Root-associated fungal communities along productivity gradients in a perennial alfalfa

Background and Aims Perennial forage legume leys such as alfalfa are a cornerstone of organic production and integrated crop-livestock systems. Spatial yield variability is common in agricultural fields but the belowground factors contributing to this variation are poorly understood. This study examined how soil chemical properties and soil- and root-associated fungal communities correspond to persistent productivity gradients in an organically managed alfalfa ( Medicago sativa L.) ley. Methods Alfalfa plants and rhizosphere soil were sampled from high- and low-productivity field zones over two consecutive years to assess plant biomass, root health and soil chemical properties. Fungal communities were profiled using ITS1 amplicon sequencing. Diversity, community composition, temporal stability and the distribution of core, indicator and putative pathogenic taxa were evaluated. Results Plant biomass in high-productivity zones was ~ 55% higher although plants in both zones appeared healthy. Soil P and K levels were similar between zones, whereas Mg differed strongly but remained within sufficiency ranges. Soil pH differed by one unit and mineral N showed no consistent spatial pattern. Fungal communities were primarily structured by compartment. Plant productivity explained only ~ 9% of β-diversity. About one-third of root-associated taxa persisted across years and productivity zones, forming a dominant and stable community enriched in putative pathogens. Core and indicator analyses identified only few zone-associated taxa, including a Glomeraceae indicator detected in high-productivity roots. Conclusion Soil nutrients and broad fungal community patterns did not explain the persistent productivity gradient. Differences were confined to a small number of root-associated taxa, suggesting that additional edaphic and biological factors beyond fungi likely contribute to the observed biomass differences.