Assessing the Polysaccharide Degradation Potential in Marine Microbial Genomes and Metagenomes

Abstract

Summary Carbohydrate-active enzymes (CAZymes) account on average for only 1-2% of the bacterial genes [1-4], yet they are responsible for the metabolism of carbohydrates (sugars) - one of the most important class of biological macromolecules. Besides their functions as structure and storage compounds, sugar molecules act in various other functions, such as protein stabilization and osmoregulation. Sugars also constitute important intermediates in the food web, can function as signal molecules and serve as precursors for biosyntheses. It is becoming more and more common to address the carbohydrate turnover in modern environmental microbiology studies. However, it is hard to directly assess the sugar composition and concentrations on a cellular level, let alone their in situ turnover rates. Despite these technical difficulties, it is still possible to characterize the carbohydrate metabolisms indirectly via the study of their metabolic genes, namely CAZymes. This is possible because CAZymes catalyze the turnover of sugars. To be specific, they are synthesized by glycosyltransferases (GT) and degraded by glycoside hydrolases (GH), polysaccharide lyases (PL) and carbohydrate esterases (CE). Therefore, gene frequencies and expression levels of CAZymes should be indicators of the in situ availability of distinct sugars. The current knowledge on CAZymes is largely derived from carbohydrate synthesis and degradation of terrestrial plants, whereas their marine counterparts are still largely unknown. This asymmetry is also referred to as the "knowledge gap" of marine CAZymes. This limits not only our interpretation of the 'omics (in particular metagenomic) data and understanding of marine ecosystems, but it also keeps us from utilizing this vast enzyme repertoire for biotechnological purposes. This doctoral project focuses on CAZyme distributions in marine genomic and metagenomic studies with a focus on the MIMAS (Microbial Interactions in Marine Systems) Project and a sediment sample from the Logatchev hydrothermal vent site. Although each project has been described in previous studies, the carbohydrate metabolisms in these habitats were still largely under-researched. At first, the metagenome sequences were taxonomically classified and clustered into 'taxobins'. Afterwards, I studied the carbohydrate metabolic capacities of the dominant taxobins. In the MIMAS study, I also discuss possible trophic relations among different taxa based on their CAZymes profiles and extend the discussion to the niche adaptation of Flavobacteriaceae. In summary, this thesis demonstrates the usefulness of CAZyme profiling as a tool for interpreting 'omics data in microbial ecology. This thesis constitutes the first attempt so far to apply CAZyme analyses to elucidate a multi-level food web as well as to characterize the carbohydrate metabolism in a deep-sea habitat. Such studies are necessary for an in-depth understanding of the marine carbon cycle and could also provide a guideline for the selection of promising candidate CAZymes for industrial applications.