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A simple path to complexity: horizontal gene transfer in microbial communities

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Buffard,  Pauline
IMPRS for Evolutionary Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society;
Department Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Buffard, P. (2023). A simple path to complexity: horizontal gene transfer in microbial communities (PhD Thesis, Christian-Albrechts-Universität, Kiel, 2023).


Cite as: https://hdl.handle.net/21.11116/0000-000D-A5DF-E
Abstract
In nature, microbial communities are inherent components of all ecosystems, actively shaping and being shaped by complex eco-evolutionary feedback processes. Importantly, these communities have a substantial impact on the health and disease of eukaryotic organisms. Genetic variation is the ultimate driver of phenotypes and ecosystem functioning, and Horizontal Gene Transfer (HGT) plays a crucial role in generating this variability. Nonetheless, a consequent knowledge gap remains in understanding the dynamic role of HGT in biologically meaningful microbial communities, and detecting HGT in complex microbial communities is challenging. Recent work has shown that Mobile Genetic Elements (MGEs) impact the movement of ecologically relevant genes, influencing community function. Building upon this, my thesis investigates HGT dynamics and its influence on community function in ecologically relevant microbial communities. For this, I experimentally evolved the nematode Caenorhabditis elegans with compost-derived microbial communities cultured on a single carbon source of cellulose paper. Regular transfers of communities, incorporating pooled MGEs, enabled the tracking of HGT. In Chapter 3, I demonstrate the effectiveness of a bioinformatic pipeline to identify and trace HGT events facilitated by MGEs across diverse free-living communities, using metagenomic data from cellulose paper-grown microbial communities. Chapter 4 explores the impact of HGT on the functioning of host-associated communities. Periodic nematode counting in repeated evolution experiments revealed fitness changes due to HGT, with both detrimental and beneficial effects observed. Microbial community composition was unaffected by HGT. Approaches were then sought to follow HGT dynamics in the nematode gut. Metagenomics proved challenging to use in this context. An in-house barcoded library of Pseudomonas fluorescens SBW25 was not suitable to track single lineages due to the strain's inability to establish a long-term association with C. elegans, despite observed beneficial interactions. The gut was dominated by Ochrobactrum and Pseudochrobactrum, diverse genera with a high propensity for gene gain. Individual genomes from these genera were successfully tracked in real-time, and multiple horizontally transferred sequences carrying ecologically relevant genes were detected. Overall, this thesis demonstrates the utility of simplified experimental designs in comprehending the intricate eco-evolutionary dynamics of microbial communities, and paves the way for a deeper understanding of the significance of HGT in shaping community function.