Microbial landscape associated with micritized carbonate sediments from tidal environments of the Arabian Peninsula

  • Rawan Alhazmi

Student thesis: Master's Thesis


The relationship between the biosphere and geosphere is a pivotal process in Earth's history and life's evolution. Prokaryotes and carbonate minerals established one of the most ancient geo-biological partnerships, which persists to this day, manifesting in various geobiological processes such as ooid and mud production, as well as carbonate diagenesis. Among the latter, micritization involves the obliteration of shallow marine carbonate grains promoted by microorganisms and the re-crystallization of fine carbonate materials into microcrystalline calcite (micrite). Microorganisms have been recognized as playing an important role in micritization through their bio-pitting activity and capability to promote the nucleation and reprecipitation of carbonate crystals. In this thesis, the microbial diversity and composition of four subtropical carbonate lagoons where micritization occurs were investigated using an integrated geological and microbial ecology approach. Sediment and seawater samples were collected from four different sites around the Arabian Peninsula: Rabigh, Dammam, Abu Dhabi, and Oman, for a total of 120 samples. DNA extraction and high-throughput sequencing of the bacterial 16S rRNA gene were performed, as well as sediment characterization by means of optical and electron microscopy. Environmental parameters such as water pH, temperature, salinity, micritization biosignatures, grain porosity and granulometry were also collected to be correlated with microbial community data. Functional capabilities of sediment microbial communities were also inferred by comparing the data with relevant literature and 16S rRNA databases. The results revealed significant differences in microbial communities across different sites, mainly driven by the environmental factors characterizing each specific location. The most micritized sediments were found in Abu Dhabi, populated by microbial assemblages enriched with endolithic cyanobacteria and sulphate-reducing bacteria, potentially contributing to carbonate precipitation. The study highlighted the complex biogeochemistry, i.e., the interplay between microbial communities, geochemical conditions, geological factors, and environmental parameters in shaping the carbonate sediment nature of subtropical carbonate lagoons. The findings contribute to our understanding of the diverse role microorganisms can play in carbonate alteration processes and provide valuable information for future research in the field.
Date of AwardJun 2023
Original languageEnglish (US)
Awarding Institution
  • Biological, Environmental Sciences and Engineering
SupervisorDaniele Daffonchio (Supervisor)

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