Targeting spatiotemporal dynamics of planktonic SAGMGC‐1 and segregation of ammonia‐oxidizing thaumarchaeota ecotypes by newly designed primers and quantitative polymerase chain reaction

The annual dynamics of three different ammonia‐oxidizing archaea (AOA) ecotypes (amoA gene) and of the SAGMGC‐1 (Nitrosotalea‐like aquatic Thaumarchaeota) group (16S rRNA gene) were studied by newly designed specific primers and quantitative polymerase chain reaction analysis in a deep oligotrophic high mountain lake (Lake Redon, Limnological Observatory of the Pyrenees, Spain). We observed segregated distributions of the main AOA populations, peaking separately in time and space, and under different ammonia concentrations and irradiance conditions. Strong positive correlation in gene abundances was found along the annual survey between 16S rRNA SAGMAGC‐1 and one of the amoA ecotypes suggesting the potential for ammonia oxidation in the freshwater SAGMAGC‐1 clade. We also observed dominance of Nitrosotalea‐like ecotypes over Nitrosopumilus‐like (Marine Group 1.1a) and not the same annual dynamics for the two thaumarchaeotal clades. The fine scale segregation in space and time of the different AOA ecotypes indicated the presence of phylogenetically close but ecologically segregated AOA species specifically adapted to specific environmental conditions. It remains to be elucidated what would be such environmental drivers.