Is it possible to manipulate the microbiome of growing medium for disease suppression during cucumber cultivation in soilless systems?

Abstract: Vegetables are at the basis of a healthy human diet. Traditionally, vegetables were
produced in soil-based cultivation, but due to problems with soil bound diseases soilless
cultivation systems were developed. These systems can provide increased productivity per unit of area and reduce the input of water and fertilizers.
Relatively little is known about the micro-organisms present in soilless cultivation systems.
Therefore, we studied the bacterial microbiome of growing media, using a. o. metabarcoding
and qPCR, in different experiments with cucumber cultivation in soilless cultivation systems. We also attempted to manipulate the microbial diversity and functionality present in the cultivation system by addition of different organic C sources, for example compost teas.
Results show that bacteria can quickly colonize the growing media during cucumber
cultivation, for example with numbers of 16S rRNA gene copies reaching 1010 copies/cm3
of stonewool or coco coir within a first few weeks of greenhouse cultivation. As expected the
taxonomic diversity of bacterial microbiomes in growing media differs significantly and is
influenced by growing medium type and organic C added. Interestingly, addition of organic C in the form of biochar or spent mushroom substrate (SMS) had significantly greater effect on
bacterial microbiome in inert growing medium than in organic growing medium.
This research provides evidence that steering diversity of microbiome in soilless growing
media towards higher disease suppression is possible. Still, there remains a lot to be unraveled about the taxonomic diversity and metabolic functioning of microbiomes in soilless cultivation systems, before we will be fully able to harness the potential of microbes naturally present in these systems.