Indian River (Fla. : Lagoon)

Impoundments in the Indian River Lagoon, originally built to control saltmarsh mosquitoes, led to the isolation of fish nursery habitats. Rotational Impoundment Management (RIM) aims to mitigate this by hydrologically reconnecting impoundments during mosquito non-breeding seasons. However, current practices may not effectively facilitate juvenile fish emigration. This study incorporates summer openings (drawdowns) of culverts into RIM to improve the emigration of juvenile tarpon and snook. Tagged fish were monitored with RFID technology for 18 months in four impoundments. The abundance and size distribution of tarpon and snook populations differed among impoundments, reflecting variations in habitat structure and water quality. Summer drawdowns did not significantly increase emigration rates. However, tarpon detections increased during closed-culvert periods in all impoundments, and snook detections increased in one impoundment. Despite low emigrations, the study offers insight into the behavior of juvenile fish in these impoundments and suggests ways to enhance their nursery functionality.

In the inter-coastal waters of Florida, green sea turtles (Chelonia mydas) are regularly exposed to regional blooms of harmful algae which produce biotoxins. A retrospective analysis was conducted on stranded green sea turtles along the Indian River Lagoon, FL, USA. Stranding, necropsy, and histopathology reports were analyzed for 40 juvenile turtles. Liver (N=40) and kidney (N=36) tissues were analyzed for a suite of 14 harmful algal bloom (HAB)-associated biotoxins. Thirty-four (85%) turtles tested positive for at least one biotoxin, including 21(53%) liver and 22(61%) kidney tissues. Statistically significant relationships were identified between the presence of common histopathological abnormalities and biotoxins of: melanomacrophage/hyperplasia and brevetoxin-3 (P=0.03) in liver tissues, and renal fibrosis and nodularin (P = 0.04) and lymphocytosis and neosaxitoxin (P=0.03) in kidney tissues. These data demonstrate that wild turtles are commonly exposed to HAB-associated biotoxins with potential chronic health effects that contribute to strandings in the Indian River Lagoon.

Eutrophication of urbanized estuaries is a global issue that continues to worsen as coastal development increases. The Indian River Lagoon (IRL) on Florida’s east-central coast is a eutrophic estuary that is experiencing harmful algal blooms of macroalgae and phytoplankton, as well as widespread seagrass losses. This is concerning as seagrasses provide many ecosystem services, including the provision of essential habitat. These alterations in benthic cover can have ecosystem level effects and require further investigation. Thus, drivers and effects of primary producer alterations in the IRL were investigated through analysis of long-term monitoring data, field surveys of faunal densities inhabiting macroalgae and bare bottom habitats, and stable nitrogen isotope (δ15N) analyses of primary producers, primary consumers, and secondary consumers. Long-term monitoring data from the northern IRL (NIRL) and Banana River Lagoon (BR) demonstrated there have been major seagrass losses coupled with increases in occurrence of the rhizophytic green macroalgae Caulerpa prolifera, which is now the dominant benthic cover in many locations. Multivariate analyses of long-term monitoring data spanning 2011-2020 suggested that the carbon to phosphorus ratio (C:P) of macroalgae is an important factor related to annual changes in benthic cover in the NIRL and BR; increased P-availability is correlated with these primary producer shifts. In situ collections of macroinvertebrates and resident fishes showed the current function and importance of macroalgae as habitat in the NIRL and BR, particularly in the relative absence of seagrass.

