How Lichens Work: Functional Aspects of Symbiosis Viewed through Metagenomics and other Culture-Free Methods

• Author / Creator

  Tagirdzhanova, Gulnara

• Lichens are symbiotic organisms formed around the relationship between a hyphal fungus and a phototrophic unicellular organism, usually a green alga or a cyanobacterium. In addition to the main two partners, lichens often include bacteria and yeasts. Together, the symbiotic partners create architectures that are both fascinating and challenging to study.
  In this thesis, I studied how the lichen symbiosis works, and attempted to understand how different symbiotic partners contribute to the symbiotic outcome. I focused primarily on the under-studied yeasts and bacteria of the lichen symbiosis. My other goal was to develop approaches that can be used in the future to better understand lichen symbiosis.
  My analyses of metagenomic data generated from lichens gave three main results: 1) I obtained the first genomes of lichen yeasts, thus providing the first direct evidence on their biology and role in the lichen symbiosis. The genomes of the yeasts were smaller than that of the main fungal partner and showed signs of nutrient limitation and scavenging. Compared to the main fungal partner, the genomes of lichen yeasts harboured fewer secondary metabolism gene clusters and pathogenicity signatures, but a larger repertoire of genes potentially involved in the biosynthesis of acidic polysaccharides. 2) I discovered that bacterial communities in lichens are unexpectedly structured, and the majority of bacterial occurrences come from just four families. The two most frequent families, Beijerinckiaceae and Acetobacteraceae, included lineages that I identified as aerobic anoxygenic phototrophs. These bacteria were present in samples across all major lichen groups and geographies. I established that these bacteria are not capable of fixing atmospheric nitrogen, but have biosynthetic pathways for vitamins essential for the eukaryotic symbionts. 3) Finally, I tested a recently published hypothesis that lichen fungi rely on algae for the synthesis of ATP. I showed that contrary to the hypothesis, lichen fungi have not lost a gene essential for oxidative phosphorylation, and therefore the proposed mechanism of lichen symbiont interdependence is not valid. In addition to my metagenomics work, I developed a protocol for measuring relative abundances of lichen symbionts via ddPCR. Using this method, I tested hypotheses on the role yeasts play in lichens.
  This research has significantly expanded our knowledge of lichen yeasts and bacteria, and also provided resources for future exploration. This includes both methods developed during this project, and genomes of lichen symbionts that will be publicly available for future use.

• Subjects / Keywords

  • symbiosis
  • metagenomics
  • genomic
  • lichen

• Graduation date

  Fall 2022

• Type of Item

  Thesis

• Degree

  Doctor of Philosophy

• DOI

  https://doi.org/10.7939/r3-nhd9-n153

• License

  This thesis is made available by the University of Alberta Library with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.