Uncovering the dark side of agriculture: How land use intensity shapes soil microbiome and increases potential plant pathogens

Abstract

Soil microbiome plays a critical role in maintaining key soil processes such as litter decomposition, nutrient cycling, and plant productivity. In this study, we aimed to investigate the variability of soil chemicals, microbial diversity, and composition in seven ecosystems i.e., Fagus sylvatica and Quercus ilex forests, a Mediterranean grassland and shrubland, a vineyard, a horticultural cultivation in open field and under greenhouse, across a gradient of land-use intensity in Southern Italy. Soil chemistry included pH, organic matter, total nitrogen, and C/N ratio, and soil microbiota was characterized by high-throughput sequencing of 16S and ITS genes. Our results showed that greenhouse soils had the highest pH, while Fagus had the lowest. Horticultural, greenhouse, and grassland soils had low levels of OM and total N, while shrubland had relatively high levels of OM, total N, and C/N ratio. Fagus soils, on the other hand, had the highest levels of OM, total N, and C/N ratio. Bacterial diversity was lowest in horticultural soils, whereas fungal diversity was highest in shrubland soils. Pseudomonadota were the predominant bacteria in Fagus, grassland, and vineyard soils, while Actinomycetota dominated in Quercus, shrubland, and greenhouse soils. However, Cyanobacteria was predominant in horticultural soils. On the other hand, the Ascomycota was predominant in all ecosystems except Quercus soils, where the Basidiomycota was dominant. Our bipartite network analysis revealed that bacteria are often the same in different ecosystems while fungi tend to be specific to a particular habitat. Moreover, in agricultural ecosystems, fungal pathogens belonging to Alternaria, Fusarium, Gibellulopsis, Stemphylium, Acremonium, and Curvularia are more abundant, especially in greenhouse. The findings of this study provide important insights into the variability of soil microbial diversity and community composition in different ecosystems, highlighting the essential role of preserving natural ecosystems while managing agricultural ones, given their higher abundance of pathogens.