The fungal microbiome, or “mycobiome” of plants is diverse and important to
host health, but the fluxes of fungi among plant hosts and with the surrounding
environment are poorly understood. In chapter two, we employed sterile culture
techniques and spatial sampling to examine leaves as possible vectors for transfer of their
endophytic fungi from the canopy to substrate on the forest floor, as predicted by the
Foraging Ascomycete hypothesis. Some foliar endophytic fungal species are also present
as wood-decomposing fungi on the forest floor, that transfer of mycelium across these
two life history stages can occur, that endophytic life history stages are buffered from
environmental conditions in comparison to wood-decomposing fungi, and that spatial
linkages between the two life history stages can be observed. In another study, described
in chapter 3, wood and leaf wood endophytes were sampled across a 25 ha plot, to
explore landscape patterns of mycobiomes, and to explore the concept of a core
microbiome in aerial plant tissues. We found that core microbiomes may be observed in a
real ecological setting, but that the concept of core must be carefully defined and that
some level of buffering from disturbance may be necessary to allow core microbiomes to
assemble. In chapter four, we return to examine some of the assumptions and
implications of the Foraging Ascomycete hypothesis, with an agent-based model. We
model the conditions under which dispersal through falling leaves may represent a
fitness-enhancing dispersal strategy for fungi, and that deforestation as is currently
underway throughout the world may have impacts on fungi that rely upon a canopy-
inhabiting life stage for dispersal. In chapter five, some challenges associated with
environmental sampling of microbes using illumina© MiSeq sequences are critically
examined. We find that biases introduced by random sampling at various stages of
IVenvironmental DNA extraction and illumina© MiSeq sequencing are not well corrected
by currently accepted bioinformatic algorithms. In addition, information loss from
differential extraction, PCR amplification, and sequencing success, requires that users of
MiSeq read libraries to interpret read abundances carefully.
This dissertation includes previously published, co-authored material.
| Identifer | oai:union.ndltd.org:uoregon.edu/oai:scholarsbank.uoregon.edu:1794/23141 |
| Date | 10 April 2018 |
| Creators | Thomas, Daniel |
| Contributors | Roy, Bitty |
| Publisher | University of Oregon |
| Source Sets | University of Oregon |
| Language | en_US |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Rights | Creative Commons BY-NC-SA 4.0-US |
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