Crop rotations in organic greenhouse production - effects of increased crop diversity on the soil microbiome

Soil health and biodiversity are fundamental features for both organic production systems and of an agroecological approach. Crop rotations and soil fertility management are important for nutrient flows, soil health, and economic sustainability, but little information for the incorporation of crop rotations in organic greenhouse production is available. Within the project GreenResilient (Core Organic Co-fund), and a project based in Sweden (Ekhaga Foundation) the issue of crop rotations have been investigated in a total of six European countries (Belgium, Denmark, France, Italy, Sweden and Switzerland) with crop choices designed according to the local climatic preconditions. Choice of crops is crucial in terms of soil and crop health, and can either increase or decrease the presence of soil borne pathogens and thereby make the production system vulnerable or resilient. Soil microbial activity and diversity were analyzed using fluorescein diacetate activity (FDA) and metagenomic analysis (Illumina MiSeq) of fungi (ITS) and bacteria (16S) at key events of the different crop rotations. Soil bacterial and fungal alpha diversity varied between the different sampling incidents with respect to both species richness and evenness. More complex production systems, where there was an increase in plant diversity, did not necessarily lead to higher microbial diversity. A presence of several types of fungal pathogens were observed in all countries, irrespective of production system, indicating a build-up of pathogens in short crop rotation practices. Microbial activity did not conclusively explain variations in microbial diversity for fungi or bacteria.