Factors Shaping Endophyte Communities Associated with Selected Cultivated Plants in Arizona
AdvisorArnold, Anne E.
MetadataShow full item record
PublisherThe University of Arizona.
RightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
AbstractSymbiotic microbial communities can be found in all plant species in all major terrestrial ecosystems including wild, horticultural, agricultural and residential garden settings. Microorganisms such as some bacteria and fungi that colonize the interior of a plant tissue without causing apparent disease – endophytes -- can be acquired through horizontal transmission or via vertical inheritance. Studies have shown that endophytes inhabit all tissue types of host plants and play vital roles in plant health and productivity, providing tolerance against biotic and abiotic stresses. However, the diversity of endophytes occurring in different plant tissues such as leaves, stems and seeds, and the factors that influence the endophytic diversity in those tissues is not well known. The knowledge gap is especially large for semi-arid areas such as Arizona, where endophytes may be especially important for plant survival under environmental stress.In the first part of this study, I evaluated colonization of three different types of crop seeds by soilborne fungi under different agricultural, residential and wild grassland settings in central and southern Arizona, USA. I found that fungal colonization differed among plant varieties, even when placed into the same soil. Seeds recruited distinct fungal communities in different locations, and fungal communities differed among agricultural, residential, and grassland settings. Variation in fungal communities was consistent with variation in soil chemistry. This work provides a case study regarding the diversity of fungal endophytes that can infect seeds in Arizona soils and highlights the prevalence of certain taxa, such as Fusarium and Alternaria, that are especially common and may be beneficial for plants, despite their reputations more broadly as undesirable pathogens or producers of mycotoxins. In the second part of this study, I provide a first perspective on endophytic biodiversity associated with common plants in a residential garden setting (i.e., the garden endobiome). I surveyed leaf and stem tissue of 17 different plant varieties late in the growing season in a garden environment in Tucson, Arizona. I found that the isolation frequency of bacterial and fungal endophytes from leaves, and bacterial endophytes from stems, varied among plant families. Different plant species in a given family showed similar isolation frequencies of endophytes. In general, bacteria were more common in leaves, and fungi were more common in stems. Edible and inedible leaves harbored fungi with similar frequency overall, but I did not observe bacteria in edible leaves. Because this study used inexpensive methods, I develop it further as the basis for an educational module to be used for students at the high school or college level, with limited resources, to study endomicrobiomes of cultivated plants in developing countries. Ultimately, my dissertation provides an overview of the endophytic communities that colonize various tissues and plant species in a variety of settings in Arizona. Such studies can help in mapping the distributions of endophytic microbes important for plants and provide a road-map for identifying the drivers of their community composition. These studies also can provide a basis for selecting potentially beneficial fungi and bacteria to aid in plant resilience in a changing world. Finally, this body of work provides a basis for teaching students in the developing world about biodiversity, ecology, mycology, and plant biology through endophytes, Earth’s most widespread symbionts of plants.
Degree ProgramGraduate College
Degree GrantorUniversity of Arizona
Showing items related by title, author, creator and subject.
Responses of endophyte-bearing and endophyte-free varieties of Lolium perenne L. to fungicide treatment and simulated herbivoryBoerner, R. E. J.; Scherzer, A. J.; Sturgis, B. G. (Society for Range Management, 1990-01-01)The effects of the presence of fungal endophytes, treatment with a systemic fungicide, and simulated herbivory on growth and biomass allocation were investigated in 2 varieties of perennial ryegrass (Lolium perenne): 'Repell', an endophyte-bearing variety, and 'Pennfine', a low-endophyte variety. In the absence of herbivory or fungicide there were no significant differences in the growth or pattern of biomass allocation between varieties. Treatment with the systemic fungicide benomyl reduced growth of both varieties by approximately 50% and reduced root growth more than shoot growth; fungicide effects were similar in the 2 varieties. Simulated herbivory reduced root growth more in endophyte-bearing Repell plants than in endophyte-free Pennfine plants, and root:shoot ratios of Repell plants were significantly lower than those of Pennfine plants following either moderate or severe herbivory. Statistically significant interactions between fungicide treatment and simulated herbivory were frequent in Repell plants but absent in Pennfine plants, suggesting that the fungicide had both direct phytotoxic effects and indirect effects mediated through the loss of endophytes by the Repell plants. While the proximate cost to seedlings bearing endophyte seemed small, the presence of the endophytes altered the allocation pattern of biomass following herbivory in such a way as to increase the probability of mortality.
