The Bahamas are thousands of islands stretching along the coast of Florida and south to the tropic of cancer. An aerialv iew, spectaculaar s it is, shows only a small part of the islands, a larger part is submerged and discernible only by the abundance of blue dots onshorea nd in the shallow water around the islands. The blue holes are entrancesto an underwater world wherein biology seems to have slowed down to offer a fascinating view of species rarely seen elsewhere, and of rock formations that tell a story of the subterranianw orld below the islands. My studies were inspired by curiosity and the desire to make a contribution to the preservationo f this unique and irreplaceablew indow into the pastf or geologistsa nd biologists alike. Important questions as to how the caves formed and when and what the role of cavel ife might havep layed in the excavationp rocessesa re addressedin this thesis. As a result of these studies bacteria must be considered as possibly active participantsi n the formation processesa fter the time when the rising watertablef looded all the Bahamian caves. The layering, often in hypersharp zones of biological material, matches or is perhaps caused by, equally dramatic changes in hydrogen ions and acetate and sulphate concentrations. In both caves, pH profiles were observed that varied sharply over very short distances. In all three study sites it could be shown that, vertically and horizontally, the geochemical perimeters varied dramatically. Organically mediated processes are a dominant control on dissolution within the fresh, mixing, and saline zone. The combined generationof C02 results, known from earlier studies, and 112S and other bacterially measured activity, supports this finding. Retention of suspended organic matter was directly proportional to the salinity gradient. Elevated levels of DOC, POM, and acetate at the two major density interfaces confirm this finding. In the results, generated from CHN&S methods, wall rock material was found to contain residual carbon for potential microbial use, and large bacterial populations were identified through the SEM method in excess of what was measured within the water column. Significant lepidocrocite deposits (dimorphose iron oxihydroxide) were identified as a fraction of the cave sediment, and material known as "mung7, based on amino-acid analysis, was shown to be proteinaceous. This mung appears to be unique to caves in the Bahamas. In a sense the cave system is an underground geo-biosphere wherein the peculiar water flow patterns foster a specific, sometimes rich and unusual, fauna and flora that is a treasure for science and a sight for humans to enjoy.

Sea-level change during the Quaternary has had significant impacts on the geology of the Bahamas and the global carbon budget. During periods of low sea-level position conduit caves form in the Bahamas as a function of their respective water budgets. These conduit caves can then collapse and if this collapse reaches the surface a progradational collapse blue hole can be made. Upon subsequent sea-level rise these blue holes can become sediment inilled. Tidal pumping through these sedimentilled blue holes can result in the formation of whitings. Whitings are formed when the tidally pushed water warms and degasses CO2, driving the precipitation of CaCO3. Whitings are also formed on the shallow banks by resuspension by fish. As sea-level fluctuates the amount of land in the Bahamas and other carbonate regions increases or decreases with sea-level fall or rise, respectively. As the amount of land increases in the Bahamas and other carbonate regions, there is a decrease of carbonate rock exposure at high latitudes due to glaciation. The loss of high latitude carbonates is made up for in the gain of low latitude carbonates in terms of rates of inorganic carbon drawdown associated with karst processes. Additionally, this inorganic carbon draw down from karst processes represents approximately 16% of the unknown carbon sink as reported by the IPCC. This study is significant in that it contributes to the understanding of sea-level fluctuations in relation to the geology of the Bahamas and the global carbon budget.

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.