Dynamics of a Soil Fungal Community in a Three-Year Green Garlic/Cucumber Crop Rotation System in Northwest China

A decreased soil biological environment in terms of an unstable microbial population and diversity index is primarily caused by intensive continuous cropping systems. In this study, a crop rotation system was established to evaluate the soil fungal diversity using a pyrosequencing-based analysis during three successive growing seasons (2013, 2014, and 2015) under a field pot investigation. We found that overall green garlic/cucumber rotational effects increased cucumber productivity under these growing practices. Analysis of fungal communities in rhizosphere soils by high-throughput pyrosequencing showed that the estimated treatment effects were more obvious during the three-year trials, and OTU richness was much higher than the control in cucumber-planted soils. The relative frequencies of fungal diversity showed variable responses before and after rotation practices, and mainly alpha-diversity of fungi increased in garlic planted soil and again decreased after cucumber planted soil in each year. The phylogenetic classification illustrated that the fungal communities were dominated by the taxa Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, and Zygomycota across all samples. Particularly, the relative abundance of the taxon Ascomycota was largely and predominantly enriched with the increasing number of garlic bulbs during the three years. Moreover, the majority of abundant taxa positively correlated with available P and K contents, while being highly negatively correlated with soil pH, EC, and SOC. These results indicate that garlic-cucumber-based crop rotations induce fungal richness and diversity and promote the sustainability of agricultural ecosystems, thus enhancing crop growth and production.