Understanding the mechanisms that control sedimentation in the anchialine caves of the Yucatan Peninsula, Mexico is vital for interpreting the sedimentary deposits therein. External forcing mechanisms of varying scales, such as eustatic sea-level rise and large storm events, can have a significant influence on the rate and composition of sediment transported and deposited in the cave. Using sediment cores, high resolution radiocarbon dating, cave mapping and continuous aquifer attribute data, it was shown that sedimentation patterns in the cave were not controlled by sea-level rise/fall alone. Overlying vegetation and cave physiography were controlling factors which resulted in sedimentation in the cave being transient in time and space. The coastal aquifer responded to seasonal variations in precipitation but also showed a broad regional response to intense rainfall associated with Hurricane Ingrid in 2013. Due to the extensive hydraulic conductivity of the aquifer, the hydrologic response to Hurricane Ingrid was shorted lived (weeks) while its effect on sedimentation in the cave lasted for months. Sedimentation rates in the cave did not respond to elevated precipitation alone but showed a link with overlying vegetation. In regions of the cave with overlying mangrove forest, sedimentation was significantly higher than areas with tropical forest coverage. Mangrove forests baffled sediment creating an aquitard which resulted in the ponding of meteoric waters and subsequent enrichment in nutrients. Nutrient rich meteoric waters were funneled into cenotes increasing primary productivity for organic matter sediment production. Sedimentary deposits in anchialine caves are subject to punctuated sedimentation as a result of external forcing mechanisms or triggers. In the case of Yax Chen the trigger for sedimentation was not contemporaneous with Holocene sea-level rise. This has important implications for the use of cave sediments as proxies for sea-level research and paleo hurricane studies. / Thesis / Candidate in Philosophy

The overall goal of this dissertation is to define the hydrological, geochemical, and biological characteristics of a Karst Estuary. These types of estuaries represent a unique ecosystem created by freshwater inputs from direct flow through karst conduits and/or diffuse flow through a karst matrix. In order to determine the characteristics of a Karst Estuary we monitored short-term tidal fluctuations, long-term rainfall patterns, aquifer levels, spring discharge, multiple geochemical parameters, microbial communities in the water column and sediment, and macrofaunal communities in the sediment along a transect from a submarine spring through the Gulf of Mexico. Four sites were selected along a spring/marine transect and one nearby freshwater spring was used as a reference site. Datasondes were deployed in the nearshore brackish submarine spring to measure discharge volume, tidal fluctuations, and physical water parameters for two years. Water column and sediment samples were collected quarterly from both springs and the surrounding surface sites over the same time period. An isotopic/trace element mass balance method was used to determine the hydrogeological conditions of the spring discharge with three possible sources: 1) freshwater from the upper portion of the Upper Floridan aquifer, 2) freshwater from the lower portion of the Upper Floridan aquifer, and 3) saltwater from the Gulf of Mexico. Archaea, Bacteria, and microbial eukaryote communities were analyzed using molecular techniques, and macrofauna communities were determined using light microscopy. Correlation analyses were conducted to compare all studied biological communities to the hydrological and geochemical data in order to determine the influence of aquifer discharge. Within the water column of the submarine spring conduit, there were no significant differences of the sampled parameters over short sampling distances (m) and periods (hr). Spring discharge was found to be negatively correlated with tidal level and directly correlated with aquifer level. The brackish nature of the spring discharge is primarily due to simple mixing between the Gulf of Mexico saltwater and freshwater from the lower portion of the Upper Floridan aquifer originating from the mixing zone beneath the estuary. The composition of the spring discharge varied seasonally, showing increased marine influence at the beginning of the wet season. Tropical Storm Debby, June 2012, resulted in measurable freshwater inputs to spring discharge from the upper portion of the Upper Floridan aquifer. The number of spring reversals (salt water intrusion events) increased as the dry season progressed, stopped reversing immediately after Tropical Storm Debby, and then gradually increased into the next dry season. Statistically significant geochemical differences were found along the spring/marine transect on each collection date and seasonally at the individual sites. The major finding was that the primary driver of change in all of the studied biological communities of this Karst Estuary is the volume of aquifer discharge and the gradients formed by aquifer discharge and not the geochemical fluctuations within the system. Events that result in shifting the mixing zone inland have dramatic impacts on the biological communities of these environments. Karst Estuaries are a newly discovered type of ecosystem that are different from surface estuaries in that they are formed by aquifer discharge which is more stable in terms of geochemistry than water discharged to the sea via surface rivers.

