Exploring temporal changes in the malting barley seed microbiome with meta-omics to understand nitrogen content effects

Abstract

Barley (Hordeum vulgare L.) is a critical cereal crop, particularly in beer production, where it plays a significant role in the economy, especially in South Africa. Despite its importance, the barley seed microbiome, which affects seed storage and quality, is not well understood. This research addresses two key questions: (1) how microbial composition and function evolve during storage and (2) how the inherent nitrogen content of the grain affects these dynamics. Using metagenomic and metaproteomic approaches, eight barley samples from the Kadie cultivar, stored for various durations (harvest, three, six, and nine months) with high and low nitrogen content, were analysed. Metagenomic sequencing revealed a predominance of bacterial sequences and minimal fungal presence, with storage time having a greater impact on microbial diversity than nitrogen content. However, specific bacterial genera such as Erwinia, Pantoea, Pseudomonas, and Stenotrophomonas showed nitrogen-dependent prevalence. Metagenome-assembled genomes (MAGs) were reconstructed, representing 26 bacterial genera, with minimal shared orthologues, highlighting taxonomic diversity. Functional analysis identified key metabolic pathways and carbohydrate-active enzymes (CAZymes) essential for microbial adaptation during storage. Metaproteomic analysis further showed the active expression of proteins related to nutrient transport and stress response, indicating functional changes over storage time. Overall, this research enhances the understanding of the barley seed microbiome, providing valuable insights into storage practices that could improve brewing quality and agricultural sustainability.