Isolation of oak microbiota

Microbial isolation methods are a key factor for the production of comprehensive microbial culture collections that represent the richness and diversity of the natural microbiota. In this study, we evaluated the number and taxonomic richness of bacterial and fungal isolates from the oak microbiota obtained by (1) agar plating using various types of growth conditions and (2) dilution-to-extinction. Microbial isolates were characterized by 16S rRNA gene and ITS profiling along with the endogenous microbial communities from oak tissue samples. We found that the type of agar, incubation conditions and type of samples inoculated influenced the number taxonomic richness of the isolates obtained. Most of the bacterial and fungal ASVs obtained from microbial isolates originated from one of the two isolation methods, with only 12 % ASVs being detected in both. Moreover, isolation methods captured ASVs that were not detected by culture-independent analysis of the microbiota, suggesting that isolation approaches can complement culture-independent analysis by enriching low-abundant taxa. Our results overall suggest that dilution-to-extinction and agar plating capture different fractions of the cultivable oak microbiota and that a combination of isolation methods is required in order to capture higher taxonomic richness.