NITRICARE · Nitrification Reloaded - a Single Cell Approach

Nitrification is a central component of the Earth’s biogeochemical nitrogen cycle. This process is driven by two groups of microorganisms, which oxidize ammonia via nitrite to nitrate. Their activities are of major ecological and economic importance and affect global warming, agriculture, wastewater treatment, and eutrophication. Despite the importance of nitrification for the health of our planet, there are surprisingly large gaps in our fundamental understanding of the microbiology of this process. Nitrifiers are difficult to isolate and thus most of our current knowledge stems from a few cultured model organisms that are hardly representative of the microbes driving nitrification in the environment. The overarching objective of NITRICARE is to close some of these knowledge gaps and obtain a comprehensive basic understanding of the identity, evolution, metabolism and ecological importance of those bacteria and archaea that actually catalyze nitrification in nature. For this purpose innovative single cell technologies like Raman-microspectroscopy, NanoSIMS and single cell genomics will be combined in novel ways and a Raman microfluidic device for high-throughput cell sorting will be developed. Application of these approaches will reveal the evolutionary history and metabolic versatility of uncultured ammonia oxidizing archaea and will provide important insights into their population structure. Furthermore, the proposed experiments will allow us to efficiently search for unknown nitrifiers, evaluate their ecological importance and test the hypothesis that organisms catalyzing both steps of nitrification may exist. For non-model nitrifiers we will develop a unique genetic approach to reveal the genetic basis of key metabolic features. Together, the genomic, metabolic, ecophysiological and genetic data will provide unprecedented insights into the biology of nitrifying microbes and open new conceptual horizons for the study of microbes in their natural environments.""