The Core Aquatic and Terrestrial Ecosystems Courses
The SES program emphasizes learning by doing – students spend over 20 hours each week in the lab and field investigating forests, ponds and estuaries on Cape Cod. Virtually all ecosystems have been impacted by human activity, and so this is also a curriculum about how human-caused changes in the environment are affecting the globe.

Core course lectures cover both aquatic and terrestrial ecosystems from the point of view of biogeochemistry and important ecological processes. Course research takes place in local ecosystems — ponds and estuaries within the Waquoit Bay watershed adjacent to Vineyard Sound, West Falmouth Harbor on Buzzards Bay, and grassland, forest and suburban sites in the towns of Mashpee and Falmouth. Read more about the four credit aquatic course and the terrestrial course.

Terrestrial Ecosystems Analysis Overview
The core course lectures cover both aquatic and terrestrial ecosystems from the point of view of biogeochemistry and important ecological processes. In the field and laboratory we will start out in the first eight weeks of the core courses with an intensive study focused mainly on local ecosystems.

Terrestrial Fieldwork Sites
Terrestrial fieldwork is conducted in grassland, forest and suburban habitats in the Crane Wildlife Management Area in Mashpee and other sites in Falmouth. The sites are chosen to represent a disturbance chronosequence and allow comparison of ecosystems processes, such as primary production and nitrogen mineralization, and properties such as standing stock, plant diversity and soil carbon and nitrogen content across the disturbance gradient.

Aquatic Ecosystems Analysis Course Overview
The core course lectures cover both aquatic and terrestrial ecosystems from the point of view of biogeochemistry and important ecological processes. In the field and laboratory we will start out in the first eight weeks of the core courses with an intensive study focused mainly on local ecosystems –ponds and estuaries within the Waquoit Bay watershed adjacent to Vineyard Sound, West Falmouth Harbor on Buzzards Bay, and grassland, forest and suburban sites in the towns of Mashpee and Falmouth, MA.

Aquatic Field Work Sites
There are four local sites used for aquatic fieldwork that offer an array of conditions to be studied: West Falmouth Harbor, Childs River/Waquoit Bay, John’s Pond, and Sider’s Pond.

West Falmouth Harbor: Small salt water embayment adjacent to Buzzards Bay on the west coast of Falmouth that is impacted by the plume from the Falmouth Wastewater Treatment Plant.

Child’s River/Waquoit Bay: This is a system of small estuaries on the outwash plain along the south coast of Falmouth. This site has been eutrophied by groundwater contaminated with nitrogen from septic systems in densely settled sections of the watershed, resulting in the disappearance of eel grass in this system.

John’s Pond: A freshwater kettle hole pond with a deep basin (~ 20 meters) that is seasonally stratified.

Sider’s Pond: A salt- stratified meromictic pond about 15 meters deep that displays strong vertical gradients in oxygen, sulfate, nitrate and ammonia, which illustrates anaerobic processes in marine and brackish water systems.

Electives

In addition to the Core Courses, SES students take one four credit elective which meets twice a week. The elective is intended to deepen understanding in a specific sub-discipline of ecosystems science. Choose from Mathematical Modeling or Microbial Methods.

Ecology is a relatively young science that grew from the largely descriptive discipline of Natural History. As the science has matured, it has begun to develop a firm quantitative foundation. For the most part, this foundation has been statistical (Regression, Correlation, Analysis of Variance, Ordination). The purpose of this course is to introduce the students to the other component of this quantitative foundation, dynamic simulation modeling of ecological processes.

The students will first be exposed to the role of models in science and the relationship of models to scientific theories. Then the basics of calculus are reviewed in the context of the mass-balance concept. Next the students are introduced to numerical (as opposed to analytical) solutions of the mass-balance equation; that is, they are taught how to get a computer to do all the hard math. They then apply these techniques to a series of examples like the growth of an individual organism and of a population of organisms, the interactions within species communities (competition for resources, predator-prey systems), the cycling of elements within ecosystems, the hydrology of a watershed, and an analysis of the CO2 balance of the atmosphere.

The students will use what they learn over the course of the semester to develop their own simulation model of an ecosystem. They are provided with a model shell that includes a Windows™ interface, integrator, and graphical-output package. The student then provides a set of equations describing the ecological processes they want to simulate. These equations are typically based on the simple concept of a mass balance and can be applied to ecosystem element cycles, population dynamics, or community interactions.

Required Text
Students will be assigned chapters from selected texts and papers from the primary literature.

What to expect
The students will complete about six programming problems that illustrate the topics covered in lecture. Students will be evaluated predominantly on a term project. In that project they will develop their own simulation model, address some ecologically significant question with the model, and write a manuscript describing the model and analysis. The manuscript is to be written as if it were to be submitted to a scientific journal (e.g., Ecology). Students are encouraged to relate their project to topics covered in other courses, and may use the model they develop as part of their independent research project undertaken during the last four to six weeks of the semester. Students are encouraged to discuss their projects with one another during the semester and seek one another’s advice. In addition, each student will make an oral presentation describing her or his project to the class.

