Microbial Community Composition, Diversity, and Activity across Oxygen Gradients within the Eastern Tropical North Pacific Oxygen Minimum Zone

Oceanic oxygen minimum zones (OMZs) play a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control ocean biogeochemical cycles remains undefined. We analyzed microbial communities across vertical and horizontal oxygen gradients present in the oceans’ largest OMZ, the Eastern Tropical North Pacific (ETNP), to determine how dissolved oxygen, nutrients, and organic matter influence the structure and activity of microbial communities. DNA and RNA samples were collected in parallel from depths ranging from 12 to 300 meters, targeting specific oxygen concentrations, at each of five sampling stations along a cruise track spanning the northern margins to the heart of the ETNP OMZ. Sampling stations included three functionally anoxic (AMZ) stations extending out from the coast of mainland Mexico, as well as two OMZ (but not AMZ) stations along the coast of Baja California. Corresponding DNA and RNA samples were subjected to high-throughput 16S rRNA amplicon sequencing, and sample-wise abundances of amplicon sequence variants (ASVs), taxonomic classification, and species-level assignments were evaluated. Our results show expected variations in microbial communities (based on DNA) and active microorganisms (based on RNA) with depth in OMZs/AMZs—including a shift from aerobic to anaerobic organisms, and declining alpha diversity within the OMZ. We also found systematic differences among stations with sharper and more substantial changes with depth at stations with compressed OMZs. While DNA- and RNA-based analyses were largely congruent, key differences were observed within the OMZ. Comparing corresponding DNA and RNA-based analyses across natural oxygen gradients along with complementary organic biogeochemical measurements provided new insight into community structure and composition, and collectively indicated that oxygen is a strong driver of microbial community dynamics and activity in the ETNP OMZ.