Abstract
Summary Ocean oxygen deficient zones (ODZs) host 30%–50% of marine N 2 production. Cyanobacteria photosynthesizing in the ODZ create a secondary chlorophyll maximum and provide organic matter to N 2 ‐producing bacteria. This chlorophyll maximum is thought to occur due to reduced grazing in anoxic waters. We first examine ODZ protists with long amplicon reads. We then use non‐primer‐based methods to examine the composition and relative abundance of protists in metagenomes from the Eastern Tropical North and South Pacific ODZs and compare these data to the oxic Hawaii Ocean Time‐series (HOT) in the North Pacific. We identify and quantify protists in proportion to the total microbial community. From metagenomic data, we see a large drop in abundance of fungi and protists such as choanoflagellates, radiolarians, cercozoa and ciliates in the ODZs but not in the oxic mesopelagic at HOT. Diplonemid euglenozoa were the only protists that increased in the ODZ. Dinoflagellates and foraminifera reads were also present in the ODZ though less abundant compared to oxic waters. Denitrification has been found in foraminifera but not yet in dinoflagellates. DNA techniques cannot separate dinoflagellate cells and cysts. Metagenomic analysis found taxonomic groups missed by amplicon sequencing and identified trends in abundance.