Beyond detection: unveiling microbial dynamics in oak seedlings using fungal isolation and amplicon sequencing

Forest nurseries are critical for producing resilient nursery stock for reforestation and planting of ornamental trees, yet the microbial communities associated with nursery grown plants remain poorly characterized. Quercus robur L. seedlings from seven Czech forest nurseries were analyzed to assess microbial diversity, co-occurrence patterns, and environmental drivers.

Microbial communities were characterized using fungal ITS2 and bacterial 16S rRNA gene amplicon sequencing, fungal isolation, and comprehensive soil chemistry. HTAS revealed broader taxonomic and functional profiles compared to isolation, which selectively enriched for fast growing pathogens. Both methods were found to be complementary, emphasizing the value of methodological integration. Fungal communities exhibited pronounced site specific beta diversity and responded to inorganic soil parameters, particularly calcium, phosphorus, and pH/CaCl₂. Bacterial communities were more spatially cohesive and primarily associated with humification related factors. Trends in fungal alpha diversity were observed in relation to organic matter fractions (e.g., C_ox, D_H). SparCC genus level association analyses revealed high magnitude compositional association patterns, but no network edges remained significant after FDR correction; these patterns are therefore interpreted as exploratory and hypothesis generating rather than as evidence of direct microbial interactions.

Mineral soil properties were associated with microbial community structure and fungal trophic composition. Despite standardized nursery conditions, edaphic variability exerted strong filtering effects on fungal and bacterial communities. These findings provide ecological insight into seedling microbe interactions and offer a basis for microbiome informed nursery management strategies.