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Alyssa Joyce, Mike Timmons, Simon Goddek, and Timea Pentz

Abstract The growth rates and welfare of fish and the quality of plant production in aquaponics system rely on the composition and health of the system's microbiota. The overall productivity depends on technical specifications for water quality and its movement amongst components of the system, including a wide range of parameters including factors such as pH and flow rates which ensure that microbial components can act effectively in nitrification and remineralization processes. In this chapter, we explore current research examining the role of microbial communities in three units of an aquaponics system: (1) the recirculating aquaculture system (RAS) for fish production which includes biofiltration systems for denitrification; (2) the hydroponics units for plant production; and (3) biofilters and bioreactors, including sludge digester systems (SDS) involved in microbial decomposition and recovery/ remineralization of solid wastes. In the various sub-disciplines related to each of these components, there is existing literature about microbial communities and their importance within each system (e.g. recirculating aquaculture systems (RAS), hydroponics, biofilters and digesters), but there is currently limited work examining interactions between these components in aquaponics system, thus making it an important area for further research.

Keywords Microbiota · Aquaponics · Biofilters · Bioreactors · RAS · Hydroponics · Metagenomics


A. Joyce

Department of Marine Science, University of Gothenburg, Gothenburg, Sweden

M. Timmons

Biological & Environmental Engineering, Cornell University, Ithaca, NY, USA

S. Goddek

Mathematical and Statistical Methods (Biometris), Wageningen University, Wageningen, The Netherlands

T. Pentz

Eat & Shine VOF, Velp, The Netherlands

© The Author(s) 2019 145

S. Goddek et al. (eds.), Aquaponics Food Production Systems,


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