Ecology and annual dynamics of Thaumarchaeota-driven freshwater nitrification

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Nitrification is essential step for the nitrogen cycle and converts ammonia to nitrate via nitrite. It prevents build-up of ammonia in freshwaters, which is critical for drinking water supply. Ammonia oxidation to nitrite is the rate limiting step in nitrification. Ammonia-oxidizing Thaumarchaeota (AOA) sustain large populations in the deep ocean and in soils (up to 40% and 5% of prokaryotes, respectively). A similar picture is emerging for deep oligotrophic freshwater lakes as based partially on our own research (Herber et al., 2019). Besides (relative) abundance and diversity surveys, we currently have no understanding on the ecology and ecosystem service dynamics of these chemolithoautotrophic microorganisms in freshwater environments. This stands in strong contrast to knowledge already gained on marine and soil nitrification. Our previous research established that in Lake Constance, which is an important drinking water resource for over 4 million people, a single phylotype of AOA constituted 13-21% of prokaryotic picoplankton in the hypolimnion throughout the year. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and comammox bacteria were not detected. This natural setting provides the unique opportunity to quantify the ecosystem functions exerted by planktonic AOA and at the same time to link this information to the genetic make-up of a single phylotyp. This proposal aims to elucidate environmental controls of freshwater AOA populations and the annual dynamics of ecosystem services they provide. Two hypotheses will be tested: (I) Dynamics of AOA-driven nitrification and CO2 fixation follow the yearly cycle of plankton succession as a major ammonia resource to deep waters. (II) Dynamics of the AOA population size are primarily driven by viruses. Both hypotheses will be tested in two work packages (WP). In WP1, CARD-FISH in combination with a fluorescent label binding to ammonia-monooxygenase will be established as a fast monitoring strategy of the total versus active fraction of planktonic AOA and applied to a yearly cycle. Selected time points throughout the year will be analyzed in more detail in respect to AOA-driven nitrification and dark CO2-fixation rates at both the bulk and single-cell level using 15N-ammonium and 13C-bicarbonate labeling coupled to GC-IRMS, EA-IRMS and nano-SIMS measurements. In WP2, electron microscopy and mini-metagenomics of FACS-sorted AOA cells will be used to explore the rate of viral infection and identity of infecting viruses. An ultimate goal is to isolate the planktonic freshwater AOA and its virus into pure culture. In parallel, CARD-FISH of protist food vacuoles will give insights on grazing pressure on AOA. The proposed project will be important to understand the basic principles controlling two ecosystem services provided by planktonic freshwater AOA: nitrification for safe drinking water supply and dark CO2 fixation for total lake productivity.