Effect of dietary phytase on water and fecal prokaryotic and eukaryotic microbiomes in a hybrid tilapia (Oreochromis aureus x O. niloticus) mixotrophic biofloc production system

In this study we evaluated feed and temporal effects on prokaryotic (16S) and eukaryotic (18S) microbiome dynamics in an outdoor mixotrophic biofloc system used to grow hybrid tilapia (Oreochromis aureus x O. niloticus) to market size. The dicalcium phosphate -free practical feed treated with 6-phytase (3000 FTU/kg; P-Free+Phytase) and positive (Control) and negative (P-Free) control practical feeds used were formulated to contain 27.7% digestible protein and 4% lipid. Sex reversed, all-male hybrid tilapia (28.9 g/fish) were stocked (29 fish/ m3) in 9 outdoor rectangular tanks (16.6 m3) and grown for 154 days. The Control feed was fed to all fish during the 14-day acclimation period after which each test feed was fed to fish in three tanks/feed. Biofloc water and fecal samples were collected from all tanks at time 0 (T0, study day 15) and T7, T70, and T140; prokaryotic and eukaryotic abundance and diversity were assessed using high-throughput amplicon sequencing of the 16S and 18S rRNA genes, respectively. Fecal 16S microbiome in all treatments was dominated by Fusobacteria (namely Cetobacterium) with minority representation by Proteobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Opisthokonts (namely Capsaspora) were the dominant eukaryote detected overall in all fecal samples. Fecal 16S and 18S relative abundances varied significantly with time. Relative abundance of fecal 16S differed significantly between Control and P-Free+Phytase feed treatments only at T140 (harvest). Fecal 18S relative abundance differences among feed treatments were detected only at T0 and T7 and only at the supergroup taxonomic level. Prokaryotic communities in biofloc water among feed treatments and across times were highly diverse and dominated by Proteobacteria, Bacteroidetes, Fusobacteria, Chloroflexi, Planctomycetes, and Actinobacteria. High relative abundances of Capsaspora across time characterized eukaryotic communities. Relative abundances of 16S and 18S taxa in water varied significantly over time. Control and P-Free feed 16S relative abundances in water differed significantly at T0 and T7. Time was the factor that explained most of the variation observed for 16S and 18S beta diversity. Overall, results of the present experiment suggest minimal influence of phytasetreated or dicalcium phosphate-free feeds on hybrid tilapia 16S and 18S water and fecal microbiomes throughout the experiment, particularly because the base feed formulation was the same for all treatments. During this experiment and at harvest tilapia in all treatments appeared healthy and robust, and no known pathogenic bacteria or eukaryotes were detected in any sample, suggesting the observed microbiomes may represent system-specific "healthy" core microbiomes.