Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests

Abstract

Mediterranean biomes are biodiversity hotspots and also have been historically related to wine production. During the last decades, land occupied by vineyards has increased considerably threatening these Mediterranean ecosystems. Land use change and agricultural management affect soil biodiversity, changing physical and chemical properties of soil. These changes may have consequences on wine production, especially because soil is a key component of wine identity or terroir. Here, we characterized the taxonomic and functional diversity of bacterial and fungal communities present in soil from vineyards in Central Chile. To accomplish this goal we collected soil samples from organic vineyards from Central Chile and employed a shotgun metagenomic approach. Additionally, we also studied the surrounding native forest as a picture of the soil conditions prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. In general, bacteria were more abundant than fungi in both types of habitats, including soil-living genera such as Candidatus Solibacter, Bradyrhizobium and Gibberella. Interestingly, we found presence of lactic bacteria and fermenting yeasts in soil, which are key during wine production. However, their abundances were extremely low, suggesting unlikeness of soil as a potential reservoir in Chilean vineyards. Regarding functional diversity, we found that genes for metabolism of amino acids, fatty acids, nucleotides and secondary metabolism were enriched in forest soils, whereas genes for metabolism of potassium, proteins and miscellaneous functions were more abundant in vineyard soils. Our results suggest that organic vineyards have similar soil community composition than forest habitats. Additionally, we suggest that native forests surrounding vineyards may be acting as microbial reservoir buffering the land conversion. We conclude that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions related to natural habitats.