Rainbow Parrotfish Scarus Guacamaia

Rainbow Parrotfish Scarus Guacamaia Abstract The rainbow parrotfish Scarus guacamaia is a prominent herbivore in the coastal waters of southeastern Florida whose life history is strongly linked to a dependence on both mangrove and coral reef habitats. Rainbow parrotfish also serve in maintaining the health of coral reefs by keeping algal populations in check. Using NOAA fisheries data from the Mangrove Visual Census and the Reef Visual Census, this study focused on observations of this species in Biscayne Bay and the Upper Florida Bay in order to quantify occupancy and to examine the different factors that affect the presence and absence, and the ontogenetic shifts present in this species between juvenile and adult stages. Logistic regression was used to predict abundance and occurrence using the environmental variables of temperature, dissolved oxygen, salinity, average depth, and distance from channel openings. Presence and absence were also measured against mangrove cover, bottom substrate type, and shoreline development. It was found that salinity, average depth, and distance from channel openings were significant in predicting the occurrence of this species, while temperature and dissolved oxygen were not. Conservation efforts for this species, listed as vulnerable under the IUCN, need to be given greater consideration as the health of this and other parrotfish may be useful in determining the management breadth and priorities on coral reef ecosystems across the Caribbean Sea. Key words: rainbow parrotfish, mangroves, logistic regression, conservation, land-use planning. Acknowledgements In completing this thesis research, I would foremost like to thank my advisor, David W. Kerstetter, Ph.D., and committee members John F. Walter III, Ph.D. and Richard E. Spieler, Ph.D., whose input and guidance has been critical in moving forward through this project. I would like to thank David L. Jones, Ph.D. for his assistance on equations and statistics. For their assistance in various aspects of ArcGIS, I would like to thank Brian K. Walker, Ph.D. and Kristian Taylor. Notably, I would like to thank James A. Bohnsack, Ph.D. and Joseph E. Serafy, Ph.D. and their work, without whom, this research could not have taken place. I would like to thank my lab mates, especially Bryan Armstrong, Shannon Bayse, Amy Heemsoth, Cheryl Cross, and Kerri Bolow for all their feedback, inquiries, assistance and advice throughout the entire research process. Finally, I would like to thank my family and all my friends for their tireless support and unfailing encouragement in the completion of my thesi s work. Introduction Life History of the Rainbow Parrotfish Rainbow parrotfish Scarus guacamaia is the largest herbivorous fish in the Atlantic Ocean and Caribbean Sea and is found in both mangrove and coral reef habitats (Mumby 2006). The rainbow parrotfish is a large, heavy-bodied, and laterally compressed fish, compared with other species of reef fish. It has a fusiform body shape with dull orange fins possessing streaks of green extending into the dorsal and anal fins; median fin margins are blue in color with the dental plates appearing a blue-green. In this species there appears to be no obvious color differentiation based on sex (Cervigà ³n 1994). Rainbow parrotfish are behaviorally cautious in nature, and are generally observed in isolation, though they can be found in schools of up to thirty individuals (Dunlop and Pawlik 1998). It has a daily home range of about 1000 m3 (Smith 1997), and occupies varying depths from the surface to 25 m. It depends on corals for shelter and space to inhabit (Cole et al. 2008) and seeks shelter under ledges at night or when threatened. The species has been shown to use the angle of the sun as an aid in returning to these shelters (Smith 1997). Rainbow parrotfish are herbivorous fish that, like most members of the Scaridae family, feed mainly by scraping macro-algae from coral structure (Bellwood et al. 2004). However, it has also been observed to feed directly on coral (Rotjan and Lewis 2006) and gut content analyses have revealed spicules from feeding on sponges (Dunlop and Pawlik 1998). Rainbow parrotfish life history characteristics are reasonably well known. It is a protogynous hermaphrodite, meaning individuals in this species undergo a sex change between their initial phase, where they are generally female and terminal phase, where they are male. Terminal phase male rainbow parrotfish defend a territory and a harem of females, and when the male dies, the most dominant female will become the dominant