Examining the Role of Marine Microbial Communities and Their Rare Biosphere Constituents in Mediating Biogeochemical Transformations from Surface Layers to Deep Hypoxic Waters

Marine microbes are the dominant life forms in the ocean, accounting for most of the biomass and metabolic activity. They are central to ocean ecosystem functioning, mediating biogeochemical cycling and driving the production and transformation of organic matter, responding dynamically to physico-chemical changes in the ocean. Often overlooked, rare biosphere lineages harbor a significant fraction of the microbial functional and evolutionary potential. Although comprising most marine microbial diversity, rare taxa are often ignored, considered dormant or ecologically marginal. This dissertation challenges that assumption, demonstrating that rare lineages are active, ecologically consequential, and rapidly responsive to environmental perturbations. Across three oceanographically distinct systems - the western Mediterranean Sea, the Eastern North Pacific Ocean, and the Sargasso Sea, in the North Atlantic Subtropical Gyre - and combining a wide array of techniques - including amplicon sequencing, flow cytometry and fluorescence-activated cell sorting, targeted metagenomics, and phylogenomics with physical and biogeochemical measurements - this work investigates how microbial communities respond to rapid physical forcing and explores the role of the rare biosphere across contrasting ocean habitats. Chapter 1 resolves phytoplankton community structure across a submesoscale cyclonic eddy and adjacent non-eddying waters in the Western Mediterranean Sea. Chapter 2 examines the active microbial community inhabiting an oxygen minimum zone below the highly productive upwelling system of the Eastern North Pacific. Chapter 3 examines how mesopelagic microbial communities respond to pulsed inputs of fresh particulate organic matter from the base of the photic zone, simulated experimentally in the Sargasso Sea during the spring bloom season. These studies elucidate new microbial lineages and novel aspects of their metabolic capacities advancing our understanding of how conditionally rare and understudied lineages drive microbial community responses to environmental change. Collectively, this research has direct implications for predicting how ocean ecosystems will function under ongoing warming, deoxygenation, and altered export regimes.