Proteomes in the flow: proteomic insights into engineered water environments

Abstract

Microbes have evolved to thrive in diverse and extreme environments. Understanding these microbes in engineered ecosystems, such as those used for wastewater treatment and drinking water production, is crucial for elucidating their roles in sanitation, nutrient cycling, and overall system stability. Traditional methods, such as microscopy and in situ staining, provide limited insight into microbial diversity and function, particularly for low-abundance species. The rise of culture-independent techniques like 16S rRNA and whole metagenome sequencing has revolutionized microbial ecology, enabling deeper analysis of taxonomic profiles, but does not answer questions beyond the metabolic potential.
Mass spectrometry is a powerful technology which enables the identification and characterization of proteins at a large scale from small amounts of cell material, referred to as proteomics. This has gained wide interest in the scientific community and industries, as proteins mediate fundamental processes in cells, such as enzymatic catalysis, molecular transport, signaling, cell division, and defense mechanisms.
Most recent advances in mass spectrometry allowed to transition the field of proteomics to investigate microbes, and complete microbial communities. Advantageously, microbial proteomics provides insights into the active metabolic pathways in microbes and microbial communities, thereby complementing the information obtained from DNA-based approaches.
While microbial proteomics has already been widely employed in various fields of research, including medical applications and biotechnology e.g. for understanding cell factories, much less has been done on environmental microbes, including those found in engineered ecosystems like wastewater and drinking water production systems.
This thesis aims to advance the application of microbial proteomics for studying microbial communities in engineered ecosystems, specifically within wastewater and drinking water environments. By analyzing the proteins present in these environments, this approach provides critical insights into the expressed metabolic functions of individual microbes and the protein biomass composition of microbial ecosystems. Additionally, investigating the microbial secretome provides new insights into metabolic versatility of microorganisms in nutrient-poor environments...