Microbial Communities, Activities, and Metabolisms in Earth’s
Subseafloor and Analog Oceanic Environments
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Elkassas_PhD_EAPS_2025_Final_Thesis.pdf
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8.25 MB
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Adobe PDF
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e2e4f99ef80da400615c0f6ff9ea499f
Author(s)
Elkassas, Sabrina Mariam
Advisor(s)
Huber, Julie A.
Date Issued
February 2026
Publisher
Massachusetts Institute of Technology
Abstract
The crustal subseafloor biosphere is one of the largest and most underexplored habitats on Earth. Microorganisms inhabiting this environment contribute to chemical transformations, energy flow, and the long-term habitability of the oceanic crust, while also offering insight into the potential for life on other Ocean Worlds. However, the functional dynamics of these subseafloor microbial communities remains unresolved. This thesis investigates how geochemical conditions shape microbial activity and physiology in subseafloor fluids from basalt- and ultramafic-hosted environments. The first part of the thesis uses stable isotope probing to determine the activity of subseafloor carbon-cycling microorganisms. Chapter 2 examines chemolithoautotrophs at Axial Seamount, demonstrating that variations in hydrogen and oxygen availability strongly influence the composition and function of active subseafloor communities. Chapter 3 quantifies microbial activity in hyperalkaline fluids (pH > 12.5) from the Mariana forearc, where mineral-associated microbial methanotrophs were detected, though microbial methanogenesis was not observed. The second part of the thesis focuses on cultivation-based approaches to characterize newly isolated microbes and their responses to high-pH and low-energy conditions. Chapter 4 investigates Methanocalculus natronophilus, a methanogen from an alkaline soda lake, to identify growth parameters and genomic adaptations that support methanogenesis in extreme pH environments. Chapter 5 introduces a growth medium designed to approximate the chemistry of the ocean on one of Saturn’s moons, Enceladus, and evaluates the genomic and physiological characteristics of microbial enrichments and isolates that may be relevant for survival in such extraterrestrial ocean environments. Chapter 6 characterizes six novel Marinobacter shengliensis strains from Mariana forearc fluids and sediments, highlighting adaptations that facilitate persistence in a submarine serpentinite-hosted system. Together, this work links microbial activity, function, and physiology with the geochemical conditions of the subseafloor, advancing our understanding of how life persists in Earth’s oceanic crust and informing ongoing efforts to assess the potential habitability of Ocean Worlds beyond Earth.
MIT Department
Joint Program in Oceanography/Applied Ocean Science and Engineering
Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences
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