Biogeochemical mechanisms employed by key organisms, or symbiotic associations of organisms, transform the function and structure of their environment through processes recognized as ecosystem engineering. This dissertation seeks to investigate organism-ecosystem interactions that serve globally significant ecological functions in marine systems and impact how systems respond to environmental change. Using two model ecosystems that are quite unique from one another, deep-sea methane seeps and tropical coral reefs, I consider the ecosystems from a bottom up perspective, constraining the biogeochemical interactions that manifest in the hotspots of production and complexity associated with both of these systems. Through investigating seep systems that span the Cascadia margin in the N.E. Pacific, I reveal never before seen latitudinal variations in the microbial communities at the center of globally relevant seep processes, highlighting connections to the persistent oxygen minimum zone of the region, and increase the biogeographic ranges of two key seep taxa. Expanding these results, I explore the trophic connectivity of the chemosynthetic production that is at the base of seep systems to commercially important, non-seep fauna typically connected to sparse food supply from surface production in the food-limited deep-sea. With this, I provide the first evidence of the assimilation of seep-derived chemosynthetic nutrition by commercially harvested species in the deep sea and provide crucial context on the importance of the ecosystem provisioning services of seeps to overall ocean health and productivity. I also reveal a methodological bias that may have underestimated the contribution of seep nutrition to deep-sea fauna in past studies, elucidating the importance of matching the spatial and temporal scales of methods used with the interactions being studied. I then shift to tropical coral reef ecosystems and employ both field- and experiment-based methodologies to identify a novel mechanism in coral decline, wherein coral bleaching releases globally significant amounts of dissolved organic carbon that fundamentally alters the biogeochemistry of the reef scape. This in turn ignites a positive feedback mechanism of coral mortality, with consequences that are substantial enough to impact global carbon budgets. Overall, my dissertation uses multiple systems to identify the variability and flow of energy through marine ecosystems through both disparate habitats and episodic events that together inform the function of the marine realm.