Pathobiome Analyses Reveal Structural Changes in Maize Microbiomes Associated with <i>Phyllachora maydis</i> and Tar Spot Disease

Pathobiomes, the complex microbial communities associated with plant diseases, play a crucial role in shaping host–pathogen interactions. In crops such as maize, understanding these microbial dynamics is essential for managing diseases such as tar spot, caused by the fungus Phyllachora maydis. Thus, the objectives of this study were to investigate the mycobiome composition associated with tar spot disease in corn and to evaluate the genetic diversity of P. maydis in Florida. Amplicon sequencing of the internal transcribed spacer (ITS) region revealed 1,267 unique amplicon sequence variants (ASVs) across asymptomatic and symptomatic (tar spot stroma) maize tissues, with Ascomycota dominating both tissue types. Although the overall fungal diversity was similar between symptomatic and asymptomatic tissues, P. maydis was significantly more abundant in symptomatic samples. Key taxa, such as Fusarium and Epicoccum, were enriched in tar spot lesions, contributing to a distinct fungal community structure. Co-occurrence network analysis further demonstrated a more complex fungal interaction network in tar spot-affected tissues, suggesting the importance of Fusarium, Curvularia, and Phaeosphaeria, among others, in shaping these interactions. Low genetic diversity within the P. maydis population in Florida was confirmed based on nucleotide diversity and phylogenetic analysis of 16 ASVs and 88 individual isolates collected from single tar spots across different fields during 2022 and 2023, showing minimal nucleotide variations across the ITS, large subunit, and small subunit regions. These findings enhance our understanding of the fungal community dynamics and P. maydis population structure in tar spot disease. By framing these dynamics within a pathobiome perspective, this study offers insights that could inform future microbiome-based management strategies. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .