First Advisor

Daniel J. Ballhorn

Date of Publication

Spring 5-23-2018

Document Type


Degree Name

Doctor of Philosophy (Ph.D.) in Biology






Endophytic fungi -- Ecology, Fungal communities, Polystichum, Ferns -- Pacific Northwest



Physical Description

1 online resource (xii, 131 pages)


Fungal endophytes are highly diverse, cryptic plant endosymbionts that form asymptomatic infections within host tissue. They represent a large fraction of the millions of undescribed fungal taxa on our planet with some demonstrating mutualistic benefits to their hosts including herbivore and pathogen defense and abiotic stress tolerance. Other endophytes are latent saprotrophs or pathogens, awaiting host plant senescence to begin alternative stages of their life cycles. Most, however, are likely plant commensals with no observable benefits to their hosts while under study. Yet, when considering the context-dependence that may determine plant resistance to pathogen attack, the consortium of endophytes present in the host could alter these outcomes, thereby affecting plant evolution. Despite the excitement of exploiting endophytes for their potential to produce bioactive compounds that are useful to medicine and agriculture, fungal endophyte community ecology is a lagging field. Much remains unknown regarding their colonization patterns within hosts, their spatial and temporal turnover and their diversity. Further, a severe deficiency exists in work on endophytes in seed-free plants, particularly ferns. Since ferns exist in free-living forms in both the haploid and diploid stages, are the second largest group of vascular plants, occupy important ecological niches and represent an older lineage of land plants, this is a major shortcoming in our understanding of plant-fungal ecology and evolution. For these reasons, I have examined endophyte community ecology in a widespread fern host in the Pacific Northwest, Polystichum munitum, addressing several gaps in the endophyte literature. Since an understanding of the degree of early endophyte colonization, temporal turnover and the relative contribution of priority effects to community composition are unknown, I conducted a temporal survey of fern endophyte communities utilizing culture-independent, next-generation sequencing on a monthly basis for an entire growing season. A high degree of temporal turnover was observed early in the growing season, where a late colonist rapidly took over the fern population and persisted throughout the year. This colonist, which was isolated from several of the same plants, appears to support growth rates of the host plant when in the gametophytic stage, but is not highly competitive against other endophytes in vitro. Additionally, in an effort to examine host and habitat specificity I examined the spatial turnover of endophytes across four distinct habitat types: a coastal site, a coniferous understory site, a montane site near Mount Saint Helens but not impacted by the 1980 eruption, and a secondary succession site at Mount Saint Helens, spanning 150-km at a single point in time. A high degree of host specificity was found when compared to endophyte communities in neighboring plant taxa and a lack of distance decay was also observed contrasting with other work examining endophyte biogeographic patterns. We conclude that a high degree of host filtering, combined with an abundance of senescent fern material around the base of the plant--which potentially serves as a reservoir of endophyte inoculum--is likely responsible for the observed results. In the process of the ecological studies described above, I isolated over 500 strains of endophytes that corresponded to ca. 100 operational taxonomic units (OTUs). Four of these OTUs are previously undescribed and form a new family and genus, Catenosporaceae and Catenospora, respectively. One of these taxa is responsible for the strong spatial and temporal signals found in the ecological studies. We emphasize that future work should examine if the same phenomena are observed in other fern systems and further encourage endophyte researchers to expand the scope of their investigations into non-traditional plant lineages, as exciting ecological interactions that contribute to our understanding endophyte ecology--and community ecology as a whole--are waiting to be discovered.


In Copyright. URI: This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).

Persistent Identifier