Underwater (phreatic) caves are a ubiquitous landform on coastal karst terrain, but the marine geological processes operating in these systems are largely unknown. This dissertation redresses the problem by asking if Bermudian phreatic cave sediments archive sea-level and climate information? An important premise is that coastal cave environments are not identical. They can be categorized based on whether they are terrestrially-influenced (anchialine), completely flooded by saline groundwater (submarine), positioned at sea level (littoral) or in the vadose zone (vadose). For the first time the boundary between modern anchialine and submarine cave environments has been distinguished in Green Bay Cave using a multi-proxy approach (benthic foraminifera, sedimentary organic matter content and carbon isotopic composition - ?13Corg, and grain-size analysis). Twelve push cores were extracted from Green Bay Cave and dated with twenty 14C dates, recovering the first underwater cave succession spanning the Holocene (13 ka to present). Green Bay Cave transitioned through all major cave environments during Holocene sea-level rise (vadose, littoral, anchialine, and submarine), providing a sedimentary model for global cave successions. These relationships provide a novel means to solve Quaternary sea-level and climate problems. For sea level, two examples indicate that the littoral cave can be used as a sea-level indicator, distinguished stratigraphically by microfossil or sedimentary proxies. First, the elevation and timing of when Green Bay Cave was a littoral environment indicates Bermuda experienced an abrupt ~6.4 m sea-level rise at 7.7 ka, coinciding with final collapse of the Labrador sector of the Laurentide Ice Sheet. Second, microfossils preserved in elevated caves at +21 m above modern sea level and dated to marine isotope stage 11 (U-series, amino acid racemization) are consistent with modern Bermudian caves and co-stratigraphic sea level. For climate problems, annual temperature monitoring in Walsingham Cave indicates that cave water is thermally comparable to regional oceanographic conditions in the Sargasso Sea. Three sediment cores dated with sixteen radiocarbon dates indicate that Bermuda’s coldest and stormiest conditions of the last 3.2 ka occurred during the Little Ice Age (proxies: ?18Oc, grain size, bulk organic matter).

Submerged caves, locally referred to as cenotes, can be found throughout the Yucatan Peninsula of Mexico. These nutrient poor, aphotic “underground estuaries” lack photosynthetic primary productivity, but are often found underlying high primary productivity areas such as mangroves and tropical forests. Adjacent ecosystems contribute organic carbon to the cave systems via percolation, where it is then utilized by the obligate, cave-dwelling fish and invertebrates. Another potential pathway through which organic carbon can enter the cave food web is through chemosynthesis. Chemoautotrophic sulfur-oxidizing or nitrifying bacteria have been found in the hydrogen sulfide layer or in the sediments of some anchialine caves. Our study utilizes 13C/12C and 15N/14N stable isotopes as well as 14C radiocarbon dating to determine and compare the sources of organic matter entering a coastal anchialine cave (Cenote Aak Kimin) versus an inland cave (Cenote Maya Blue) in the Yucatan Peninsula. Stable isotopes have long been employed in tropic investigations. This study, however, is the first to utilize radiocarbon isotopes in anchialine caves. The use of both stable and radiocarbon isotopes as source indicators provides greater discrimination in systems that contain numerous carbon sources or indistinct trophic levels, particularly to distinguish between chemoautotrophic versus photosynthetically derived carbon. Results indicate that chemosynthetically derived organic carbon contributes substantially to the diet of some crustaceans, such as the stygobitic shrimp Typhlatya, while other species remain dependent on detrital inputs. Depleted δ13C values and aged radiocarbon values (as low as -47.51‰ and 1840 yrs. for Typhlatya spp.) in comparison to particulate and sediment δ13C values (lowest -32.07‰ and -28.43‰, respectively). A comparison of isotopic values between Cenote Aak Kimin and Cenote Maya Blue suggests that the trophic web of the coastal cave incorporates more photosynthetic or detrital carbon, while the inland cave, with more depleted 13C and 14C values, relies more heavily on chemoautotrophic carbon. Within both systems, however, distinct photosynthetic and chemoautotrophic levels were identified. Water quality parameters, especially dissolved oxygen and pH, support the hypothesis of bacterial activity at the halocline. Anchialine systems in the Yucatan Peninsula are threatened due to increases in tourism, development, and pollution. Quantifying and qualifying the inputs of organic carbon is vital for the management and conservation of the area’s freshwater resources.

