Despite their crucial role in the nitrogen cycle, freshwater ecosystems are relatively rarely studied for active ammonia oxidizers (AO). This study of Lake Lucerne determined the abundance of both amoA genes and gene transcripts of ammonia-oxidizing archaea (AOA) and bacteria (AOB) over a period of 16 months, shedding more light on the role of both AO in a deep, alpine lake environment. At the surface, at 42？m water depth, and in the water layer immediately above the sediment, AOA generally outnumbered AOB. However, in the surface water during summer stratification, when both AO were low in abundance, AOB were more numerous than AOA. Temporal distribution patterns of AOA and AOB were comparable. Higher abundances of amoA gene transcripts were observed at the onset and end of summer stratification. In summer, archaeal amoA genes and transcripts correlated negatively with temperature and conductivity. Concentrations of ammonium and oxygen did not vary enough to explain the amoA gene and transcript dynamics. The observed herbivorous zooplankton may have caused a hidden flux of mineralized ammonium and a change in abundance of genes and transcripts. At the surface, AO might have been repressed during summer stratification due to nutrient limitation caused by active phytoplankton. 1. Introduction Nitrogen cycling is one of the major biogeochemical processes on Earth. The discovery of novel nitrogen-converting pathways in the past decades [1] has shown the lack of knowledge we had and still have on global nitrogen cycling. Additionally, intensified use of fertilizers and nitrogenous precipitation derived from industry and traffic has led to large changes in the N-cycle in many ecosystems [2]. A major recent discovery in relation to the nitrification process was the role of Archaea in ammonia oxidation [3–5]. This notion has led to a great interest in the presence of ammonia-oxidizing archaea and bacteria in many ecosystems, often determined by the occurrence of archaeal and bacterial amoA genes (e.g., [6, 7]). In most analyses, the presence of archaeal amoA genes outnumbered those of bacteria by orders of magnitudes. What this means for the relative activities of both groups has only been investigated in a few environmental studies [8, 9]. The ecological importance of AOA and AOB has been determined in several studies; the relative abundance of AOA and AOB in soils is thought to be influenced mainly by pH [10, 11], temperature [12], and ammonium [13, 14], while in marine systems, next to ammonium [15], oxygen concentrations are expected to play a major role
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