male, with her ovaries becoming functional male testes (Streelman et al. 2002). Like other species in this family, peak spawning occurs primarily in warmer summer seasons from May to August, but can occur year-round, and there is an active period of recruitment into the population occurring around February in this region (Haus et al. 2000). Spawning is found to take place generally around dusk, and may correlate to either the lunar cycle or the high tide, as this is an optimal time for egg dispersal. The initial phase is composed of females while the terminal phase i s composed of sexually mature males. Rainbow parrotfish aggregate into territories that contain a group of females and the dominant male, which pair-spawns almost exclusively within this group (Munoz and Motta 2000). The rainbow parrotfish is a relatively large reef fish, compared to most species of reef fishes in the Caribbean, and can achieve a maximum length of 120 cm (TL). The estimated K value of 0.293 equates to a minimum population doubling time of approximately four and a half to fourteen years (Robins and Ray 1986; Randall 1962). Observations of rainbow parrotfish have been made in waters with temperatures ranging from 12-36  °C, salinities ranging from 23.74 to 39.1 †° (parts per thousand), and dissolved oxygen concentrations ranging from 2.4 to 14.07 †° (Serafy et al. 2003). The species wide range of tolerances to these factors is most likely an adaptation to the wide range of its known habitats. These habitats range from estuaries to offshore areas, both of which are subject to large pulses of freshwater and storm events. The varied thermal and oxic conditions cannot be exploited by less tolerant species and may be beneficial in providing refuge from predators, foraging gr ounds, or potential nursery areas (Rummer et al. 2009). The diet of rainbow parrotfish has been shown to be variable across life stages and habitats. In the Dunlop and Pawlik (1998) study, sponge spicules were found in higher masses in the individuals collected from the mangrove sites as compared to those from coral reefs, suggesting there are shifts in diet preference based on the food sources available. A secondary food source is coral, as rainbow parrotfish has been classified as a facultative corallivore based on direct observations, meaning coral can be either a majority of their diet or only a minor component. These fish impose more permanent and chronic pressures on scleractinian corals (those that generate a hard skeleton such as Montastrea and Porites species) meaning there is repeat scraping activity on these corals, and the damage caused is longer lasting. However, chronic predation may play a factor in regulating distribution, abundance, and fitness of certain prey corals (Cole et al. 2008). Though not fully known, this corall ivory may be part of an ontogenetic diet shift, meaning coral is only an important food source for part of their lives, accounting for less than five percent of their bites (Cole et al. 2008). Along with this diet selectivity comes the ability to cause significant damage to corals by biting off growing tips or large portions of skeletal material, which means they are capable of having a disproportionately large impact on the physical structure of Caribbean reefs (Cole et al. 2008). It has also been observed that grazing reduced the density of zooxanthellae and increased the severity of a bleaching event in Belize (Cole et al. 2008). Rainbow parrotfish use a feeding method of scraping or grinding algae from the coral or other rocky substrate, and sometimes inadvertently ingests coral animals as well. The hard coral substrate is broken down through its digestive system, and the excretion of this limestone material is one of the main sources in the creation of the sand surrounding cora l reefs in the Caribbean. Parrotfishes are known to become progressively more important to coral reef ecosystems upon reaching a certain key size around 15-20 cm, at which point they become functionally mature (Lokrantz et al. 2008) and their actions provide a significant impact on the coral reef. This impact increases exponentially as there is a non-linear relationship between body size and scraping function. Calculations have suggested that up to 75 individuals with a size of 15 cm are required to functionally compensate for the loss of a single 35 cm individual, and a 50% decrease in body size can result in a 90% loss of function provided to the ecosystem (Lokrantz et al. 2008). In addition, the level of grazing impact in mangrove systems is also a power function of body length. A