Abundant rather than rare fungi perform a vital role in maintaining the growth of continuous cropped cut chrysanthemum

Soil fungi play key roles in agricultural ecosystem. Yet, little is currently known about the dynamic pattern and driving factors of the rare and abundant fungal subcommunities in response to the short- and long-term continuous cropping. Here, we comparatively investigated the diversity and structure of rare and abundant fungal subcommunities with varying histories of continuous chrysanthemum (Chrysanthemum morifolium Ramat.) cropping, that is, cropping for 1 year (CP1), 6 years (CP6) and 12 years (CP12). The alpha diversity (estimated as Shannon index) of abundant and especially rare fungal subcommunities increased with continuous cropping years. The structure of both rare and abundant subcommunities varied notably with the increasing of continuous cropping years, but the value of dissimilarity for rare taxa (average of 0.988) was significantly higher than for abundant taxa (average of 0.243). The abundant taxon Mortierellomycota and rare taxa Nitrospirae and Elusimicrobia were significantly enriched in the CP12 treatment. Soil rare fungal taxa were mainly affected by the available nutrients (i.e., carbon, nitrogen and phosphorus) and pH, while the abundant fungal taxa were majorly influenced by soil total nutrients. The growth indicators (e.g., plant biomass, plant height, and flower diameter) of cut chrysanthemum significantly decreased under 12-year continuous cropping system. Random forest models showed that abundant rather than rare fungi played key roles in the chrysanthemum growth even though the rare fungi were more significantly affected during continuous cropping.