"Manipulation of naturally occurring microbial communities to reduce plant diseases or increase crop yields requires a thorough understanding of interactions within the phytobiome, in particular, how microbial communities change as plants age, across plant species and organs, and under different land management regimes. Plants were sampled from a wheat-maize-soybean crop rotation site that implements four different land management strategies (conventional, no-till, reduced inputs, and organic). The fungal and bacterial communities of leaves, stems, and roots of wheat, maize, and soybean throughout the growing season were analyzed using fungal internal transcribed spacer and bacterial 16S rRNA gene amplicon sequencing. Analysis of sequence-based fungal communities has some limitations due to the unreliable phylogenetic resolution of DNA sequence alignments. To improve this deficiency, a tool that improved phylogenetic resolution was developed. This tool increases the number of operational taxonomic units which are identified at genus and species levels. Endophytes were isolated from the wheat plants used for microbial community analysis and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum during wheat seedling and head infection. Endophytes on crops can be developed to manage disease, and endophyte-based biocontrols could solve current limitations in F. graminearum disease control. Additionally, functional analysis of F. graminearum secondary metabolite genes provides insight into the function of their gene products for this fungal pathogen. Microbial community structure is affected by various genetic factors of the host plant, environmental factors, and interactions with other organisms. Understanding community responses to these factors is necessary for targeted manipulation of communities to reduce plant disease."--Pages ii-iii.
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