Syllabus (2 sessions per week)

Session 1: Computer & software orientation, model examples and intro to the original Multiple Element Limitation Model (MEL)
Session 2. Why Model?
Session 3. Fountain experiment and MS Excel model
Session 4. Mass Balance and fountain model in Lazarus
Session 5. Numerical integration
Session 6. Class model
Session 7. Class model
Session 8. Forest Nitrogen budget
Session 9. The Michaelis-Menton equation
Session 10. Catchment hydrologic budget
Session 11. Population logistic and competing populations
Session 12. Predator-prey systems
Session 13. Parameter estimation and curve fitting
Session 14. In class help with projects
Session 15. The Multiple Element Limitation (MEL) Model
Session 16. Island model
Session 17. Forest model
Session 18. In class help with projects
Session 19. Student Presentations
Session 20. Student Presentations and Final Modeling Projects due

The usual methods of microbiology were developed to study microbes affecting human health (Lynch and Hobbie 1988). When these methods are used for field studies they have many problems; to begin with, less than one percent of the bacteria found in a sample of ocean water will grow on laboratory petri plates. Recent methodological advances, such as the application of fluorescently-labeled immunochemical or nucleic acid probes, provide a new way to taxonomically identify individual cells in the mixed populations of soils and waters. Yet, the application of these methods is limited to the detection of physiologically active cells with a large number of ribosomes, a rare occurrence in nature. Despite these and other problems, ecological microbiologists have developed a number of methods for enhancing our ability to measure the activities, abundances, and types of microbes found in soils, waters, and sediments of natural systems (e.g., the methods book of Kemp et al. 1993).

In this course, we will present the scientific rationale behind a number of methods suitable for determining the role of microbes in ecosystems. The methods will be described and students will carry out the procedures in a series of hands-on laboratories. One theme will be choosing methods and temporal and spatial scales appropriate to the question being asked (e.g., the review by Pearl and Pinckney 1996). The course will be taught, under the leadership of Joseph Vallino, in collaboration with scientists from the Ecosystems Center, the permanent staff of the Marine Biological Laboratory, and other Woods Hole institutions.

Lectures will describe the biology and logic that underlie the various methods used by microbial ecologists. In the laboratory, students will work with the latest techniques to measure microbial biomass, activity, extracellular enzymes, biogeochemistry and species diversity. These include epifluorescence microscopy, radioisotopic tracers for bacterial production, fluorescent substrates, hydrogen sulfide and methane production, and molecular probes for classes of bacteria. Students will be required to turn in answers and calculations to problem sets that are associated with each lab topic. These problem sets will form the basis of the grade. In addition, students will be asked to present their laboratory results and participate in group discussions on the findings by the entire class. Students will be encouraged to use the methods developed in this course for their individual research projects associated with the SES course.

For more information go to the Microbial Methods in Ecology website.

2019 Syllabus

Session 1: Introduction
Session 2: Construct Winogradsky Column: field trip to Little Sippewisset Marsh
Session 3: Bacterial Abundance: prepare dilution and coliform plates, fix samples for direct DAPI counts
Session 4: Bacterial Abundance: DAPI staining and counts; examine plates
Session 5: Bacterial Production: lecture on bacterial production method; count dilution plates
Session 6: Bacterial Production: measure bacterial production using C14
Session 7: Bacterial Production: 14C activity results, scintillation counter demonstration, explain calculations
Session 8: Extracellular Enzyme Assays: lecture on extracellular enzymes and fluorometry
Session 9: Extracellular Enzyme Assays: measure enzyme activities
Session 10: Chemolithotrophy: lecture on Winogradsky column, column observations
Session 11: Chemolithotrophy: measure hydrogen sulfide profiles in columns
Session 12: Chemolithotrophy: measure methane gradient in columns
Session 13: Microbial Food Webs: lecture on flagellate and ciliate grazing on bacteria
Session 14: Microbial Food Webs: lab on bacterial grazing with fluorescent beads
Session 15: Molecular Techniques: lab on DNA extraction
Session 16: Molecular Techniques: lab on electrophoresis and PCR
Session 17: Molecular Techniques: lecture on Molecular methods
Session 18: Microbial Food Webs: lecture on bacterial phytoplankton competition
Session 19: Microbial Food Webs: microcosm start-up and sample microcosm
Session 20: Microbial Food Webs: sample microcosm
Session 21: Microbial Food Webs: sample microcosm
Session 22: Microbial Food Webs: sample microcosm
Session 23: Microbial Food Webs: sample microcosm, analyze samples
Session 24: Microbial Food Webs: analyze microcosm samples
Session 25: Microbial Food Webs: present and discuss microcosm results and calculations
Session 26: Microbial Food Webs: bacteria phytoplankton competition

Independent Research Projects
The structured laboratory experiences and techniques of the core courses and electives set the stage for the most rewarding part of the SES program, the Independent Research Projects (4 credit course). During the last five weeks of the course, students will be able to devote full time to a project of their choosing.

Science Writing Seminar

SES students all take part in a one credit seminar that introduces the art of science writing. This course is taught by Claudia Geib, freelance science journalist and producer of the podcast Gastropod, with the help of guest experts across the science writing industry. The goal is to help students understand how scientific work can be made more accessible to the public, and to produce writing that engages readers as well as educates them. Students will interview pre-eminent scientists, learn to write short news stories, and work to produce a long-form feature of their choice as a final project. Along the way, they'll learn from podcast producers, documentary filmmakers, investigative journalists and institutional science writers who can share their experience and expertise in this diverse field. With this and other programs at the Marine Biological Laboratory, we hope to begin training a new generation of writers who can communicate critical scientific and environmental issues with the public.

Prerequisites
Because of the diversity of curricula at the schools participating in the Environmental Science Consortium, we are providing a description of the knowledge we hope students will have, rather than specific course requirements. We have grouped these under three categories: Biological Science, Chemistry and Mathematics. Students who are deficient in a given area may still qualify for entrance in the program at the discretion of the on-campus advisor and selection committee.