Metataxonomic analysis reveals that the farming system has minimal effect on soil microbiome variation in cereal fields

Abstract

The soil microbiota, particularly mycotoxin-producing fungal communities, has garnered increasing attention owing to its implications for human and animal health. Mycotoxins commonly contaminate cereal crops and their by-products, with their associated health risks intensified by climate change. The growing demand for organic food, driven by perceptions of enhanced safety, contrasts with the inconclusive research on mycotoxin contamination in organic versus conventional cereals. Here, metagenomic techniques such as amplicon sequencing offer valuable tools for elucidating this issue. In this study, we employed metataxonomics to investigate potential variations in fungal and bacterial community diversity between organic and conventional farming systems in cereal fields, with a focus on toxigenic fungi. Our analysis revealed that geographic location of the samples, rather than farming practice (organic/conventional), was the primary driver of diversity differences. Furthermore, we found no significant evidence of differential abundance across toxigenic fungal groups between the two systems. To validate taxonomic assignments, we constructed a phylogenetic tree using sequences classified under the genus Fusarium. Additionally, we assessed the potential activity of biocontrol agents from certain bacterial genera against toxigenic fungi by analysing their co-occurrence patterns in both conventional and organic soils. Most correlations were weak, although a few significant associations involved Bacillus, Streptomyces, and Pseudarthrobacter. Notably, we detected mycotoxigenic species of concern (e.g., potential producers of aflatoxins or trichothecenes) in cereal fields irrespective of the farming system.