Factors Shaping Endophyte Communities Associated with Selected Cultivated Plants in Arizona

Symbiotic 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