Differential contributions of nitrifying microorganisms to nitrification in oligotrophic groundwater from the Hainich Critical Zone Exploratory

This study investigates the spatial distribution and niche differentiation of the prokaryotic ammonia oxidizing community from oligotrophic groundwater of karstic limestone aquifers (Hainich Critical Zone Exploratory, Germany). Sampling for sequencing was conducted between 2018 to 2021 from eight groundwater wells with heterogenous hydrochemical conditions. Community composition was assessed by amplicon sequencing of amoA genes using an Illumina MiSeq device, with the primer combinations amoA-1F/ amoA-2R for ammonia oxidizing bacteria, Arch-amoA-104F/ 616R_mod for ammonia oxidizing archaea and comamoAF/ comamoAR for complete ammonia oxidizing Nitrospira.