Simulating productivity changes of epipelagic, mesopelagic, and bathypelagic taxa using a depth-resolved, end-to-end food web model for the oceanic Gulf of Mexico

•Oceanic systems are difficult to model due to a lack of long-term datasets and complex dynamics such as particle sinking and diel vertical migration (DVM).•Data collected after the Deepwater Horizon Oil Spill provided the opportunity to develop an end-to-end food web model for the northern Gulf of Mexico that tracks energy flows vertically through the water column as a whole as well as within and between epipelagic, mesopelagic, and bathypelagic depth zones.•Decapods and non-copepod mesozooplankton are important nodes of energy transfer, especially in meso‑ and bathypelagic depth zones.•Increases in large jellyfish biomass had a negative overall impact on other functional groups, while decreases in strongly migrating mesopelagic fish biomass had a generally positive impact on competing mesopelagic fish functional groups. Open-ocean and deep-sea ecosystems can be difficult to model due to the challenges of incorporating important dynamics such as diel vertical migration and particle sinking, as well as the absence of long-term datasets for deep-sea taxa abundance, distribution, and physiological parameters. The data collection that followed the Deepwater Horizon Oil Spill provided the unique opportunity to model the oceanic Gulf of Mexico in a way that was not previously possible. Using new biomass datasets, we developed a depth-resolved food web model to better understand the trophic dynamics of the oceanic Gulf of Mexico. The model tracks vertical energy transfer in the water column between three depth zones: the epipelagic (0–200 m), mesopelagic (200–1000 m) and bathypelagic (>1000 m). This functionality allows us to demonstrate how changes in the biomass of specific functional groups, such as large jellyfish, non-copepod mesozooplankton, decapods, and strongly migrating mesopelagic fishes affect the food web within each depth zone. Non-copepod mesozooplankton and euphausiids were shown to have greater importance in energy transfer, particularly in meso‑ and bathypelagic depth zones, than other functional groups. Increasing large jellyfish biomass by 25 % resulted in decreases in biomass of most of the other forage functional groups, particularly mesopelagic fishes and small gelatinous carnivores, two groups that actively compete with and are consumed by large jellyfish. A simulated decrease in strongly migrating mesopelagic fish biomass of 25 % increased the biomass of functional groups presumed to be in competition with strongly migrating mesopelagic