Rivers span the boundaries between terrestrial, freshwater, and marine ecosystems. Thus, alteration of river flow regimes can have profound effects on aquatic organisms, both within river basins and within estuarine and nearshore and offshore marine systems. The effects of altered river flow interact with other sources of anthropogenic stress and environmental degradation. Further, they are embedded within larger regional and global changes, such as atmospheric deposition of pollutants and sea-level rise, that are expected to further change the hydrologic cycle and the nature of interactions at the land-sea interface.

Oyster Reefs

Oyster reefs provide habitat and other services that are important to ecosystem health and of direct benefit to humans.  Their ability to filter particles from the water column, for instance, leads to greater water clarity that contributes to healthy sea grass meadows; and the structure they create provides refuge and nursery habitat for a suite of economically and ecologically important species as well as shoreline protection from storm surge.

To learn more about oysters, estuaries, and how weather and environmental factors impact these ecosystems, check out a WeatherSTEM lesson done in collaboration with the FSUCML here.

Hardbottom Reefs

Hardbottom reefs provide homes for many types of organisms and make for an ecologically diverse ecosystem. The collection of sessile macroinvertebrates in the Apalachee Bay region that inhabit these hardbottom reefs are numerous, including bryozoans, corals, tunicates, and sponges. FSU graduate student, Jennifer Schellinger, put together a collection of the above groups of species that she found in her studies here at the FSUCML.

Offshore Reef

Along the edge of the West Florida continental shelf (50-100 m deep) exists a broad band of limestone "drowned reefs" or "fossil reefs" that are embedded in sand with a veneer of silt. The limestone is composed of the remains of numerous species of coral,  algae, and many other benthic organisms, and is perforated with holes bored by clams and dissolved by water, leaving many holes and crannies in which other organisms live. It is covered with crustose coralline algae, sponges, sea fans, sea whips, and scattered clusters of Oculina coral and home to arrow crabs, hermit crabs, and basket stars and numerous species of fish, from the small planktivorous reef fish to large predators such as amberjack, scamp, and red snapper. These biologically diverse reefs support spawning aggregations for many economically important reef fish species. Yet little is known about these ecosystems. Given the potential for human-induced threats to these habitats from fishing impact, oil and gas exploration and development, and water rediversion projects, the need is acute to identify and classify the area into spatially and temporally specific regions.

Seagrass Meadows

The seagrass meadows of the northwest Florida coast form the only structurally complex habitat in these waters. These meadows are dominated by turtle grass Thalassia testudinum, followed by shoal grass Halodule wrightii, manatee grass Syringodium filiforme, and widgeon grass Ruppia maritima. Turtle grass forms particularly dense beds directly west of the Florida State University Coastal and Marine Laboratory (FSUCML) off Lanark, whereas shoals grass is locally dominant in areas of physical disturbance or areas exposed to salinity and temperature stress. Manatee grass occurs at greater depths than turtle grass. Widgeon grass occurs on Turkey Point Shoal. These grasses support diverse communities, providing essential habitat for juveniles of several economically important species of fish. Seagrasses are also particularly important in the diets of manatees and endangered sea turtles. They have diverse ecological functions, including improving water clarity, filtering pollutants from seawater, and nutrient cycling. In the northeastern Gulf of Mexico, where the FSUCML is located, seagrasses are mostly deciduous, dying back in winter and producing new leaves in spring. Damage to seagrass beds caused by propellers from motorboats is a major source of harm to this habitat, and may take several years to recover.

Salt Marsh

Most of the estuarine habitat of the northwest Florida, Gulf of Mexico Big Bend is bordered by intertidal salt marshes, primarily Spartina alterniflora at the shoreline then S. patens, Salicornia virginica and Juncus roemerianus to landward. These plants are adapted to rapid and sometimes extreme variation in salinity, temperature, and dissolved oxygen, allowing them to dominate this biotope. After salt marsh plants slough leaves or die, their material is broken down by bacteria to form detritus. In this form, the salt marsh nutrients fuel food webs both within the marsh and in the adjacent waters. Detritus, diatoms and other microorganisms in the marsh are the food source for dense populations (hundreds per square meter) of fiddler crabs, Uca spp. and marsh periwinkles, Littoraria irrorata, as well as clams, mussels, and other invertebrates. Nutrients that are washed out to sea support the food chain of pelagic larvae of fish and commercial shrimp. Many marsh creeks also host oyster (Crassostrea virginica) reefs that form an important substrate and habitat for many invertebrates and fishes. All of the above elements are highly interactive and constitute an exceedingly productive ecosystem. The ecological functions of salt marsh also include the provision of nursery and adult habitat for invertebrates, fish, and birds; protection of shorelines from erosion; and removal of excess nutrients from the water column.

