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A major concern in potato and onion production worldwide is the sustainability of crop production systems using short-term rotations. Although rotation crops are known to influence soil microbial communities, few long-term field studies have investigated effects of potato and onion crop rotations on soil microflora and soilborne diseases. A long-term trial (10 years) was established in New Zealand in the 2004–05 season to determine changes in soil characteristics, soil biological communities, plant productivity and soilborne diseases resulting from different crop rotations. Six different crop rotation ‘treatments’ were used: three were onion-focused and three were potato-focused. For both the onion- and potato-focused rotations, one treatment was continual monoculture, one was biennial alternating onion and potato (‘conventional’ rotation, common local commercial practice) and one was a 4-year cycle where the onion or potato crops were grown every fourth season with different crops in the intervening seasons (‘sustainable’ rotation). The results of the rotations were evaluated at the end of 2012–13, nine growing seasons after the trial began. Soils from the three potato-focused rotations had similar microbial biomass carbon (C) and nitrogen (N), total C and N, and enzyme activity, but had different microbial activity parameters. Soils from the three onion rotations differed in organic matter content, total C and N, enzyme activity and carbohydrate utilization. The main factor correlated with potato diseases (stem canker, black scurf) and crop yields was the amount ofRhizoctoniainoculum in the soil. Onion yields in 2012–13 were correlated with the severity of pink root during the growing season. Total microbial activity in soil gave better relationships to soilborne disease incidence (Rhizoctonia stem canker of potato or pink root of onion) and to crop yields, than soil chemical parameters (pH, nutrient status, C:N ratio) or other microbiological parameters (microbial biomass, total culturable bacteria and fungi, and microbial diversity). This research has broadened understanding of effects of crop rotations on soil microbial community characteristics, soilborne diseases and crop productivity of potatoes and onions grown in a soil and an area where intensive vegetable production is common. This knowledge will assist growers to increase crop yields and reduce soilborne pathogens in a sustainable manner. Based on the results from this study, intensive potato and onion production should require these crops to be grown within 4-year crop rotations in order to foster sustainable yields and minimize soilborne diseases. [ABSTRACT FROM PUBLISHER]