conservative estimate places the home range of S. guacamaia at 1600 m3 (Mumby and Hastings 2008), which is larger than that of many other scarids. Rainbow parrotfish also represents approximately 14% of the total grazing intensit y measured for mangrove depauperate systems (Mumby and Hastings 2008). The majority of the rainbow parrotfish diet consists mostly of short epilithic turf algae, cropped algae, red coralline algae, and filamentous algae (Mumby and Hastings 2008), and they feed heavily upon Halimeda opuntia, a green calcareous alga. Juvenile scarid abundance has also been shown to be positively related to the percent cover of Dictyota spp. algae at site level in the Florida Keys (Kuffner et al. 2009). Similar parrotfish species have been observed consuming whole pieces of the thallus rather than grazing on the attached epiphytes, and taking more bites from H. opuntia and fewer bites from coral than would be expected from the percent cover of different microhabitats (Munoz and Motta 2000). While not quantitatively known for rainbow parrotfish, a mean home range for similar parrotfish species, redband parrotfish and redtail parrotfish, in the Florida Keys was observed to be 4371.5 +/- 5869.5 m2 (Munoz and Motta 2000); the standard error was found to be high due to a low nu mber (n = 7) of study sites. Due to overlap in microhabitat and foraging areas in these home ranges, interspecific aggression between parrotfish species takes place when one species attempts to use defended resources to the detriment of the defending species. This aggression involves vigorous chasing over comparatively large distances, as well as biting. Engaging in resource defense behavior was found to be advantageous as the benefits gained outweighed the cost (Munoz and Motta 2000). Aggression has also been observed to be greater when encountering other parrotfish species as opposed to non-parrotfish species and rainbow parrotfish were instigated into these aggressive encounters most often by redband parrotfish Sparisoma aurofrenatum (Munoz and Motta 2000). Scarus guacamaia is most closely related phylogenetically to midnight parrotfish Scarus coelestinus and striped parrotfish Scarus iseri, with Scarus clades having root nodes at between 2 and 3 million years ago, thus implying that most Scarus species are products of recent speciation. This speciation likely occurred around the time of the complete closure of the Isthmus of Panama at approximately 3.1-3.5 million years ago (Smith et al. 2008). The pantropical distribution and the relatively recent ages of the divergence of the four main clades of Scarus imply that fluctuations in sea level and patterns of differential cooling of the oceans during the Pliocene and Pleistocene may be the driving forces behind the rapid radiation in this genus, which is today largely restricted to the complex reefs built by hard corals (Smith et al. 2008). Alternatively, processes of ecological speciation and divergence due to sexual selection remain a possible explanation for the rapid radiation of parr otfishes, which all have pelagic larval phases and highly similar morphology (Smith et al. 2008). The protogynous mating system of parrotfishes, where species aggregate and have male-dominated haremic systems organized by color recognition, has also been proposed as a possible driving force for speciation via sexual selection mechanisms (Smith et al. 2008). The phylogeny of parrotfish suggests a gradual shift from browsers living in seagrasses to excavators inhabiting rock and/or coral reefs to scrapers found exclusively in association with coral, with Sparisoma being considered the transitional genus (Streelman et al. 2002). It can be assumed that the Scarus genus has always had a habitat association with coral reefs as the Scarus genus is the third radiation off of the Sparisoma lineage (Streelman et al. 2002). Of the parrotfishes, S. guacamaia is the only species that possesses an obligate and functional dependence on the mangrove habitats (Nagelkerken 2007; Mumby 2006). This dependency has been shown quantitatively in the Mumby et al. (2004) study in which the species suffered local extinctions that corresponded with the removal of mangrove stands, and the extent of mangrove coverage in a region is one of the dominant factors in structuring reef communities. Mangrove connectivity enhances the biomass of rainbow parrotfish on neighboring coral reefs, because grazing influences the cover of macroalgae on reefs and high levels of parrotfish grazing has been shown to lead to a twofold increase in recruitment of Porites and Agaricia corals in