Quantitative Assessment of Tuber lyonii DNA Distribution and Microbial Diversity in a Pecan Orchard

Understanding variability in truffle fruiting patterns is critical for improving productivity. A cultivated Tuber lyonii pecan orchard comprising 9-year-old trees in sections A - D and 4-year-old trees in Section E was investigated to determine whether orchard age, soil microbial communities, and soil physicochemical properties were associated with spatial variation in truffle abundance. Soil cores were collected from ten trees per Section and an outlier site ( n = 60). T. lyonii DNA was quantified using species-specific quantitative PCR (qPCR), microbial communities were characterized using ITS and 16 S rRNA genes, and soil physicochemical properties were analyzed. Quantitative PCR revealed that T. lyonii DNA abundance was highest in Section E (1.95 × 10⁴ ± 3.91 × 10 3 ng g⁻¹ soil), low in sections A-D (3.60 × 10⁻¹ ± 0.18, 5.30 × 10³ ± 1.60 × 10³, 1.14 × 10⁴ ± 4.72 × 10⁴ and 1.05 × 10⁴ ± 1.54 × 10³ ng g⁻¹ soil, respectively) and absent in outlier. Fungal communities were dominated by Mortierellomycota, Ascomycota, and Basidiomycota, while T. lyonii accounted for 92.2% of detected Tuber sequences. Proteobacteria (Pseudomonadota), Acidobacteriota, and Actinobacteriota dominated bacterial communities. Beta-diversity analyses revealed differences in microbial community composition among sections. Soil pH and organic matter did not differ across the orchard, whereas cation exchange capacity (CEC) was significantly lower in Section E than in sections A-D. These findings demonstrate spatial heterogeneity in T. lyonii abundance and microbial community composition and suggest that orchard age and localized soil conditions may be associated with n T. lyonii distribution.