Abstract:

Per- and polyfluoroalkyl substances (PFAS) are persistent organofluorine contaminants widely distributed in the environment. Coastal sediments receive substantial anthropogenic inputs and act as important long-term repositories for these compounds. Although microbial biotransformation may provide a sustainable approach to PFAS remediation, most evidence derives from isolated strains, enriched consortia or laboratory microcosms. The genetic basis of PFAS biotransformation potential in indigenous marine microbiomes and whether the associated candidate genes contribute to measurable PFAS transformation processes under natural conditions remain poorly understood. Addressing these knowledge gaps is further constrained by the lack of a unified framework for annotating genes associated with PFAS biotransformation and classifying the strength of evidence linking them to specific substrates and reactions. Combining metagenomics, metatranscriptomics, functional annotation guided by curated evidence and field sediment experiments, this study aims to achieve three interlinked objectives: (1) characterize the diversity, abundance, transcription and potential microbial hosts of PFAS-associated candidate genes in coastal sediments, and assess the roles of mobile genetic elements, potential horizontal gene transfer and environmental factors in shaping their distribution and transcription; (2) establish a reference framework that links genes to specific substrates and reactions, grades the supporting evidence and distinguishes experimentally supported functions from predicted functions, and apply it to approximately 2,000 metagenomes spanning nine marine habitat types to investigate functional diversity, biogeographic patterns and potential microbial hosts; and (3) investigate PFAS biotransformation in coastal sediment microcosms deployed in the field by integrating measurements of biotransformation products with microbial genomic and transcriptional responses. This thesis will connect functional annotation grounded in curated evidence with local and global environmental patterns and experimental assessment, advancing understanding of microbial PFAS biotransformation potential in marine ecosystems and identifying candidate functions and microorganisms for subsequent validation.