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Hitchhiking in the Canopy: Ecological Patterns of Forest Mycobiomes

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.

Identiferoai:union.ndltd.org:uoregon.edu/oai:scholarsbank.uoregon.edu:1794/23141
Date10 April 2018
CreatorsThomas, Daniel
ContributorsRoy, Bitty
PublisherUniversity of Oregon
Source SetsUniversity of Oregon
Languageen_US
Detected LanguageEnglish
TypeElectronic Thesis or Dissertation
RightsCreative Commons BY-NC-SA 4.0-US

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