SUPERVISOR: Thomas ERTL

PROJECT ASSIGNED TO: Aurora GITTO 

The presence of a variety of microorganisms (bacteria, virus, fungi) in surface water and ground water represent an important issue for human health all around the world. As part of European union, Austria, adopts several EU regulations for water quality which defines specific parameters to follow in order to achieve the water quality in all the water bodies. To determine the microbiologic water quality, the count of bacterial colonies on selective media (e.g. Escherichia Coli or Intestinal Enterococci) or the cultivation on heterotrophic growth media is an important parameter. Especially on unspecific media organisms often remain unidentified, which makes troubleshooting even harder. For these reasons several methods are available that allow the taxonomic assignment of cultivated bacteria. Unfortunately, those techniques are based on either classical physiological properties or on genetic analysis, which both are time consuming and pretty much laborious. In recent years different high-throughput screening technologies have been developed to simplify the analysis in term of work and time like the mass spectrometry-based proteomics using matrix-assisted laser desorption/ionization–time of flight (MALDI–TOF MS). MALDI-TOF-MS has emerged as a promising and reliable tool for bacteria identification not only in clinical diagnostic microbiology but in recent years also for environmental strains. It is capable of rapidly and reliably assigning taxonomy of a wide range of bacteria in species, sub-species, and strains level with high accuracy, thanks to an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation.

The PhD thesis is part of the project WHAM (Wasserbürtige Heterotrophen – Analyse mit MALDI-TOF-MS) which aims to firstly investigate the suitability of MALDI-TOF-MS for the rapid identification of bacteria in Austrian water environment, then, to develop an adapted protocol for this use including a suitable bioinformatic workflow. An important task of the PhD study is to conceptualize and set-up library information to fasten taxonomic assignment for future bacterial isolates and to create a comprehensive database of MALDI-TOF-MS spectra from environmental water samples. The database would help not only to rapidly identify bacteria, but also to ease source tracking for the investigation of entry paths of microorganisms into water bodies. Further on, this thesis will investigate which extend cultivation dependent community analysis based on MALDI and cultivation independent community analysis based on high throughput sequencing of bacterial 16S-rRNA genes correspond on different taxonomic levels and apply advanced data analysis to gain more insights into abundance patterns of culturable and non-culturable microorganisms.

The project WHAM and the PHD's topic are well related to the metabolism and vulnerability research cluster proposed by the Doctoral School HR21. In regards of metabolism cluster, the thesis connects the biological and social metabolic processes with the identification of the bacteria community in the water bodies as an important issue for human health. For the same reason, the vulnerability focuses more on the importance of the water security and ecosystem health.