Coastal wetlands across the Indian River Lagoon (IRL) on the east coast of Florida have been impounded for mosquito control purposes, which have been known to have adverse effects on overall fish populations. The objective of this project was to assess the use of culverts by species of larval fish at three impounded mangrove sites in the IRL. Light traps were used to collect samples of larval fish (both inside the basins and in the surrounding lagoon) which were humanely euthanized, preserved, and examined under a digital microscope. A total of 3,926 fish were collected from 24 taxa in 576 samples over the year-long study. Larval seasonality generally followed known reproductive seasonality of the species captured. Inside the impoundments were dominated by species known to spawn in and around mangroves such as the Gambusia holbrooki and Poecilia latipinna. Species that spawn in the IRL or in coastal waters that subsequently use the IRL as a nursery (such as Anchoa mitchilli and Gobiosoma robustum) had relatively low catches in the impoundments. Larvae of the main sportfishery species that have juveniles known to utilize the studied impoundments (Megalops atlanticus, the Atlantic tarpon, and Centropomus undecimalis, the common snook), were rarely caught inside the impoundments or in the surrounding IRL. The low numbers of IRL and offshore spawning larvae that enter the impoundments may be hindered by restricted water flow through culverts connecting the habitats, or by their inability to survive the low DO conditions often found inside the impoundments, especially during the summer. The lack of larval tarpon and snook in the light collections suggest that these species metamorphose from the larval to juvenile stage outside of the impoundments, before they enter the mangrove-dominated nursery habitats. The results of the study can be used to further modify impoundment restoration and management strategies to enhance their role as fish nursery habitats.

Sponges (Phylum Porifera) are hardy organisms persisting and predicted to become more dominant world-wide under climate change scenarios. However, we lack baseline knowledge on sponge biodiversity in transitional areas (subtropical to warm-temperate) that are more susceptible to climate change such as The Indian River Lagoon (IRL) (estuary) and Saint Lucie Reef (northern most coral reef) ecosystems in south Florida. The aims of this master’s thesis are to 1) evaluate if sponge assemblages reflect the previously defined ecotone between subtropical and warm-temperate biomes in the IRL (Chapter one), 2) determine how porifera communities are associated to their respective environment (temperature, water velocity, photosynthetically active radiation, carbonate chemistry, and nutrients) in the IRL and St. Lucie Reef (Chapter two), and 3) establish a distribution baseline for future studies aiming to assess Porifera range shifts during climate change (Chapter one and two). Porifera biodiversity surveys across the IRL and Saint Lucie reef were carried out at different spatial and time scales. Environmental parameters (ocean acidification, temperature and eutrophication) were obtained and compared for sites in Fort Pierce Inlet and St Lucie Reef. Chapter one results show that sponge assemblages do not reflect the previously defined ecotone between subtropical and warm-temperate biomes in the IRL, instead they structure in relation to the inlets (distance from the inlet). The most diverse sponge assemblages are found in Sebastian, Fort Pierce, and Jupiter Inlets, and are significant different among habitats; oyster reefs host a unique assemblage of excavating sponges.

Cultivation of microbial populations is a necessity for the use of microbes within the biotechnological and pharmaceutical industries, however, approximately only 1% of bacteria have been successfully cultivated in the lab. Dilution to Extinction (DTE) is a technique which involves serially diluting a microbial suspension to single cell inoculum prior to inoculation in a liquid medium designed to replicate natural aquatic environments. This technique was used here for the cultivation of diverse, potentially novel microbes from the marine sponge, Mycale microsigmatosa. One hundred thirty-six samples were successfully sequenced and identified with the majority belonging to the classes Alphaproteobacteria and Gammaproteobacteria. Furthermore, when combined with miniaturized fermentation, DTE allowed for the isolation and identification of marine natural products (3-Heptyl-3-hydroxy-2,4 (1H, 3H)-quinolinedione and 2-Heptyl-4-hydroxyquinoline) active against Methicillin-resistant Staphylococcus aureus. These metabolites originated from Pseudomonas aeruginosa, an isolate obtained from Mycale microsigmatosa using this technique.