Anchialine blue holes found in the interior of the Bahama Islands have distinct fresh and salt water layers, with vertical mixing, and dysoxic to anoxic conditions below the halocline. Scientific cave diving exploration and microbiological investigations of Cherokee Road Extension Blue Hole on Abaco Island have provided detailed information about the water chemistry of the vertically stratified water column. Hydrologic parameters measured suggest that circulation of seawater is occurring deep within the platform. Dense microbial assemblages which occurred as mats on the cave walls below the halocline were investigated through construction of 16S rRNA clone libraries, finding representatives across several bacterial lineages including Chlorobium and OP8. In many blue holes, microbial metabolism of organic matter in the presence of seawater sulfate leads to anoxic and sulfidic conditions at or below halocline. Sunlight penetrating this sulfidic layer allows for in situ primary production to be dominated by bacterial anoxygenic phototrophs. Although water column chemistry and molecular genetic diversity of microbial mats in Cherokee Road Extension Blue Hole were investigated in this study, the full scope of the biogeochemistry of inland blue holes throughout the Bahamas Archipelago is complex and poorly understood. However, these microbial communities are clearly influenced by several factors including solar insolation, terrestrial and marine inputs of oxygen, carbon, and nutrients, water residence times, depth to the halo/chemocline, and cave passage geometry. The biogeochemistry of inland blue holes throughout the Bahamas is so distinctive which makes Abaco Island and the rest of the archipelago valuable as natural experiments, repositories of microbial diversity, and analogs for stratified and sulfidic oceans present early in Earth's history.

West Central Florida is a complex karst environment with numerous sinkholes, springs, and submerged cave systems. Many of these karst features are anchialine, located within the subterranean estuary where freshwater and saltwater mix. Water quality data and/or fauna data were obtained from twenty-one karst features and their associated cave systems. The anchialine karst environment of the study area has a wide range of habitats with measured salinities ranging from freshwater at <0.2 ppt to sulfidic, hypersaline water at 38.5 ppt and measured pH readings ranging from 6.39 in water impacted by sulfur oxidizing bacteria to 10.3 in an isolated room of a cave. Stygobitic crustaceans were identified in conduits extending beneath the Gulf of Mexico supporting the hypotheses that freshwater crustaceans could survive higher sea levels in freshwater conduits beneath saltwater. The fauna associated with the anchialine cave systems included Sabellidae and Polychaeta worms, hydroids, cnidarians and hydrobiid snails. Jewfish Sink, like other anaerobic marine basins that were submarine springs, has four zones: oxic zone, transition zone, upper anoxic zone and anoxic bottom water. The upper zones have seasonal water quality variations from winter cooling and sinking of surface water and changes in the microbial communities. Activity of sulfate reducing bacteria is carbon limited in the anoxic zones, where sulfate reduction is the major metabolic process, and primary production is phosphate limited in the oxic zones. Organic input from the Gulf of Mexico drives the bacterial anaerobic ecosystem, resulting in a “sulfide pump”, in which sulfide percolates upward removing oxygen from the overlying sediment.