Vol.:(0123456789) 1 3 Arch Microbiol (2017) 199:613–620 DOI 10.1007/s00203-016-1334-1 ORIGINAL PAPER Microbial diversity in diferent compartments of an aquaponics system Zala Schmautz 1  · Andreas Graber 1,2  · Sebastian Jaenicke 3  · Alexander Goesmann 3  · Ranka Junge 1  · Theo H. M. Smits 4   Received: 3 August 2016 / Revised: 20 December 2016 / Accepted: 28 December 2016 / Published online: 10 January 2017 © Springer-Verlag Berlin Heidelberg 2017 Keywords Community analysis · Metagenome · Tilapia · Lettuce · Nitrospira Introduction Aquaponic (AP) systems are sustainable multi-trophic-inte- grated quasi-closed-loop food production systems with low environmental impact considering that food is produced with low water consumption (Endut et al. 2011; Somerville et al. 2014; Goddek et al. 2016). AP combines a recirculat- ing aquaculture system with a hydroponic unit. One of its most important features is the reliance on bacteria and their metabolic products. Bacteria serve as the bridge that con- nects the fsh excrements, which is high in ammonium con- centration, to the plant fertilizer, which should be a combi- nation of low ammonium and high nitrate (Somerville et al. 2014). However, the total microbial community in diferent compartments of the AP systems has not been character- ized yet using—omics technologies (Munguia-Fragozo et al. 2015). As the AP systems can have diferent subunits, i.e., fsh tank, bioflter, drum flter, settler, or hydroponic, with each of them having diferent possible designs and diferent optimal conditions, the microbial communities in these components may difer drastically, and are, therefore, interesting to analyze, the ultimate goal being improved steering of the processes. Until now, nitrifying bacteria are the best studied group of environmental importance in the AP systems (Tokuyama et al. 2004; Revsberg et al. 2006; Zou et al. 2016a, b). Within this group, the ammonium-oxidizing bacteria (AOB), who convert ammonium to nitrite, are of particular interest. This group of chemolithothrophic bacteria was restricted to two evolutionarily distinct line- ages of the class Proteobacteria (Kowalchuk and Stephen Abstract Aquaponics is a solution for sustainable pro- duction of fsh and plants in a single semi-closed system, where nutrient-rich water from the aquaculture provides nutrients for plant growth. We examined the microbial communities within an experimental aquaponics system. Whereas the fsh feces contained a separate community dominated by bacteria of the genus Cetobacterium, the samples from plant roots, bioflter, and periphyton were more similar to each other, while the communities were more diverse. Detailed examination of the data gave the frst indications to functional groups of organisms in the diferent compartments of the aquaponic system. As other nitrifers other than members of the genus Nitrospira were only present at low numbers, it was anticipated that Nitro- spirae may perform the nitrifcation process in the bioflm. Communicated by Erko Stackebrandt. Electronic supplementary material The online version of this article (doi:10.1007/s00203-016-1334-1) contains supplementary material, which is available to authorized users. * Theo H. M. Smits theo.smits@zhaw.ch 1 Ecological Engineering Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland 2 UrbanFarmers AG, Zurich, Switzerland 3 Bioinformatics and Systems Biology, Justus-Liebig- University Giessen, Giessen, Germany 4 Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland