Abstract

Low-oxygen environments harbor intense biogeochemical transformation. Some areas of the Eastern Tropical North Pacific (ETNP) hold profuse oxygen minimum zones (OMZ) and yet, their microbial diversity has scarcely been studied. This is the case for the microbiota of the Southern Gulf of California (GC). It is documented this area is a biological diversity hotspot experiencing increasing warming. We performed a prokaryotic assemblages cross-comparison of diverse marine environments of the GC, including coastal and marine surface environments, and vertical profiles including OMZs. Our data show regional increasing warming in the Southern Gulf of California, and revealed the microbial potential for N fixing in GC OMZs. An active N cycling, including N loss and N fixation, was indicated by different sources of evidence: oxygen and nutrient patterns, as well as the distribution of known diazotrophs in deep layers. Dissolved oxygen and nutrient patterns suggest nutrient replenishment mechanisms should operate to counterbalance nutrient loss. Metabarcoding allows for a comprehensive prokaryote profiling across varied environments that results in a regional diversity baseline that holds a vast potential related to carbon and nitrogen cycling. Nostocales cyanobacteria offer the N-fixing potential in surface waters while diazotrophs Rhizobiales do in deep layers. A vast diversity of potential diazotrophic and methylotrophic taxa populate oxycline and OMZ and significant correlations of their abundance is revealed at genus level. © 2025 The Authors