Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution–environment relationships.

Nitrification plays a key role in marine ecosystems where Thaumarchaeota are thought to be responsible for most of the ammonia oxidation in the water column. Over a 2‐yr, near‐monthly time series at two sites in Monterey Bay we observed repeatable seasonal and depth‐based patterns of Thaumarchaeota ecotype abundance that highlighted a clear delineation between populations in shallow euphotic (< 50 m) vs. deeper mesopelagic (60–500 m) depths. Euphotic depths show greater seasonality and influence from light, while mesopelagic waters have trends based on water mass and other covarying features with depth. Three major ecotypes were recovered: a Nitrosopumilus‐like (NP) group, a Nitrosopelagicus‐like ecotype containing "shallow" water column A (WCA) members, and an ecotype affiliated with the "deep" water column B (WCB) Thaumarchaeota. These ecotypes show a strong depth distribution, with WCB dominant at ≥ 200 m depth and WCA most abundant in surface (5–100 m) waters. The NP ecotype was found throughout the water column with the highest abundance in summer, and was the only ecotype showing a correlation with measured nitrification rates. We also found three abundant taxa related to Nitrospina—the major nitrite‐oxidizing bacteria in the ocean; these showed clear connections to each of the three Thaumarchaeota ecotypes, suggesting a specific relationship between both steps of nitrification. Our results support the importance of ecotype‐based analysis of Thaumarchaeota and show that their abundance and distribution are controlled based on their water column position, with a distinct shift at 50 m between euphotic and mesopelagic depths. [ABSTRACT FROM AUTHOR]