Universität zu Köln

Freudenthal, Jule ORCID: 0000-0002-1745-9171 (2025). New approaches for investigating microbial food webs across ecosystems. PhD thesis, Universität zu Köln.

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Abstract

Microbial communities drive essential ecosystem processes such as organic matter decomposition and nutrient cycling. However, the complex dynamics of microbial food webs, including the role of trophic interactions and environmental factors, are not yet fully understood, as disentangling biotic and abiotic factors remains challenging. This thesis explores microbial food webs across various ecosystems, ranging from wastewater treatment plants and maize rhizospheres to alpine soils and forest canopies. Using metatranscriptomics or metabarcoding with group-specific primers, the complex interplay of biotic and abiotic factors that drive microbial diversity, community composition, and function are uncovered. In addition, this thesis facilitates the exploration and integration of functional traits for protists by providing a functional trait database for Amoebozoa - a widespread and dominant protist group - as well as introducing workflows for the investigation and comparison of physiological traits of individual protist taxa based on de novo transcriptomes. We show that microbial food webs are strongly shaped by predation. In wastewater treatment plants, predation by protists and microscopic metazoans facilitated the removal of parasites. In the maize rhizosphere, predation by protists drove prokaryote community turnover, along with plant immune responses, root zones, or the effects of root manipulations. However, biotic interactions are not limited to predation. On canopy bark surfaces, microbial community assembly was shaped by an interplay of biotic and abiotic factors, specifically by competition between bacteria and fungi, symbioses between algae and fungi, bark topology, and environmental conditions. Furthermore, abiotic factors partly influenced microbial communities indirectly through biotic interactions. For example, seasonal changes affected predator communities in alpine soils and wastewater treatment systems, which, in turn, shaped the prey communities through selective predation pressure. In addition, analyses of the functional traits of protists revealed: First, variations in Amoebozoa and Cercozoa communities across ecosystems affected not only the taxonomic composition but also the functional composition. Second, even the physiological traits of individual protist taxa, including closely related strains, exhibit remarkable variation. Collectively, these findings highlight the central role of biotic interactions in structuring microbial communities and emphasize the advantages of functional traits and holistic, molecular-based approaches for studying microbial communities. The insights into the complexity of microbial food webs, combined with the established methodologies and tools, will allow future studies to deepen our understanding of the astonishing diversity of microorganisms – particularly of protists.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Freudenthal, Jule jule.freudenthal@uni-koeln.de orcid.org/0000-0002-1745-9171 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-780692
Date:	2025
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Zoologisches Institut
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language Protists; Microbial ecology; Food web; Biotic interactions; Functional traits; Metatranscriptomics; Metagenomics; Phylogenomics; Metabolism; Rhytidome; Wastewater treatment; Soil; Rhizosphere English
Date of oral exam:	12 March 2025
Referee:	Name Academic Title Bonkowski, Michael Prof. Dr. Lampert, Kathrin PD Dr. Boenigk, Jens Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/78069