Ecology and spatiotemporal dynamics of Nitrososphaerota-driven nitrification and dark CO2 fixation in deep oligotrophic Lake Constance

Large planktonic populations of Nitrososphaerota inhabit deep oligotrophic lakes. They are thought to be the key ammonia oxidizers in these freshwater reservoirs, and as such responsible for the rate-limiting step in nitrification. In addition, their autotrophic metabolism is hypothesized to influence the carbon budget of these habitats. However, the impact of these ammonia-oxidizing archaea (AOA) on nitrogen and carbon cycling in oligotrophic lakes is yet to be quantified. Using 15N-ammonium and 13C-dissolved inorganic carbon (DIC) labeling techniques, linked with quantification of AOA by CARD-FISH, this thesis followed spatiotemporal dynamics and the contribution of these planktonic AOA to nitrification and dark CO2 fixation in Lake Constance , which is an important drinking water reservoir for >5 million of people. Previous studies have showed that a single AOA phylotype dominated the nitrifying community in this lake. Seasonal and spatial analyses revealed stable ammonia oxidation and CO2 fixation rates in the hypolimnion, with higher variability below the thermocline of the lake. Ammonia oxidation rates peaked below the thermocline, with a maximum of 139 nmol l─1 d─1, during summer months. Below the thermocline and in the deeper hypolimnion, dark CO2 fixation rates ranged from 0.27 to 14.60 nmol C l─1 d─1, which is in line with the published fixation rates in aquatic systems. Dark NH4+ assimilation rates were higher than rates obtained in other lakes, with different trophic states. It was estimated that nitrifiers were potentially responsible for 25 – 100% of the total dark CO2 fixation, with more seasonal variability below the thermocline, likely due to higher contributions from other microbial groups, like heterotrophic bacteria, or changing environmental factors. In the hypolimnion, AOA constituted between 0.24 and 10.91% (average: 3.31 % ± 2.47) of total prokaryotes, and displayed stable populations throughout the seasons. In the upper layers of the lake, seasonal mixing increased AOA populations and led to fluctuations in environmental parameters. However, the exact drivers of these changes are not fully determined. Experiments demonstrated the temperature sensitivity of nitrification, dark CO2 fixation, and NH4+ assimilation, with CO2 fixation and NH4+ assimilation increasing, while nitrification decreased in response to higher temperatures. Alongside key findings providing guidance on storage of non-saline samples for nitrification rate measurements in freshwater environments, and strategies to enrich planktonic freshwater nitrifiers, this study offers insights on spatiotemporal shifts of AOA populations and their contribution to the nitrogen cycle and carbon cycle in a deep oligotrophic lake, emphasizing their importance in the ammonia and CO2 removal, to sustain a safe drinking water supply.