There is considerable interest regarding the composition of the microbiome in aquaculture systems. The objective of this project was to evaluate how the microbiome changes in an aquaponics system with changes in the plant component.
Five aquaponics systems were set up and inoculated with water from an established Koi aquaponics system. Three guppies (Poecilia reticulata ) were added to each system . Two s ystems grew B asil, two grew Arugula and one was left as a control. The duration of the project was 8 weeks. For each system 50 0 mls of water were sampled at the beginning and end of the experiment, and passed through a 0.45 micron filter. Bacterial DNA was extracted using the ZymoBiomics DNA miniprep kit and libraries were prepared using the Oxford Nanopore 16s Barcoding kit . Libraries were sequenced using an Oxford Nanopore MinIon . A preliminary test of the sequencing method was also done by comparing the microbiome of an established Tilapia aquaponics system with the Koi/Goldfish aquaponics system and also bacteria from a 3% and 10% NaCl cabbage lactofermentation experiment.
Results for the plant treatment s are still pending, but some interesting results arose from the two preliminary tests. While the 3% NaCl microbiome was predominantly Lactobacillus, the 10% NaCl harbored mostly Staphylococcus and Lactobacillus. The Tilapia system had a variety of bacteria but was dominated by Polynucleobacter whereas the Koi/goldfish was more diverse with the most abundant genus being Devosia and Flectobacillus (see diagram) . We are still working to identify the species of nitrogen bacteria in each system.
Clearly the microbiome varies with water chemistry and species composition of the system. Understanding factors that effect the bacterial species of the aquaculture microbiome will help to promote beneficial species and avoid pathogens.