Spatial and Temporal Variation in Fungal Endophyte Communities Isolated From Cultivated Cotton (Gossypium hirsutum): Implications for Sustainable Agriculture Practices

Communities of endophytic fungi in a single plant species can vary both temporally and geographically and depend on multiple factors such as plant density, nutrient availability, local environmental conditions and interactions with soil fungi and bacteria. In order to better characterize communities and functional roles of fungal endophytes in cotton, plant tissue samples of asymptomatic leaves, squares and bolls were collected at two different times of the season (June and August 2011) from multiple commercial cotton varieties grown during variety trials at eight sites distributed across two ecologically distinct growing regions in north and central Texas, USA. We also surveyed cotton grown on organic farms in comparison to non-organic farms. We identified fungal endophytes using morphological and molecular approaches and calculated several ecological parameters to characterize their patterns of diversity and community composition. We found a total of 71 different endophytic fungal taxa grouped into 44 different genera. We found evidence of differences in community composition between the two growing regions and the tissues surveyed. Our findings in cotton are consistent with analyses of endophtyes in other plants, showing variation in community composition associated with different tissues, locations, and time of the season sampled. However, the Shannon-Wiener biodiversity index values were not significantly different, indicating that the overall species richness and relative abundance of fungal taxa isolated per plant sample is relatively constant. Among the fungal endophytes isolated, several are candidates for potential use as beneficial endophytes in the management of plant pathogens, insect pests and nematodes, based either on their known effects as endophytes in other plants or their ecological roles outside the plant. Our spatial and temporal analysis results will be useful for the targeted implementation of these fungi as beneficial endophytes for the management of specific pests, at specific locations and times of the season.