the Bahamas (Mumby and Hastings 2008). Biomass of rainbow parrotfish has been shown to more than double when coral reefs were located adjacent to rich mangrove resources, defined as mangrove stands with 70 km or greater of fringing red mangrove Rhizophora mangle located in a region of 200 km2, equating to coverage of 35% (Mumby 2006). Juveniles of this species, those less than 30 cm total length (TL), are observed almost exclusively in mangrove habitats, while all individuals observed on the coral reef were greater than 25 cm TL (Dorenbosch 2006). Average sizes of 10.1 cm and 14.6 cm TL have been recorded in mangroves and seagrass beds, respectively (Nagelkerken et al. 2000). The species of juvenile reef fishes that utilize mangroves and seagrass beds do so because of the high food availability, the presence of shade and shelter that the mangroves provide, and a reduced risk of predation due to the plant and root configurations. There is also a lessened chance of interaction with predator species as well as low predator abundance and efficiency (Verweij et al. 2006). Shallow water habitats such as mangroves and seagrasses, are believed to contain less piscivores than the reef (Verweij et al. 2006) possibly because the energetic cost s of chasing the smaller fish in these habitats outweigh the gains of catching one of the prey fish. The turbidity of the water can also negatively affect predator efficiency due to scattering and reduction of light by suspended particles (Verweij et al. 2006). There is significant interannual variability in species composition that may be expected in mangrove fish communities, but spatial factors have been found to contribute more to differences in fish community structure than seasonality (Robertson and Duke 1990). Verweij et al. (2006) tested the effects of plant structure, shade, and food upon rainbow parrotfish foraging behavior using artificial seagrass leaves and artificial mangrove roots. Rainbow parrotfish showed the same trends as those of pooled herbivores, showing highly significant Poisson regression results for the tested variables of structure, food, structure*food, and location of the experimental unit. In this study, 72 individuals were observed ranging in size from 7.5-15.0 cm. The behavior observed was broken down into 2.8% of individuals resting (spaced evenly throughout the water column), 91.7% foraging, and 5.6% swimming. Eighty-four percent of the rainbow parrotfish observed foraging in the study were found in the artificial mangrove roots, with six percent foraging on artificial seagrass leaves. It was determined that the presence of higher surface area on the root structure provided more substrate for algae, which allowed for diurnal feeding (feeding that occurs in the da ytime) on the fouling algae and epiphytes in mangroves and seagrass beds. Rainbow parrotfish observed in this study were also found to be preferential to experimental units with the highest structural complexity. Caribbean region mangroves and seagrass beds function as foraging habitats, but are not used continuously as shelter during the daytime (Verweij et al. 2006). The value of these habitats is diminished with decreased water clarity from turbidity originating from terrestrial run-off, leading to population declines in this and other species (Freeman et al. 2008). Seagrass minimum light requirements differ between species and systems. Halodule and Syringodium seagrass species often require more than 24-37% surface light intensity (Freeman et al. 2008). These seagrass species consistently require minimum light levels that are an order of magnitude higher than the requirements of terrestrial plants or other photosynthetic marine organisms. Reduced subsurface light intensity has c aused seagrass declines and the subsequent re-suspension of unstabilized sediments has impeded recovery of these seagrass systems, increasing the pressure placed on species such as the rainbow parrotfish that depend on them (Freeman et al. 2008). However, presence of preferential habitat is not the only contributing factor determining abundance. It is possible that habitat configuration has an influence on the connectivity between mangroves, seagrasses, and coral reefs and this configuration in terms of providing pathways and connections to the reef affects fish assemblage composition, fish density and size, and species richness (Dorenbosch et al. 2007). Local recruitment patterns can also play a major role. In a study off Curaà §ao, juvenile densities on the reef were comparable to those in seagrass beds, suggesting that this species can also use