreme care and caution. Some of you will be working with volatile and harmful chemicals, others will be near the water on floating docks, while others will be on a boat for at least one trip. If everyone uses his/her common sense, we will have productive and enjoyable days. Team One: Water Quality Sampling Along a Hypothetical Pollution Gradient-- Objective: To make measurements of water quality along a gradient. Utility: With these samples we will be able to see the broad range of water quality variation from the opening of Jamaica Bay to the ocean, all the way east to areas with urbanized waters. Time allowing we will make the same comparison in a transect in Stony Brook Harbor. Necessary materials and equipment: Van Dorn sampler for water sampling near the surface and near the bottom YSI Model 85 Temperature-Salinity-Oxygen meter Turner Aquafluor fluorescence analyzer, for measuring fluorescence related to chlorophyll, and ammonium ion, a nutrient necessary for phytoplankton. Also possible: Propeller driven current meter. To take water samples, we will use the Van Dorn water sampler and sample in Jamaica Bay from a fishing boat provided by a local conservationist, Daniel Mundy, Sr. Water will be collected from near the surface and the bottom and will be analyzed by our two sampling instruments on deck. Water sampling will also be done from floating docks at Gateway Marina and Inwood Marina, Jamaica Bay. The latter samples will help the nutrient experiment team understand their results. a. Collecting Water. At each station, or at each marina, the Nisken bottle will be put over the side and we will bring up a sample from near the bottom and at the surface. We will measure the five variables in water samples poured from the Nisken spout into a beaker. For monitoring from the two marinas, water will be taken back to Stony Brook. We will extract chlorophyll from water and this will involve a series of procedures that will be covered in a laboratory demonstration. Monitoring at the docks will occur biweekly to monthly. The transect across the Jamaica Bay transect from the boat will occur once. As mentioned if time permits we will do a similar comparison in Stony Brook Harbor.

4 This team will also pick a couple of data sources to plot water quality changes over time and do statistical analyses to estimate changes in water quality at a series of stations. Possible areas to study are Jamaica Bay, lower Hudson River. The report will include an analysis of trends in water quality (e.g., temperature, salinity, dissolved oxygen, other properties such as bacterial counts). Team Two: Nutrients and Plankton Response Objective: To start water samples from Jamaica Bay and study their responses to nutrients in comparison to water collected at a cleaner site in Stony Brook Harbor. Utility: Four waste-water treatment plants release nutrient-rich waters into Jamaica Bay. The question is what nutrients might be limiting when so much nitrogen is released into the Bay? We will study this by enrichments of other potentially limiting nutrients such as silicon and phosphorus. We will collect batches of water from Jamaica Bay and at Stony Brook, bring them back to the laboratory and keep them under light (why?) and will set up a balanced experiment that one team will monitor regularly. Water will be collected from Jamaica Bay and Stony Brook. The team will be ready to set up ca. 2L water containers under light. Each locality will have 5 bottles: control, nitrogen added, phosphorus added, silicate added, and all three added. We have to decide about replicates. Bottles will be sampled 72 hours later and we will sample for chlorophyll larger and smaller than 5um, nutrients, and for plankton, using a special preservative known as Lugols solution. The different responses will give us information as to what nutrients are limiting on each side of the Bay. We will discuss the issue of nutrient limitation in a lecture in class. Equipment and materials: Culture bottles with aerators Environmental chamber Nutrients Lugols solution Filtration equipment Analytical balance (to weigh filters) Team Three Oyster performance Objective: to measure the feeding rates and oxygen consumption rates of oysters maintained in central Jamaica Bay and in Stony Brook Harbor in cages. Utility: If oysters are restored to Jamaica Bay, how will they succeed, at least as adults? We can understand this by choosing two sites at either end of a water quality gradient and studying their performance. Also the rates can be used to study the impact oysters might have on the bay in removing plankton and also perhaps reducing water quality by lowering oxygen by consuming it. This team will place oysters brought from a site in Shelter Island, New York (unpolluted) and will bring them in cages to Jamaica Bay and Stony Brook Harbor. They will be kept there for about one month to experience the local waters. We will count live and dead to see how they survive the transplant. They will then be

5 retrieved and studied quite rapidly to examine their feeding rates and oxygen consumption. We hope to do this twice at different temperatures. Equipment: Turner fluorometer Strathkelvin oxygen meter with six electrodes Filtration equipment Analytical balance Initial Class Schedule August 31 - General introduction: Seawater properties, estuaries, tides, Hudson and Jamaica Bay September 7 Oysters: Biology, Ecology, Ecosystem Influences (Quiz 1) September 14 - Class Field Trip to Jamaica Bay, depart 8 AM September 21 - Nutrients and Their Effects on the Water Column; Salt Marshes - Structure and Use in Coastal Restoration, Lab on measurement of chlorophyll, quiz 2 September 28 Water quality team trip to Jamaica Bay, other groups to be determined October 5 - (whole class, restoration of Big Egg Marsh led by George Frame, research scientist, National Park Service, depart 730 AM bad weather date October 20) October 12 Goals of Restoration of Oysters and Problems, (Quiz 3) Lab on oyster biology October 19 (quiz 4) set aside for team field trips, class field trip to SB Harbor oyster restoration project 330 P.M. - tentative October 26 Exam on lectures and readings (ca. one hour), Team experiments and analyses November 2 continue experiments, analyses November 9 Progress Report 1, Oral Presentations (10 min each group) continue experiments November 16, Continue experiments November 23, Thanksgiving Break

