Abstract

Dissolved oxygen regulates microbial distribution and nitrogen cycling and, therefore, ocean productivity and Earth's climate. To date, the assembly of microbial communities in relation to oceanographic changes due to El Niño Southern Oscillation (ENSO) remains poorly understood in oxygen minimum zones (OMZ). The Mexican Pacific upwelling system supports high productivity and a permanent OMZ. Here, the spatiotemporal distribution of the prokaryotic community and nitrogen-cycling genes was investigated along a repeated transect subjected to varying oceanographic conditions associated with La Niña in 2018 and El Niño in 2019. The community was more diverse during La Niña and in the aphotic OMZ, dominated by the Subtropical Subsurface water mass, where the highest abundances of nitrogen-cycling genes were found. The largest proportion of the Gulf of California water mass during El Niño provided warmer, more oxygenated, and nutrient-poor waters towards the coast, leading to a significant increase of Synechococcus in the euphotic layer compared with the opposite conditions during La Niña. These findings suggest that prokaryotic assemblages and nitrogen genes are linked to local physicochemical conditions (e.g. light, oxygen, nutrients), but also to oceanographic fluctuations associated with ENSO phases, indicating the crucial role of climate variability in microbial community dynamics in this OMZ. © 2023 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley & Sons Ltd.