the coral reef as a nursery (Dorenbosch et al. 2004). Dorenbosch et al. (2007) concluded that for rainbow parrotfish, migration among these habitats most likely takes place along the coastline. The presence of seagrass-mangrove bays along the coasts of these islands strongly influences the distribution pattern of this species on the coral reef (Dorenbosch et al. 2004). The absence of seagrass beds and mangroves was shown to lead to reduced density of those species that utilize seagrass-mangrove bays in juvenile stages (Dorenbosch et al. 2004). For island sites, this migration was observed to occur on the sheltered or leeward shores, where most adult individuals were observed on coral reefs between 0 and 10 km from mangroves. However, no significant linear relationship was present between mean total density of adult rainbow parrotfish on these reefs and the distance to the nearest stands of mangroves (Dorenbosch et al. 2006). There was also reduced density or complete absence of juvenile rainbow parrotfish on the coral reefs that were farther than nine kilometers from the mangrove and seagrass habitats used by fish of juvenile ages. The density of these species is additionally regulated on local scales by variable habitat structural complexity and the available vegetation. Herbivory, measured by rates of grazing, was found to be highest at the maximum habitat complexity site (Unsworth et al. 2007). This suggests that the increased shelter and food abundance provided by denser seagrass beds may have increased fish abundance resulting in these higher levels of herbivory (Unsworth et al. 2007). Herbivory was found to increase away from patchy seagrass areas whilst increasing distance from a reef reduced the rate of herbivory due to a reduction in fish migration. Observed high levels of herbivory, however, may only be a short-term effect of irregular grazing by shoals of juvenile and sub-adult scarids (Unsworth et al. 2007). Rainbow parrotfish migrate across habitats in accordance with its life history stage, and will grow as large as possible before moving on to the next habitat (Mumby et al. 2004). Utilization of intermediate nursery habitats has been hypothesized to increase survivorship of small fish (Mumby et al. 2004). The intermediate nursery stages between mangroves, seagrass beds, and patch reefs serve the function of alleviating predatory bottlenecks in early demersal ontogeny (Mumby et al. 2004). A predatory bottleneck occurs when pressure from predation prevents a large percentage of a population from reproducing. The presence of seagrass beds has also been linked to significantly higher densities of rainbow parrotfish on coral reefs (Dorenbosch et al. 2006) while other studies (e.g., Gonzalez-Salas et al. 2008) have found differing results with respect to these nursery habitats. Noting high abundance of juveniles and adult members of S. guacamaia in coral reef habitats and a total absence in mangrove stands, it appears that mangroves in certain regions do not function as obligate habitats and that seagrass and coral rubble become the primary alternative for nursery, growth, and reproduction (Gonzalez-Salas et al. 2008). It is possible that with removal of mangrove forests the rainbow parrotfish are adapting to utilize other habitats that offer similar survival benefits. The reduced benefits of these marginal habitats may not provide rainbow parrotfish with the resources necessary to survive across their entire life history, allowing only temporary survival through one life stage or another (Rummer et al. 2009). This selective use, which is defined as use of a particular habitat patch disproportionately relative to its availability, can be exhibited either seasonally or spatially, and proximity rather than suitability has been found as the dominant pattern of habitat use (Faunce and Serafy 2008). Mangrove shorelines across broad spatial scales are not equivalent in thei r value as fish habitats due to the inherent patchiness within the ecosystem. A measure of total habitat area may therefore overestimate the amount of functional habitat utilized by these fishes. In addition, species richness and total number of fishes collected adjacent to mangrove shorelines has been shown to decline with increasing inland distance from creek mouths and oceanic inlets, with water depth greatly related to fish use (Faunce and Serafy 2008). Rainbow parrotfish are valuable members of the communities with which they are associated. The grazing activities of these parrotfish are beneficial in preventing algal overgrowth and enhance coral reef resilience to algal