Mangrove Forests

Mangrove forests are very productive ecosystems that provide habitat and shelter for many fish and invertebrate species, from larval and juvenile stages through adulthood. These habitats serve as valuable nursery areas by providing a rich source of food and offering safety from predation. They also help protect coastlines by using their roots to stabilize sediment and prevent erosion from waves and storms. Florida’s fisheries would suffer greatly if species did not have access to healthy mangrove habitat. One such species that relies heavily on this habitat is the Goliath Grouper. They remain primarily in nearshore mangrove habitats as juveniles until they mature and move to offshore reefs. Learn about Chris Malinowski’s (FSUCML graduate student) mangrove field work on juvenile Goliath Grouper here

Sand Dunes

Sand dunes occur along high-energy shorelines, extending from the beach to the inland forest. They are formed by the interaction of wind and "pioneer" plants that establish along the beach and help trap the sand. Plants that establish in the sand dunes, such as Sea Oats grass that lives in the fore zone--must be able to withstand harsh winds and salt spray. Their success is essential for maintaining the structural stability of the dunes. As sand is piled shoreward, it accumulates around roots of the pioneer plants, creating large mounds that protect the inner area from wind and salt spray. Winds push the dunes landward, where nutrients accumulate and different plants establish, while new foredunes are formed near the shore. This cycle reflects the formation of barrier islands, with dunes in different stages of succession supporting a large diversity of plant and insect species.


A bog is a type of freshwater wetland that is characterized by highly acidic soils and generally dominated by sphagnum moss. These conditions create a unique habitat where a number of highly specialized plants can be found, including bog buttons, blueberries, and a number of beautiful orchids. However, they are also ideal conditions for insectivorous plants such as sundews, bladderworts, butterworts, and pitcher plants. Bogs are important ecological areas for the rare species and high diversity that they support. Many bog communities are located in pine savannas in the Apalachicola National Forest, just a short drive from the FSU Coastal and Marine Laboratory.

Pine Communities

Sandhills and flatwoods are pine communities that are common in northwest Florida. They share a sparse canopy consisting of longleaf (Pinus palustris) or slash pine (Pinus elliotti) but the understories, fire regimes and soils differ. Sandhills occur in areas with deep, sandy, well-drained, low nutrient, soil and are characterized by longleaf pine overstories and wiregrass groundcovers. Flatwoods occur in flat, sandy areas, and can be either wet or mesic. Wet flatwoods occur in depressions or over clay hardpans that impede drainage while mesic flatwoods occur in areas that are inundated less frequently. Slash and longleaf pines both form the canopy of flatwoods but slash pine is more common along the coast. However, longleaf pines can still be the dominant canopy tree in some flatwoods such as the FSUCML’s North 70 tract which is home to old growth longleaf pines. Like sandhills, wiregrass is a typical component in flatwoods but unlike sandhills, shrubs are also a major component of the understory. The pine communities are all dependent on fire. Some communities naturally burned as frequently as every two years. Although sandhills, wet flatwoods, and mesic flatwoods are considered unique communities, in reality they occur in a mosaic pattern and are interspersed with each other and with other wetland and hardwood community types. The habitat diversity created by the mosaic is critical for many species including some species that are dependent on pine communities.

The FSUCML has an ongoing restoration project in the North 70 tract mentioned above. We are working to return fire to the Longleaf pine forest, which comes with a unique set of challenges. Learn about the Longleaf restoration project at the FSUCML.

Learn about Fire Weather from a WeatherSTEM lesson, which features the FSUCML restoration project here.

Last Updated: Monday, January 27, 2020 at 4:19 PM