Relation of the soil microbiota of cork oak groves and surrounding grasslands to tree decline

Cork oak ( Quercus suber L.) form low-density silvopastoral systems of great ecosystemic and socioeconomic importance in the Mediterranean Basin, as they provide bark of great industrial value. Since the 1950s, these trees have been increasingly suffering from a deadly disorder known as decline, due to different biotic and abiotic factors. Associated with these forests, grasslands of great pastoral value and as carbon sequestrators develop. The aim of this work was to study the bacterial and fungal diversity present in the soils of healthy and diseased cork oaks (due to decline) and their associated grasslands, an ecosystem whose microbiome has not been studied so far by metagenomics. Soil samples were collected from cork oak forests in southern Spain and their microbial diversity was analyzed by metabarcoding with Illumina MiSeq. With respect to bacterial families, no differences were reported between cork oak forest soils and their associated grasslands, possibly due to the presence of endemic bacteria and similar environmental conditions. However, there were differences in fungal diversity between healthy cork oak forests and their associated grasslands. In the healthy cork oak soils, the families Gemmatimonadaceae and Nocardioidaceae were massively present, while in the diseased soils the fungal genus Geminibasidium was found. Regarding the functional niche, healthy cork oaks presented mainly ectomycorrhizae in their soils, while their associated grasslands presented fungal endophytes, less present in areas with diseased trees. Therefore, fungi, but not bacteria, present in the soils of cork oaks and associated grasslands could play a key role in the presence/absence of decline in cork oaks. • Cork oak groves and associated grasslands soils show similar bacterial diversity. • Healthy cork oak groves and associated grasslands show different fungal diversity. • Gemmatimonadaceae and Nocardioidaceae families were in healthy cork oak soils. • Geminibasidium was found in diseased cork oak soils. • Ectomycorrhizal and endophytic fungal functions in healthy ecosystems were found.