blooms and other competitor species (Hughes et al. 2007). The species also facilitates settlement and survival of corals by scraping and bioeroding the hard dead coral substratum and are crucial for the regeneration and maintenance of coral reefs (Lokrantz et al. 2008). Rainbow parrotfish and other scarid species participate in not only the uptake of carbon into the food chain in their direct consumption of seagrass, but also indirectly contribute to the detrital food chain with the removal of decaying seagrass material, which potentially results in the widespread dispersal of seagrass material into surface waters. Detached seagrass may also be cast onto the shore where it decays and may re-enter the system as detritus (Unsworth et al. 2007). Rainbow parrotfish may be equally important in influencing seagrass export from the system by the high rates of material discarded during consumption. The unattached plant matter, estimated to be as high as 11% of seagrass growth, becomes subsequently removed from the system by weather and currents (Unsworth et al. 2007). This figure is in addition to the amount consumed in grazing which causes the loss of at least 16% of the seagrass growth each day (Unsworth et al. 2007). In spite of their ecological role and importance, S. guacamaia populations are thought to be in decline and to have been fished to ecological extinction in Brazil, as well as other areas of the Caribbean (Floeter 2006). Rainbow parrotfish has been listed as vulnerable on the IUCN Red List. This designation means the species is facing a high risk of extinction in the wild based on one or more of the following five criteria: reduction of population size, shrinking geographic range, a population with fewer than 10,000 mature individuals, restricted population extent, or quantitative analysis showing the probability of extinction in the wild is at least 10% within 100 years (the full explanation of which are detailed in the 2004 IUCN criteria; version 2.3, Roberts 1996). Given this information and the ecosystem role of the species developing a model that details occurrence provides a means to assess the health and function of this parrotfish in this region. In addition, one may apply the methods not only throughout the range of this species, but it may be possible to apply this model to other parrotfish species and similar families across the Florida Reef Tract and the Caribbean Sea. Characteristics of the Biscayne Bay and Florida Reef Tract Region The Biscayne Bay region receives high numbers of larvae from offshore spawning adults and functions as a source point for juveniles and adults to migrate to the reef tract (Wang et al. 2003). The region also contains some of the most pristine habitat within the Florida Keys (Ishman 1997). The coastal shelf of the Florida Keys is characterized by shallow and highly variable topography, where currents are influenced by tides, wind, and the very energetic offshore Florida current system (Haus et al. 2000). The eddies and meanders of the Florida Current make it possible for upwelling and larval transport to occur across the shelf, and the scale of these perturbations can vary from slow moving mesoscale gyres to faster moving, sub-mesoscale eddies (Haus et al. 2000). Velocities of these eddies can range from 0.53 m/s to 0.80 m/s along the inshore edge of the Florida Current (Haus et al. 2000) and the variability of those velocities can have an impact on dispersal and the resulting end loc ations of larvae (Haus et al. 2000). Patch reefs in this region occupy a significant portion of the water column, which leads to variability in the water depth. These protrusions have the potential to change the strength and direction of the tidal flow in the bay. The northern Florida Keys contain over 4,000 patch reefs, composed generally of cemented reef (47.3 +/- 2.2% cover) and pavement (20.1 +/- 2.1%), with varying amounts of rubble, boulders and sand (Kuffner et al. 2009). The benthic community observed on these patch reefs is largely dominated by macrophytes, encrusting invertebrates, and suitable settlement substratum found beneath a substantial canopy of gorgonian (soft) corals (Kuffner et al. 2009). Macroalgae occupies a large portion of space on the reefs, especially Dictyota spp. (15.4 +/- 0.8% cover) and Halimeda tuna (11.7 +/- 0.6% cover). Live scleractinian corals account for only 5.8+/- 0.6% of the benthos (Kuffner et al. 2009). The tides are generally weak, with a semidiurnal height range of approximately 0.5 m (Haus et al. 2000). As measured in Caesar Creek, tidal velocity can exceed 25 cm/s, while