Host-, Geographic-, and Ecological Specificity of Endophytic and Endolichenic Fungal CommunitiesArnold, Anne Elizabeth; U'Ren, Jana M.; VanEtten, Hans; Orbach, Marc; Bronstein, Judith L.; Sullivan, Matthew (The University of Arizona., 2011)As one of the most diverse and ecologically important clades of life, fungi are best known as pathogens, saprotrophs, mycorrhizae, and lichens. Yet an enormous amount of previously unknown diversity occurs among endophytic and endolichenic fungi--species-rich, horizontally transmitted fungi that live within asymptomatic photosynthetic structures such as leaves and lichens. Here, I explore the biodiversity of these understudied symbiotrophs and the ecological and biogeographic factors influencing their communities.To evaluate methods currently used in ecological studies of environmental samples of fungi, I assessed inter- and intraspecific divergence of a fast-evolving locus for four genera commonly found as endophytes, and compared analytical methods for identifying and delimiting OTUs. Then I used the most robust methods to show that after soil contact, seeds of a focal tree species contain diverse fungi that are closely related to endophytes and pathogens.To explore the ecological specificity of symbiotrophic fungi, I examined endophytic, endolichenic, and saprotrophic communities inhabiting physically proximate hosts in a biotically rich area of southeastern Arizona. I found that endolichenic fungi are largely distinct from plant-associated fungi, with the exception of a group of ecologically flexible symbionts that occur in lichens and mosses. Although numerous endophytes were found in non-living leaves, fungi that were highly abundant in leaf litter were seldom found as endophytes.To assess symbiotroph biodiversity and ecological specificity at a broad geographic and phylogenetic scale, I isolated>4100 endophytic and endolichenic fungi from diverse communities of plants and lichens across five climatic regions in North America. I found that the abundance, diversity, and composition of these nearly ubiquitous fungi differ as a function of climate, locality, and host. Differences among communities reflect environmental characteristics more strongly than geographic distance.Last, I addressed a series of hypotheses regarding the ecological specificity of fungi inhabiting living and non-living leaves. I show that like endophytes, saprotrophic communities are structured by environmental characteristics, and at small spatial scales by host and leaf status. Yet, differences in communities between living leaves and leaf litter suggest that most endophytes either rapidly complete their life-cycle or are out-competed by robust saprotrophs once leaves senesce.
The Effects of Endohyphal Bacteria on Anti-Cancer and Anti-Malaria Metabolites of Endophytic FungiJung, Chan; Arnold, A. Elizabeth (The University of Arizona., 2012-05)Endophytes - the diverse, ubiquitous microbes that inhabit healthy plant tissues-- have proven to play a promising role in advancements in medicine due to their bioactivity against many pathogenic agents- such as bacteria, cancer cell lines, and malarial parasites. Based on preliminary data, endohyphal bacteria that have been found to inhabit certain endophytes may affect their metabolite production. The goal of this study was to evaluate whether diverse bioactive endophytes harbor endohyphal bacteria, which frequently are fastidious and can’t be cultured independently. A molecular cloning approach, through which two PCR enzyme mixes were compared, revealed that 1 out of 14 bioactive endophytes screened was positive for endohyphal bacteria (7.14%). BLAST analysis of 16s rRNA sequence data indicated a top match to the genus Caulobacter, a Gram-negative genus of bacteria commonly found in soil and water. Previous work by colleagues has found related strains of endohyphal bacteria in other strains of endophytes, which brings attention to this particular bacterium in assessing endohyphal bacteria and their ecological roles. Further testing of endophytes immediately after isolation from plant tissue, rather than from long-term vouchers, might be more effective in documenting endohyphal bacteria. For those that do harbor detectable infections, curing the endophytes of their endohyphal bacteria then assessing their metabolic activity would reveal whether or not the bacteria plays a major role for metabolite production and efficiency of endophytes against pathogens.