Repeated applications of organic amendments promote beneficial microbiota, improve soil fertility and increase crop yield

Long-term adoption of intensive agricultural system negatively affects soil fertility, soil microbiome and may compromise the quality and amount of crop production. To avoid these problems, application of organic materials has been proposed as a potential alternative strategy for soil management. Therefore, the objective of this study was to compared the effects of conventional and organic soil management on crop yield of rocket (Eruca sativa), soil fertility, and microbiome structure through a 2-year long mesocosms experiment. Eight organic treatments, different in terms of organic amendment chemistry (i.e., alfalfa hay, biochar, glucose, manure) and application frequency, were compared with conventional management practices based on mineral fertilizer and chemical fumigation. Crop quality was assessed by measuring the NO3− content in leaves, whereas soil chemical and microbiological (i.e., FDA activity and functioning by BIOLOG EcoPlates™) properties were evaluated to understand their effects on soil fertility. Changes in soil microbiota were assessed by high-throughput sequencing of bacterial and fungal rRNA gene markers. Application of organic amendments significantly improved crop yield, especially when alfalfa and glucose were applied as a single dose. NO3− concentration in leaves was decreased with biochar and manure application, and this did not depend on the application frequency. Application of synthetic fertilizer and fumigation induced soil acidification, increased soil salinity, and reduced soil microbiota diversity, activity and functionality, with negative effects on crop yield. In conclusion, this study indicates that long-term application of organic amendments effectively improved soil fertility and promoted the development of a beneficial soil microbiota capable of supporting high plant yield under intensive agricultural system.