6 November 30 Final Oral Presentation, detailed outline of three team papers due December 7 Final Team Papers Due Other team trip Dates - To be arranged Learning Objectives for this Course 1. Through lectures and readings, you will be introduced to basic estuarine/oceanic environmental variables and their variation; the presence and disappearance of healthy oyster reefs; what variables are important in restoring bivalve populations and what are the ecosystem benefits. 2. Through laboratory exercises and specific studies you will learn how to quickly construct a research project, propose a testable hypothesis, test the hypothesis with carefully constructed experiments or measurements, and analyze the data emerging from the experiments. 3. You will learn how to work in a team and to get things done by collaboration. This is how science works these days, in the lab-field, and in the construction of written papers. 4. You will learn how to cooperate in writing a group report, while doing specific tasks agreed upon by the group. You will have an opportunity to write a draft that will be edited by Instructor and TA to improve your writing skills by constructive criticism. 5. You will learn how to make oral presentations that are organized and hopefully at a high level. 6. Ultimately we hope you will have a perspective on the environmental and ecological information needed to understand how to measure the components of a successful environmental study. How Will You Be Graded? This course will require some special approaches to grading, since team effort will be so important. Here are the approximate proportions that contribute to the value of your final grade. Quizzes: 5% Exam: 10% First Oral Report: 5% Final Oral Report: 15% Final Written Report: 40% - note that you will describe in the paper YOUR written part of the paper (e.g., methods or discussion). Participation in lab activities and field activities: 20% Self Evaluation: 5%

7 Late Policy: There basically is no excuse for being late or absent at oral presentations. The paper must be on time (10 percent penalty for each day late). Because this is a TEAM effort, we hope and expect that such penalties will not be necessary. I will ask you at the end to write a self evaluation, which will help me evaluate your grade and performance. Attendance is mandatory and the field trip times may involve leaving before the formal start of the morning session. These are mandatory and you might consider dropping the course if you have major other responsibilities on Fridays between Today s Demonstration YSI Model 85 Temperature, Salinity, Oxygen For our demonstration this afternoon (August 28), we will use an integrated instrument to measure seawater temperature, salinity, and dissolved oxygen. These three simple measures give us a great deal of information. Temperature What is it? Temperature is an estimate of the kinetic energy of molecules and atomic particles. It is therefore a crucial property of physical systems, including seawater. At higher temperature, chemical reactions are faster, but also chemical properties may change materially. For example, the solubility of oxygen decreases with increasing temperature. Since, most marine organisms require oxygen, this means that at higher temperature less oxygen can be available dissolved in seawater. We measure temperature using the centigrade scale: distilled water freezes at 0 C and boils at 100 C. Sounds simple? Well it isn t because salt in seawater (see discussion of salinity below), the freezing point of water declines. Typical oceanic seawater freezes at a temperature of -2 C. This is not very important for our purposes but dissolved salt also increases the boiling point of seawater above 100 C. In the ocean, temperature varies substantially, but let us just concentrate on our region: winter temperatures in our coastal waters usually are below 5 C in winter, but may reach C in summer. This is a plot of temperature in Long Island Sound, unfortunately in degrees F. In recent decades, temperature of seawater has increased regionally. Salinity salinity is a measure of the salt content of seawater. This subject could be discussed at a much deeper level, but for our purposes we consider a situation where we take a liter of seawater and let it evaporate. The distilled water evaporates and this leaves a number of salts behind as the concentrations of ions increases as evaporation proceeds. What you find in the end is that you mostly have sodium chloride crystals, potassium chloride, and a few other solids. The simplest definition of salinity is the mass of the solid material per liter, measured in

8 parts per thousand (ppt), or o/oo. Seawater with salt conducts electricity and salinity is usually measured by the conductivity of seawater, which increases with increasing salt content but also varies with temperature and pressure. This conductivity is compared with a standard and salinity is expressed as practical salinity units or psu. The instrument measures conductivity of seawater. In coastal waters salinity varies a great deal. River water mixes with coastal water and forms a mix of seawater from freshwater to full strength seawater. We will discuss this in lecture. But it is crucial that most marine organisms function very differently and often grow and perform more poorly as salinity decreases. That is why we measure it. In this region, open coastal salinities are psu, but Jamaica Bay is influenced by freshwater from four wastewater treatment plants and also some freshwater flow from the regional watershed. Salinities are usually Oxygen - As you probably realize marine animals, algae and plants use oxygen, so variation in dissolved oxygen is an important parameter to measure. We will go into this in more depth, but coastal environments often have low oxygen content because of a large amount of organic matter that enters the system, but this is exaggerated in a place like Jamaica Bay, where so much sewage enters into the water. It is therefore very important to measure oxygen. The nutrients in Jamaica Bay also allow phytoplankton to grow, which produce a large amount of oxygen. As we will learn, this combination can cause large swings in oxygen concentration. Oxygen can be measured as mg of oxygen per liter, but also in terms of percent saturation (a maximum amount of oxygen can be dissolved in seawater at equilibrium, which sets the 100% point). The amount of oxygen that can be held at saturation declines with increasing temperature and increasing salinity (to a lesser extent). So as summer moves along, dissolved oxygen can decline. Oxygen is measured using the Clark-type oxygen electrode. As oxygen crosses a membrane, it reacts with an electrode, which creates an electric current. The amount of current is proportional to the concentration of oxygen, so you just need an ammeter, although a rather sensitive one. The ammeter is calibrated to allow you to measure the amount of dissolved oxygen. OK, this should be enough to get you started to appreciate what will be a rather fast demonstration!