Thesis (Ph.D.)--University of Washington. / Vita. Bibliography: L. 122-128.

A series of modern sediment samples from seven sites and five sediment cores collected in central and southern Biscayne Bay were analyzed for benthic foraminifers. The goal of the research was to determine important foraminiferal assemblages in the modern environment, and use these data to assess the distributions of marine ecosystems over the past 100-400 years. Two of the cores are from localities in the mid-bay, whereas three represent near-shore sites. The latter cores were collected under the supposition that near-shore sites may be more sensitive to recent ecosystem change that may not be so readily apparent at the mid-bay sites. Seven assemblages were identified from these data that appear robust enough to be recognized at the regional level in Biscayne Bay. The assemblages identify a range of haline environments in Biscayne Bay both presently and in the recent past. None of the assemblages is typical of a continental shelf assemblage after Rose and Lidz (1977), but the conditions within Biscayne Bay include assemblages indicative of polyhaline-euhaline restricted circulation environments and mesohaline brackish environments. The near-shore cores reveal a pattern of assemblages indicative of increasing salinity. There is clearly a natural component of the ongoing Holocene marine transgression. However, there are key data which show sudden increases in salinity via rapid changes to the benthic foraminiferal assemblages. At Middle Key, salinity increases at the time of construction of the Key West Extension of the Florida East Coast Railway. Increased marine species at the top of the core corroborate the findings of Ishman et al. (1998) from a core in Manatee Bay. The foraminiferal assemblages near the top of the cores at Black Point North and at Chicken Key show a shift toward higher salinity conditions. Ostracode and mollusk data in Wingard et al. (2004) reveal an increase of genera that are tolerant of wide ranges of salinity. This manner of salinity fluctuations is not correlative to any patterns observed historically in any of the cores from Biscayne Bay. Recent changes to the marine ecosystems in Biscayne Bay reflect both natural and anthropogenic changes. It is necessary to determine appropriate restoration of natural sheet and groundwater flows to Biscayne Bay as part of the ongoing Everglades restoration to reduce the high stress of salinity fluctuations that are a recent alteration to the natural ecosystems in Biscayne Bay.

The spatial and temporal distribution of modern diatom assemblages in surface sediments, on the most dominant macrophytes, and in the water column at 96 locations in Florida Bay, Biscayne Bay and adjacent regions were examined in order to develop paleoenvironmental prediction models for this region. Analyses of these distributions revealed distinct temporal and spatial differences in assemblages among the locations. The differences among diatom assemblages living on subaquatic vegetation and sediments, and in the water column were significant. Because concentrations of salts, total phosphorus (WTP), total nitrogen (WTN) and total organic carbon (WTOC) are partly controlled by water management in this region, diatom-based models were produced to assess these variables. Discriminant function analyses showed that diatoms can also be successfully used to reconstruct changes in the abundance of diatom assemblages typical for different habitats and life habits. To interpret paleoenvironmental changes, changes in salinity, WTN, WTP and WTOC were inferred from diatoms preserved in sediment cores collected along environmental gradients in Florida Bay (4 cores) and from nearshore and offshore locations in Biscayne Bay (3 cores). The reconstructions showed that water quality conditions in these estuaries have been fluctuating for thousands of years due to natural processes and sea-level changes, but almost synchronized shifts in diatom assemblages occurred in the mid-1960’s at all coring locations (except Ninemile Bank and Bob Allen Bank in Florida Bay). These alterations correspond to the major construction of numerous water management structures on the mainland. Additionally, all the coring sites (except Card Sound Bank, Biscayne Bay and Trout Cove, Florida Bay) showed decreasing salinity and fluctuations in nutrient levels in the last two decades that correspond to increased rainfall in the 1990’s and increased freshwater discharge to the bays, a result of increased freshwater deliveries to the Everglades by South Florida Water Management District in the 1980’s and 1990’s. Reconstructions of the abundance of diatom assemblages typical for different habitats and life habits revealed multiple sources of diatoms to the coring locations and that epiphytic assemblages in both bays increased in abundance since the early 1990’s.

Seagrass beds serve critical functions in coastal Florida ecosystems. The beds serve as nursery habitat for many juvenile reef fish species and provide protection for many types of benthic organisms found in Biscayne Bay. They help stabilize sediment that would otherwise increase turbidity around coral reefs, filter the water of contaminants, and help support an entire food web. Three species of seagrass were found at the study sites in northern Biscayne Bay: Thalassia testudinum, Halodule wrightii, and Syringodium filiforme. This study focused on understanding the organism habitat interaction by determining the species diversity, seasonal densities, and the correlation between population size and individual size for Penaeid shrimp, juvenile fish, and small adult fish at each site over a one year period. Habitat selectivity of various species was determined based on the habitat complexity derived from the various different seagrasses found in each of the beds. Animals predominantly favored H. wrightii habitat (Kruskal-Wallis H test: p< 0.0001) and this was likely the result of a decrease in predation risk due to the increased habitat complexity of the seagrass beds. Species diversity did not vary significantly over the course of a year (p= 0.7790), likely due to the lack of large abiotic disturbances (e.g. boating, hurricanes, and extreme salinity changes) to the seagrass beds. Densities of inhabitants changed significantly on a monthly basis, with the overall epifauna densities greatest at the end of the wet season (p< 0.01). The lack of correlation between individual size and overall population size likely indicated the majority of the species caught did not exhibit ontogenetic migration or live in the seagrass beds for the entirety of their life cycle.

Inshore tropical and subtropical estuaries harbor a relatively high abundance and diversity of organisms. Specifically within estuaries, mangrove and seagrass habitats provide shelter and food for a plethora of organisms, through some or all their life histories. Given the biological connection between offshore coral reefs and coastal estuaries, there is a critical need to understand the underlying processes that determine distribution and abundance patterns within mangrove-seagrass habitats. The predatory fish assemblage within the mangrove and seagrass beds of Biscayne Bay, Florida (USA), was examined over 24-hr. time periods along a distance and habitat gradient from the mangrove edge and nearshore environment (0–300 m) to farshore (301–700 m) seagrass beds. This thesis also investigated the occurrence, distribution and timing of reef fish movement between offshore coral reef habitat and inshore seagrass beds over 24-hr periods. Results indicate that fish predators differed over both the sampling period and with distance from mangrove edge. The results also demonstrated reef fishes move into Biscayne Bay at dusk and exit at dawn by utilizing Broad Creek Channel as a passageway. This work supports the idea of diel migration of selected reef fishes to inshore seagrass beds and highlights the importance of connective channels between habitats. The results suggest that the degradation or loss of seagrass habitat could differentially impact the life-history stages of reef fish species.

An ecological risk assessment was conducted on the risk to fish of chemical contaminants detected in the habitat of Albula vulpes in South Florida, to evaluate whether contaminants may be a driver of declines in the recreational bonefish fishery. All available contaminant detection data from Biscayne Bay, Florida Bay, and the Florida Keys were compared to federal and state guidelines for aquatic health to identify Contaminants of Potential Ecological Concern (COPECS). For these COPECs, species sensitivity distributions were constructed and compared with recent detections at the 90th centile of exposure. Copper in Biscayne Bay was identified as the highest risk of acute and chronic effects to fish, followed by a risk of chronic effects from both the recently phased-out pesticide endosulfan in Florida Bay, and the pharmaceutical hormone estrone in the Florida Keys.