When reishi (Ganoderma lucidum) was grown in the same soil year after year, the soil microbiome shifted toward hostile bacteria. Antifungal species like Bacillus velezensis and Bacillus amyloliquefaciens blocked reishi growth by 53–83% in lab tests, and after 3 years, overall bacterial diversity dropped by about 30–40%. Beneficial nutrient-cycling microbes declined while inhibitory species took over, showing yield collapse is driven by microbial imbalance, not nutrient depletion.