Skip to main content

Introduction to Trophic Ecology: Why do we study the diets of fish?

stomach of a sport fish in gloved hand

Figure 1. A researcher holds the stomach of a juvenile sportfish taken so that stomach contents (prey species) can be analyzed.

Traditionally, fish stocks have been assessed and managed as independent populations, however, marine researchers recognize that fish populations interact with each other, often competing for resources or in predator-prey relationships. These interactions are complex and vary across ecosystems, age ranges, and habitats. Therefore, moving towards a more holistic, ecosystem-level understanding of fish populations for subsequent management requires significant work to determine what fish are eating and how their diets shift through their growth and across different habitats.

The goal of the trophic ecology lab is to provide quality diet data to understand these competitive and predator-prey dynamics. Fish are collected in routine monitoring or opportunistically and the stomachs are removed for analysis in the lab (Fig. 1). There, our taxonomists use microscopes and dichotomous keys to identify all the prey to the lowest possible taxonomic level and obtain volumetric measures and counts of each. Fish are often quickly digested and distinguishing species in stomachs without color, scales and fins, compared with other more easily identified organisms with hard parts, e.g. crabs, is extremely difficult. Often, fish jawbones and teeth are some of the last parts to be digested and remain distinguishable in stomachs. Images of representative fishes taken from regular net sampling are being catalogued to aid in the identification of these heavily digested fish, some of which are available in our Trophic Ecology Flickr album.

a map of Florida with numerous green dots showing all of the areas in the Gulf of Mexico that fish stomach samples were taken from.

Map of the locations (green dots) of fish stomach samples that have been processed by the FWRI trophic ecologists.

Since 2005, we have analyzed over 50,000 fish stomachs, from a variety of surveys and locations, primarily in the Gulf of Mexico and associated estuaries, and more recently, the Atlantic side of the state (Fig. 2). We have observed over 1,600 prey species and have observed over 90,000 predator-prey interactions. This data has already contributed to ecosystem models to support management decisions in the Gulf of Mexico such as estimating gag (Mycteropercamicrolepis) mortality and examining the effects of the invasive lionfish (Pteroisspp.) on the ecosystem (Fig. 3).  The trophic ecology lab’s data can also be used to describe the diets of important sportfish and how their diets may shift through their lifespan and across regions for species, such as redfish (Scianopsocellatus), hogfish (Lachnolaimusmaximus), spotted seatrout (Cynoscionnebulosus), and gag (Hall-Scharf et al. 2016; Fig. 4). Understanding these diets can indicate which species are strongly interacting, and what may happen if important predators or prey numbers change dramatically. Furthermore, diet data in tandem with catch data aids in understanding how the ecosystem is responding to fishery management actions, red tides, hurricanes, habitat shifts, and climate change. The trophic ecology lab is continually adding to the fish diet database and can address many emerging research questions and management-related data needs and add an important ecosystem-level perspective to how we study the fishery resources in Florida.


Figure 3. This diagram is an example of a food web model that is influenced by information provided by the trophic ecology lab.  Each point represents a different species or group of species and the lines represent predator/prey relationships between the points (Chagaris et al. 2017).

Diagram representing the energy flows (dietary linkages) between groups in the Gulf of Mexico, West Florida Shelf ecosystem


Figure 4. This diagram shows the diet of juvenile gag in the Tampa Bay and Charlotte Harbor estuaries. These results indicate that young gag prefer to prey on fish (blue stripes), especially pinfish.  Shrimp (yellow stripes) are also preyed upon by juvenile gag, but these data suggest that shrimp account for a much smaller proportion of their diet than fish.

Diagram showing the diet of juvenile gag in the Tampa Bay and Charlotte Harbor estuaries



Chagaris, D., S. Binion-Rock, A. Bogdanoff, K. Dahl, J. Granneman, H. Harris, J. Mohan, M. B. Rudd, M. K. Swenarton, R. Ahrens, W. F. Patterson, J. A. Morris, and M. Allen. 2017. An Ecosystem-Based Approach to Evaluating Impacts and Management of Invasive Lionfish. Fisheries 42(8):421–431.

Hall-Scharf, B. J., T. S. Switzer, and C. D. Stallings. 2016. Ontogenetic and Long-Term Diet Shifts of a Generalist Juvenile Predatory Fish in an Urban Estuary Undergoing Dramatic Changes in Habitat Availability. Transactions of the American Fisheries Society 145(3):502–520.