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Publication Date



UM campus only

Embargo Period


Degree Type


Degree Name

Doctor of Philosophy (PHD)


Marine Geology and Geophysics (Marine)

Date of Defense


First Committee Member

James S. Klaus

Second Committee Member

Peter K. Swart

Third Committee Member

R. Pamela Reid

Fourth Committee Member

Christopher Sinigalliano


Microbes play an important role as geological agents in mineral growth and dissolution, rock and mineral weathering and alteration, transformation of organic carbon in sediments for fossil fuel formation and cycling of elements in the global ocean. In the case of microbial depostion of calcium carbonate, most studies focus on the large sedimentary structures formed by microbes known as microbialites, which include features such as stromatolites and thrombolites. However, given the pervasive nature of bacteria in the marine environment and similar metabolisms related to calcium carbonate precipitation across environments, it remains to be understood how the same processes responsible for building meter-scale structures can influence sedimentation. The goals of this work are to apply molecular and geochemical techniques to various carbonate depositional environments to characterize bacterial communities related to early diagenesis (carbonate precipitation or dissolution) and to understand how microbial ecology, metabolic groups, and attatchment via biofilms influence sediment characteristics. Three case studies were chosen to investigate the influence of microbial communities on fundamental environmental and geological processes in three different marine environments. Florida Bay bacterial communities were dominated by bacterial groups with metabolisms whose byproducts are associated with favoring both the precipitation and dissolution of calcium carbonate (Chapter 2). Typically, bacterial groups related to precipitation of calcium carbonate occurred in diagenetic zones of the sediment column where profiles of Ca2+/Cl- ratios were well below expected seawater values, suggesting precipitation was indeed occurring. Furthermore, evidence for other processes that promote calcium carbonate precipitation and dissolution, such as the degradation of EPS by heterotrophic bacteria and microbial sulfate reduction were detected in these sediments. Similar results were found in salt pond sediments on Little Darby Island, Exumas, Bahamas. Early diagenesis in hypersaline ponds sediments was related to bacterial sulfate reduction and degradation of the organic biofilm matrix component exopolymeric substances (EPS) (Chapter 3). As was observed in Florida Bay, metabolisms related to both preciptation and dissolution were present. However, other environmental factors such as salinity and bioturbation seem to be related to the type of diageneiss occurring. Sulfate reduction was prominent in all settings, but when combined with bioturbation in moderate salinity environments, the mixing of oxygen with H2S produced by sulfate reduction may produce acid and dissolve calcium carbonate. In the hypersaline ponds of Florida Bay islands and Little Darby salt ponds, precipitation of calcium carbonate was more prevalent in the presence of sulfate reducing bacteria and a lack of bioturbation. Whereas sediment biofilms were related to calcium carbonate deposition in Florida Bay and Little Darby Salt Ponds, the complex relationship between microbial ecology and sediment biofiloms was revealed at South Florida recreational beaches (Chapter 4). Enterococci, recommended at the U.S. federal level for monitoring water quality at marine recreational beaches, have been found to reside and grow within beach sands. However, the environmental and ecological factors affecting enterococci persistence remain poorly understood, making it difficult to determine levels of fecal pollution and assess human health risks. Here we document the presence of enterococci associated with beach sediment biofilms at eight south Florida recreational beaches (Chapter 4). Enterococci levels were highest in supratidal sands where they displayed a nonlinear, unimodal relationship with extracellular polymeric secretions (EPS), the primary component of biofilms. Enterococci levels peaked at intermediate levels of EPS, suggesting that biofilms may promote the survival of enterococci, but may also inhibit enterococci as the biofilm develops within beach sands.


bacteria; biofilms; diagenesis; calcium carbonate; microbial mats