Rhizobiome data from lettuce (Batavian) grown in hydroponics and aquaponics environments.
Terrestrial plant roots mediate a complex network of prokaryotes and eukaryotes, collectively referred to as the rhizobiome. The ability to promote beneficial plant symbionts can contribute to increased crop productivity. Despite recognition of this microbial underpinning, plant cultivation strategies remain focused on plant physiology to determine crop health. The success of plant cultivation in hydroponics indicates that nutrient uptake, abiotic and biotic stress resistance is preserved in the rhizosphere regardless of the surrounding milieu. What has not been explored is how the microbial community adapts to soil-less hydroponic or aquaponic cultivation. Microbial dynamics in aquaponic systems are more complex than in hydroponics. As additional communities enter via the inflow water. This influx is shaped by microbial communities in the facility intake water, recirculating aquaculture system (RAS) environment including fish gastrointestinal tract, and the biofilter community of the soluble-waste treatment loop.  This study presents results from a series of experiments aimed at characterizing the development of the rhizobiome during the cultivation of Batavian lettuce (Lactuca sativa) in hydroponic or aquaponic systems coupled to freshwater RAS with common carp (Cyprinus carpio) or Nile tilapia (Oreochromis niloticus). In the first set of experiments, we employed standard water purification techniques (UV, ozone, H2O2) to impede microbial proliferation in hydroponic beds. This provided a macroscopic view of how sterilization processes impact rhizosphere and plant health. In the second set of experiments we investigated the dynamics of rhizosphere colonization by foreign microbial communities such as the upstream RAS microbiome, a soil rhizosphere community, and probiotic supplementation. These were compared to treatments grown in sterilized nutrient solution. The similarity of taxonomic profiles across all treatments indicated that the plant roots strongly dictate the rhizobiome regardless of other environmental pressures or microbial influences. Upstream nitrifying microbial communities were not reflected in the rhizobiome – indicating that nitrifying organisms from the biofilter in the RAS do not carry over to the rhizosphere but rather are functionally replaced by rhizosphere-specific nitrifiers. Nonindigenous communities in proximity to plants are not capable of displacing the pre-existing rhizobiome in hydroponic nor aquaponic systems.