Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean

TLDR

Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, is a central process in the global nitrogen cycle, and while it was once thought to be limited to certain bacteria, recent metagenomic studies have uncovered ammonia‑monooxygenase genes in uncultivated Crenarchaeota archaea. The study aimed to provide molecular evidence for the widespread presence of ammonia‑oxidizing archaea (AOA) in marine water columns and sediments. By designing PCR primers that specifically target archaeal amoA, the authors detected AOA throughout key oceanic zones—including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. The results revealed diverse, habitat‑specific AOA communities with minimal overlap between water columns and sediments, largely unique to individual sites but with a few cosmopolitan sequences, suggesting that AOA play a significant, previously unrecognized role in the global nitrogen cycle.

Abstract

Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the β- and γ- Proteobacteria . However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase α-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal amoA , we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.