The fungal focus on broad-scale metagenomics

The fungal kingdom is omnipresent in a multitude of ecosystems across the earth's biosphere. In this dissertation, the fungal abundance was analyzed in a broad-scale way to determine general and specific patterns. Starting with a case study of the human gut and simulations modeling the metabolic profile of fungi, a user-friendly web server was developed allowing to study all publically available fungal cohorts. Finally, a meta-study was conducted to find general patterns across soil, aquatic and host-associated environments. This facilitated insights into what happens to the fungal community in disrupted environments, e.g., after antibiotics treatment or fire events to artificially turn an ecosystem towards a more resilient state using microbial editing. Most fungi were unique to a particular environment. No single inter-kingdom co-abundance between any bacterial and fungal genus was found in all three environments. However, a major fraction of fungal dissimilarity could be explained by just a few bacterial genera. Most of them were generalists, which were highly prevalent in all three environments. They are potential candidates for microbial editing because they probably play a key role in maintaining the structure of the ecosystem. The dysbalance was much longer-lasting for fungi compared to the bacterial microbiome. Unlike the taxonomic profile, changes to the functional metabolic profile were less severe. Future studies are needed to refine fungal patterns in less explored environments. In summary, both the biotic and the abiotic contexts are required to describe and predict fungal abundance patterns.