The main purpose of Amira project is to investigate the phylogeny of ammonia oxidizing bacteria biofilm via cytochrome c-resonant Raman microscopy (CRRM), which can be applied for the analysis of ongoing and undisturbed biofilms in vivo and in situ with a resolution at cell level. Until very recently, phylogenetic methods have been inherently invasive, rendering a phylogenetically sensitive observation of undisturbed biofilm formation impossible. In this project, AOBs are selected as a reference, due to their key importance in nitrogen cycling in both natural and artificial systems. Study of the AOB behavior in both pure planktonic cultures under optimal, oxygen stress conditions as well as their biofilm formation under laminar, and turbulent flow regimes can help us better understand their mechanisms in wastewater treatment plants. Within this project, the first optical phylogenetic distance tree based on non-invasive, contact –free in vivo measurements of individual AOB bacterial cells in situ will be formed. Additionally, for the first time, Undisturbed ongoing formation of single and triple species of AOB biofilm in vivo will be studied so that the recording of phylogenetic movies of ongoing biofilm formation will be possible.

• Kniggendorf AK, Nogueira R, Nasiri Bahmanabad S, Pommerening-Röser A, Roth BW. Small Sample Stress: Probing Oxygen-Deprived Ammonia-Oxidizing Bacteria with Raman Spectroscopy In Vivo. Microorganisms. 2020 Mar 19;8(3):432. doi: 10.3390/microorganisms8030432.