The name we chose for this website, Coral Reef Systems, reflects our belief that understanding coral reefs requires us to look at them at many levels: from the microbes to the macrobes, the genes to the metagenomes, the local to the global, through evolutionary and ecologically relevant time scales.  The researchers that make up our scientific team come from a range of disciplines. Each member of our group brings unique insights to our goal of better understanding how coral reefs function and how best to ensure their survival.





I examine the dynamics between predators and their prey and how those dynamic shape the coral reef community. Typical models of predator-prey dynamics assume that predators act independently within the community. For example, doubling of predators leads to a doubling of predation threat. New evidence from coral reefs, however, calls into question the this assumption.

The populations of fish we see from remote (and unfished) coral reefs show evidence of “inverted trophic pyramids”, namely with a higher biomass of “top” predators relative to the biomass of lower trophic guilds (prey species) . In these cases, doubling the predator biomass is unlikely to double predation threat as in the typical model.

My research further examines these inverted trophic pyramids among fishes, specifically considering the role of competition among predators for food in shaping community dynamics. How do reductions in predators (from fishing pressure) create dynamic changes in coral reef fish populations? Are our assumptions about how fish populations behave based on observations of a system which is out of balance? By studying remote coral reefs I can strive to answer some of these questions and make important contributions to the understanding of how to best conserve coral reef fisheries.

Sandin Lab:





My research focuses on understanding the factors that influence community structure in benthic marine ecosystems.  The benthic community includes algae, corals, and other invertebrates. While I conduct research in a number of different systems, both pristine and degraded, my primary interests lie in determining how different anthropogenic (human caused) impacts affect coral reef community structure.

When coral reefs undergo degradation, a “phase-shift” usually occurs where reef-building corals are replaced by fleshy macroalgae. Phase-shifts are often considered to be irreversible and the end result is a macroalgal dominated community that lacks the diversity, complexity, and structure necessary to support a typical coral reef. I study the factors that cause these types of phase shifts. Specifically my research focuses on the importance of herbivory (or overfishing) and increased nutrient concentrations (in association with pollution from land) in maintaining the competitive balance between algae and coral.

My research often goes beyond basic ecology by integrating conservation, restoration, management and sustainability. In the future I plan to begin investigating the potential for reef restoration in an effort to understand if phase-shift reversal is possible.

Smith Lab:






Coral reefs worldwide are in decline. The dramatic rise in incidences of coral disease over the last two decades has been instrumental in this process. We have hypothesized that most of these diseases are actually opportunistic infections instigated by anthropogenic (human caused) stressors. Our research is focused around understanding the interactions between the microbial world and coral reefs, and how these systems change following perturbation.

Corals are host to a wide diversity of organisms, including endosymbiotic algae, protists, fungi, Bacteria, Archaea, and viruses. Together, these organisms make up the coral holobiont. In our lab, we are interested in understanding the physiological roles of these players in their interaction with the coral animal, and how this relates to coral reef health. We use a variety of techniques to better understand these complex microscopic communities and have learned that microbes play a much larger role than previously thought in the health and success of coral reefs.

Rohwer Lab:


Rob Edwards, Ph.D., is at the forefront of 21st century genome sequencing, annotation, and bioinformatics analysis, with a primary focus on microbial genomics. Using his strong background in computational science, he developed MG-RAST, a fully-automated service available for rapid functional annotation of metagenome samples–a system that has been put to work by many, including Forest Rohwer for his analysis of data from the Line Islands. A scientific SCUBA diver, Rob has studied coral reefs in both the Pacific and the Atlantic. He holds joint faculty appointments in the Biology Department, Computer Sciences Department, and the Computational Sciences Research Center at SDSU.

Edwards Lab: