Abstract
Soil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the rhizosphere remains limited. By leveraging urban farming-featuring fields of different ages and multiple genotypes-we tracked the relative abundance, richness, and microbial networks of putative plant pathogenic fungi, mycorrhizal fungi, and saprotrophic fungi across fields over two years. We observed an increase in the relative abundance of putative plant pathogenic fungi in the rhizosphere in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. The relative abundance of saprotrophic fungi remained similar between younger and older fields. While the richness of putative plant pathogenic fungi and saprotrophic fungi was similar across the examined fields, the community structure of both groups differed between younger and older fields. For mycorrhizal fungi, the richness declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogenic fungi remained similar across fields. Our study reveals contrasting dynamics of essential soil fungal functional groups in the rhizosphere and provides predictive insight into the potential shifts in soil function and their impact on plant productivity.