Photic-zone euxinia (PZE) is associated with several times in Earth's history including Phanerozoic extinction events and long parts of the Proterozoic. One of the best modern analogues for extreme PZE is Mahoney Lake in British Columbia, Canada where a dense layer of purple sulfur bacteria separate the oxic mixolimnion from one of the most sulfidic monimolimnions in the world. These purple sulfur bacteria are known to produce the carotenoid okenone. Okenone's diagenetic product, okenane, has potential as a biomarker for photic-zone euxinia, so understanding its production and transport is important for interpreting the geologic record. In the following dissertation, I examine Mahoney Lake with a multi-proxy approach. I use lipid biomarkers to understand organic matter production burial in the lake and find strong evidence of lateral transport of organic matter from shoreline microbial mats to the lake-bottom sediments. I also find evidence of okenone production in these shoreline mats and a carotenoid previously unreported in the environment, Thiothece-484, associated with the okenone synthetic pathway. Finally, I develop a new bioinformatics method to examine high-throughput metagenomic data and use this method to start understanding how the metabolic and lipid synthetic pathways of microbial communities in the lake are associated with each other. / Earth and Planetary Sciences