Unlocking biosynthetic potential of sweet corn (Zea mays L. var. saccharata) phyllosphere and rhizosphere through metagenomics and metagenome-assembled genomes

Abstract

Sweet corn ( Zea mays L. var. saccharata ) is an important economic crop in Thailand. While most maize microbiome studies have focused on characterizing microbial communities and general functions, the potential for biosynthetic gene clusters (BGCs) remains largely unexplored. We performed shotgun metagenomic sequencing on the phyllosphere and rhizosphere of two sweet corn cultivars (Hi-Brix 3 and Insee 2) to characterize their microbial composition, BGCs, and metagenome-assembled genomes (MAGs). Our results revealed that the dominant phyla in the phyllosphere were Pseudomonadota , Bacillota , Ascomycota , Euryarchaeota , and Orthornavirae , while the rhizosphere was dominated by Actinomycetota , Ascomycota , Nitrososphaerota , and Bamfordvirae . Across both cultivars and compartments (phyllosphere, rhizosphere, and MAGs), the most abundant BGC classes were non-ribosomal peptides (NRPs), polyketides, and terpenes. Moreover, the four potential bacterial isolates from the sweet corn phytobiome–identified as Bacillus siamensis (isolates SCR1-1 and SCR1-2) and Asaia bogorensis (isolates SCLAB1-1 and SCP1-16)–were recovered and demonstrated significant antifungal activity against Exserohilum turcicum SWI-1, the causative agent of northern corn leaf blight. Metabolome profiling confirmed the production of potential bioactive compounds, including 2,4-di-tert-butylphenol (from the isolated Bacillus ) and 2(3H)-furanone derivatives (from the isolated Asaia ). This study represents the first unbiased characterization of BGCs in the sweet corn phytobiome, establishing a vital resource. The findings also illuminate potential metabolite-driven interactions and provide promising bacterial candidates for developing novel biocontrol agents to support sustainable disease management in sweet corn. Copyright © 2025. Published by Elsevier B.V.