Diamondback terrapins (Malaclemys terrapin) are an exclusively brackish water turtle found along the east coast of the United States. Very little is known about the Florida east coast diamondback terrapin (M. t. tequesta). This study examined wild terrapins in the central Indian River Lagoon to establish baseline population parameters for the species in this region. Morphometrics were assessed for the sampled animals, reinforcing findings of sexual dimorphism for the species. Acoustic monitoring was used to investigate terrapin occupancy and habitat use. Occupancy differed seasonally, with the highest occupancy in the summer and fall, lower occupancy in the spring, and the lowest occupancy in the winter. Terrapins were detected most commonly and spent a high percentage of their time in the southern portion of the study site. Reference blood chemistry values were established for the population. This study provided baseline information on a Species of Greatest Conservation Need in Florida.

This study explored spatiotemporal patterns in movement, diet, and baseline phycotoxin concentrations in immature bull sharks (Carcharhinus leucas) of the Indian River Lagoon (IRL), an estuary of national significance that has been considerably impacted by multiple toxic harmful algal blooms (HABs). Long-term spatial use of the system was assessed for 29 acoustically tagged sharks over a 4 year period (2017–2020). Tissue samples for diet and toxin analysis were collected from a separate cohort of 50 individuals between 2018 and 2020. UPLC-MS/MS was used to screen tissues for 14 algal toxins. Young bull sharks were found to be mainly piscivorous and displayed high residency to the IRL as well as to specific regions of the IRL, with small activity spaces. Multiple phycotoxins were detected in screened tissues, indicating that young bull sharks in the IRL may be compromised by trophic transfer of HABs while they reside in this important nursery.

The Indian River Lagoon (IRL) spans approximately one-third of the east coast of Florida and faces numerous harmful algal blooms. The potentially toxic diatom, Pseudonitzschia, has been observed in many locations of the IRL. The goal of this study was to obtain a better understanding of the factors contributing to population dynamics of Pseudo-nitzschia in the southern IRL system. Bi-monthly surface water samples were collected for 18 months from five locations. Cell counts enumerated all microphytoplankton, and environmental data was collected at sampling sites throughout the study by the Indian River Lagoon Observatory Network. Six species of Pseudonitzschia were isolated and characterized through 18S Sanger sequencing and scanning electron microscopy, all showed toxicity. Surface water samples also showed domoic acid (DA) presence. We report the first known occurrence of Pseudo-nitzschia micropora in the IRL and the first known DA production from this taxon.

The Indian River Lagoon (IRL) FL, USA, is an Estuary of National Significance due to its economic and high biodiversity. Microbial populations are understudied in the IRL despite their numerous ecological services. A two-year, nineteen-site Lagoon-Wide Survey (LWS) was conducted to provide the first 16S rRNA amplicon sequencing data on the microbiome of the sediment in the IRL and determine how the microbiome changed in response to environmental and anthropogenic factors. The most influential variables that explained the variability between microbiomes were porewater salinity, total organic matter (TOM), and copper (Cu). These results correlated with some of the anthropogenic pressures the IRL faces such as freshwater discharges from St. Lucie Estuary (SLE), trace metal contamination, and the accumulation of fine-grained, highly organic sediment known as “IRL muck” (muck). Research then focused on determining the microbial differences between three sets of sample types: sediment from the IRL versus the SLE; sediment that had three muck characteristics versus those with zero; and high TOM sediment that had high Cu versus high TOM sediment that had low Cu. Differentially abundant prokaryotes between sample types were determined with novel indicator analysis techniques. One technique tested the effectiveness of an indicator list to separate samples based upon the product of the sensitivity and specificity of partitioning around medoids clustering in comparison to metadata classifications. The other technique allowed for the tracking of changes in the entire indicator microbiome. These new indicator analysis techniques were created using the original LWS data and tested to determine how sediment microbiomes responded during two opportunistic surveys: dredging of muck from an IRL tributary (Eau Gallie River) and Hurricane Irma. These studies have filled the knowledge gap regarding the unknown microbiome of the IRL and how sediment microbiomes respond to extreme events such as dredging and a hurricane. They also led to the development of new indicator analysis techniques that can be used by to track changes in the entire indicator microbiome.