Date of Award

Spring 2026

Document Type

Open Access Dissertation

Department

Marine Science

First Advisor

Xuefeng Peng

Abstract

Microorganisms are the primary drivers of carbon and nitrogen cycling in marine ecosystems, yet the ecological roles of marine fungi and their interactions with prokaryotes remain poorly understood. This dissertation investigates the diversity, interactions, and functional contributions of fungal and prokaryotic communities across coastal and open ocean environments, with a focus on estuaries and oxygen minimum zones (OMZs). By integrating community-level, interaction-based, and functional analyses, this work addresses key gaps in understanding how fungi contribute to organic matter degradation and nutrient transformations in marine systems. Size-fractionated metabarcoding in the eastern tropical North Pacific OMZ reveals distinct free-living and particle-associated microbial communities and identifies previously overlooked fungal- prokaryotic interactions within particle-associated niches. In coastal marsh ecosystems, targeted fungal metabarcoding demonstrates that early diverging fungal lineages are abundant and diverse, particularly in brackish environments, and that commonly used primer sets substantially underestimate their presence. Co-occurrence network analyses further reveal that fungal-prokaryotic interactions may vary across habitats, ranging from competitive to cooperative, with implications for organic matter remineralization and nutrient cycling. Metatranscriptomic analyses coupled with quantitative internal RNA standards show that marine fungi are metabolically active across the eastern tropical South Pacific OMZ. Fungal communities express a diverse suite of extracellular carbohydrate-active enzymes, indicating an important role in the degradation of complex organic matter under both oxic and anoxic conditions. Early diverging fungi remain transcriptionally active throughout the water column, underscoring their ecological relevance in low-oxygen environments. These results highlight marine fungi as integral, yet understudied, components of marine microbial communities. By integrating targeted molecular approaches, including size-fractionated sampling, fungal-specific metabarcoding, and multi-omic analyses, across coastal and open ocean systems, this dissertation improves the understanding of fungal roles in marine carbon and nitrogen cycling and establishes approaches for incorporating fungi into studies of marine microbial ecology and biogeochemistry.

Rights

© 2026, Madeleine Ann Thompson

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