Coral Reef Ecology (Kaczmarsky)


Lonnie Kaczmarsky, Ph.D.

Institute for Tropical Ecology and Conservation, and, Florida International University

2911 NW 40th Place
Gainesville Florida, 32605

Phone: (201) 704-8065


Diving certification is not necessary to enroll in this course, but is recommended. For SCUBA certified (PADI, NAUI, or SSI certified) students who will be diving, there is a $100 Lab Fee with this course which covers dive tank, air and dive weight rental. Students with SCUBA certification are expected to bring their own BC, regulators, mask/fin/snorkel and proof of certification. For those not diving certified, students are expected to bring mask/fin/snorkel.


This course is designed to provide the student with a sound foundation in ecological concepts, techniques and experimental design in field research as applied to coral reef ecosystems. The material covered is equivalent to a university upper level course in coral reef field ecology. The course will begin with a global ecosystem perspective and then will progressively narrow to assess the way in which local reefs are influenced by both global and local phenomena. We will briefly survey reef systems in various parts of the world and focus in depth on Caribbean reefs.
Using the reef at Bocas del Toro as an example, we will carry on an inventory of representative reef biota to characterize a general reef community. We will examine several theories of the origins of reefs and discuss some controversial arguments on the ecological processes ruling the dominant state and health of coral reefs. Students will learn to characterize a general reef community and its place among surrounding marine habitats. The major reef biota will be discussed in terms of their phylogeny, biology, physiology, ecological requirements and roles in species interactions on reefs. We will discuss the impacts of anthropogenic stressors to coral reefs and the role of marine reserves [and coral nurseries] in reef conservation and restoration. In the inventory we will examine and compare several experimental designs and sampling schemes with regard to their usefulness in a reef setting.

boulder-coraltube-spongesFormal Lectures
Lectures will present topics that provide a background for the field work in an interactive discussion format. Topics are selected to teach students about the biology and ecology of the reef organisms they will encounter and permit students to develop an awareness of the objectives of research on coral reefs as well as an appreciation of current theoretical and practical issues in ecology.

Lecture Topics
  • Fundamentals of oceanography, global ecology
  • Plate tectonics, formation of ocean basins, continents and ocean currents
  • Reef morphology, distribution of reef systems
  • Ecological linkages between coral reef, seagrass and mangrove ecosystems
  • Coral reef community study: sampling methods for distribution and abundance of organisms
  • Coral reef community study: components and interactions, trophic dynamics
  • Biology of coral reef organisms: Cnidarians
  • Biology of coral reef organisms: Poriferans
  • Biology of coral reef organisms: Mollusks, Annelids, Arthropods, and Bryozoans
  • Biology of coral reef organisms: Echinoderms and Ascidians
  • Biology of coral reef organisms: Fishes
  • Biology of coral reef organisms and associated plants: Macroalgae, Seagrass, and Mangroves
  • Ecosystem stability, resilience, and fragility/resistance
  • Anthropogenic effects on reefs: climate change, pollution, overfishing, and diseases
  • Marine protected areas, coral restoration, ecotourism, and environmental policy

Assignments relating to lecture topics will be made from the texts and supplementary research articles provided in the library.

Required Texts
Sheppard, CRC, Davy, S.K. and G.M. Pilling The Biology of Coral Reefs, Oxford Press, USA.
Humann, Paul. Reef Coral Identification, New World, Jacksonville, FL.
Humann, Paul. Reef Creature Identification, New World, Jacksonville, FL.

Field Work Briefings
Prior to departing for the reef site, dive teams will be formed and the objectives for the day will be outlined and discussed. Assignments will be made to the dive teams and coordinated.

Group Exercises
During the first week, students will visit several sites in the vicinity of the station to familiarize themselves with the area and to make observations that may lead to hypotheses that could be tested in individual projects. Students will be organized into dive teams and will carry out field exercises in which they will gain experience in the use of sampling equipment and techniques used in reef research and monitoring. In the evenings, students will participate in ‘debriefing sessions’ during which they will identify the reef organisms they saw during the dives of the day and record the common name and scientific name of the species in a logbook.

Individual Research Projects
Each student will be expected to prepare a research proposal for an original project in consultation with faculty.  Projects may be suggested by observations made during group exercises or from the research literature, and will be evaluated on the basis of feasibility in the available time, soundness of experimental design and concept. During the final week of the course, data analysis and writing of project reports will be carried out and students will present their results orally in an end-of-course symposium. They will present the research report on their findings in the form of a scientific journal article for evaluation.

Grades will be assigned based on exams, reports, proposals, attendance at lectures, as well as by less tangibles such as personal attitude, motivation, and contribution to the course. The instructor will provide a breakdown of points earned and final letter grade to your academic institution. The student is to provide direct evidence of course participation such as the syllabus, schedules, handouts, lecture notes, proposals, reports, etc. Please arrange for credit through your department or academic advisor.