current measurements within the inlets have shown peak tidal velocities in excess of 50 cm/s (Haus et al. 2000). These channels commonly referred to as the ABC Channels because of their names: Angelfish Creek, Broad Creek, and Caesar Creek form the main outlet from the southern end of Biscayne Bay onto the Florida reef tract. The ABC Channels convey large oscillating tidal flows and wind driven flows between the bay and the ocean, and transport through these corridors predominantly shows a semi-diurnal cycle with amplitudes of 500 m3/s, 300 m3/s, and 250 m3/s respectively (Wang et al. 2003). Based on observations, there is a net outflow at Angelfish and Caesar Creek, but an inconsistent inflow in Broad Creek (Wang et al. 2003). With the tidal flows and the input of freshwater, the residence times of the water varies widely from several months in the more enclosed Barnes Sound and circulation-restricted Card Sound (Ishman 1997), to about a month in the western parts of South Biscayne Bay, and nearly zero in the vicinity of the ocean inlets (Wang et al. 2003). The area encompassing Biscayne Bay south to Card Sound and Barnes Sound forms a barrier island lagoon system that exhibits estuarine characteristics near points of freshwater inflow during the wet and early dry season (Wang et al. 2003). This lagoon system leads to broad salinity regimes that are highly variable throughout the year, and vary greatly across relatively small areas of only several kilometers due to high freshwater input through canals (as opposed to groundwater), and limited tidal flushing. Salinity variations in Biscayne Bay primarily result from canal discharges through gated control structures, as well as smaller freshwater exchanges in the Bay driven by overland runoff, rainfall, and evaporation (Wang et al. 2003) and upwelling from groundwater (Ishman 1997). The greatest salinity fluctuations occur near canal mouths in Barnes Sound and along the western margin of Biscayne Bay. The smallest fluctuation ranges were observed near ocean inlets (Wang et al. 2003), where the vertical variations of salinity in the water column ranged from less than 0.2 †° to a maximum salinity change of 0.8 †° from top to bottom in the vicinity of the inlet mouth (Haus et al. 2000). In the Pelican Bank region of Biscayne Bay (see Figure 10), good circulation results in regular flushing and average salinities range from 33 to 35 †° (Ishman 1997). Water flow characteristics in this region are also determined by a network of drainage canals used for agricultural and industrial purposes. These canals also function to control flooding, which has greatly altered the distribution of freshwater within the watershed, as well as the quantity, quality, and timing of freshwater discharges to Biscayne Bay (Wang et al. 2003). This has led to greater pulses with larger peak discharges in the wet season and less freshwater reaching Biscayne Bay in the dry season due to reduced terrestrial storage and lowered groundwater levels (Wang et al. 2003). Increased runoff not only affects salinity conditions in coastal waters, but also can be a mechanism for increased nutrient loading (Rudnick et al. 2006). There exists a coastal ridge, bisecting the Bay, which acts as a groundwater divide, with water west of the ridge flowing toward Florida Bay. The outputs of freshwater from the canals have punctured massive holes through the ridge, changing the d irection and characteristics of the flow, and the qualities of the watershed (Wang et al. 2003). This region also is characterized by large coverage of submerged aquatic vegetation such as seagrasses, and wide availability of phytoplankton, microalgal and macroalgal species. Florida Bay is approximately 2000 km2 in total surface area, with 95% bottom coverage of seagrasses, characterized by sparse, patchy beds of Thalassia testudinum interspersed with locally abundant Halodule wrightii (Fourqurean and Robblee 1999). However, in the spring of 1991, Florida Bay exhibited a shift from a system characterized by clear water to one of extensive and persistent turbidity and phytoplankton blooms, which limits the ability of the seagrass to grow and function properly by reducing penetration of light in the water column (Fourqurean and Robblee 1999). This seagrass die-off was not accompanied or preceded by noticeable decreases in water clarity or increases in colonization by epiphytes, however. There were many hypothesized causes for this die-off which include hypoxia and sulfide toxicity , the loss of the estuarine nature of the system, overdevelopment of the seagrass beds, chronic hypersal