Ciliate diversity and growth rates in experimental recirculating aquaculture and aquaponics systems using microscopy

The function of recirculating aquaculture systems (RAS) relies on microbial communities, which convert toxic, fish-excreted ammonia into substances that can provide nutrients to plants as in the case of aquaponics systems. In the present study, heterotrophic protist communities of experimental sea water RAS and freshwater aquaponics systems were investigated using microscopy to characterize their diversity, natural abundance, and potential growth rates. Heterotrophic protist abundance was low (732 ± 21 to 5451 ± 118 ciliates L⁻¹ and 58 ± 8 to 147 ± 18 nanoflagellates mL⁻¹ in the aquaponics system and 78 ± 28 to 203 ± 48 ciliates L⁻¹ in the RAS), which is in line with values typically reported for rivers. In the aquaponics system, ciliates grew faster in the fish rearing tanks (1.9 ± 0.01 to 1.21 ± 0.03 d⁻¹ compared to 0.54 ± 0.03 to 0.79 ± 0.05 d⁻¹ in the other compartments), while heterotrophic nanoflagellates grew slower in drain tanks downstream of the hydroponics compartment (0.5 ± 0.3 to 1.37 ± 0.05 d⁻¹ and 4.09 ± 0.11 d⁻¹ to 6.03 ± 0.34 d⁻¹in the other compartments). Results indicated distinct niches and reduced microeukaryotic diversity at the end of the system’s operation cycle.