Exploring Bacterial Communities in Aquaponic Systems

Abstract

Aquaponics is a production system based on the dynamic equilibrium between fish, plants, and microorganisms. In order to better understand the role of microorganisms in this tripartite relationship, we studied the bacterial communities hosted in eight aquaponic and aquaculture systems. The bacterial communities were analyzed by 16S rRNA gene deep sequencing. At the phylum level, the bacterial communities from all systems were relatively similar with a predominance of Proteobacteria and Bacteroidetes. At the genus level, however, the communities present in the sampled systems were more heterogeneous. The biofilter samples harbored more diverse communities than the corresponding sump samples. The core microbiomes from the coupled and decoupled systems shared more common operational taxonomic units than with the aquaculture systems. Eventually, some of the taxa identified in the systems could have beneficial functions for plant growth and health, but a deeper analysis would be required to identify the precise functions involved in aquaponics.

Metabarcoding Analysis of Bacterial Communities Associated with Media Grow Bed Zones in an Aquaponic System

“…These phyla respond rapidly to carbon sources and are considered as r-strategists, as they are fast-growing bacteria [ 16 , 47 ]. The enrichment of Proteobacteria and Bacteroidetes in different units of an aquaponic system such as in the sump and biofilter was reported by Schmautz et al [ 7 ] and Eck et al [ 17 ], which is similar to the findings in our study. These phyla are mostly responsible for nitrogen cycling in aquaponic systems [ 7 , 16 ].…”

“…Next-generation sequencing (NGS) metabarcoding has been effectively used in the evaluation of microbial communities of many environmental samples and for the analysis of communities of microbes that cannot be easily cultured on selected media [ 6 , 14 , 15 ]. This technique has been applied to investigate the microbial diversity in different compartments and substrates of aquaponic systems such as plant roots, the system's sump, or the biological filter [ 7 , 16 , 17 ], but not when comparing microbial community diversity in vertically arranged zones of the media bed.…”

“…For practical reasons, such as the demand on time and computational and monetary constraints, environmental microbiologists have reported findings related to microbial diversity using limited numbers of experimental units [ 18 , 19 ]. To contribute to the database that has been generated in studies, in which data from one point in time and from one aquaponic system were generated [ 7 , 17 ], the aim of this study was to describe the diversity of bacterial communities in a flood-and-drain media bed system and to suggest biological processes that may occur in the vertical zones of this environment.…”

Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

“…In our study, all facilities, except Discovery World, reared yellow perch ( Perca flavescens ), so fish-specific microbiota relationships should have had minimal impact on the results. In a recent study, it was found that microbial community composition is dictated in part by system design, in this case, aquaculture versus coupled and decoupled aquaponic systems (25). We anticipate that further system design and operation standardization would result in microbial community assemblages that are more similar and thus more predictable among facilities.…”

Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?

“…For apple carposphere microbiota, the V3-V4 region of the 16s-rRNA gene was targeted using the modified primers to include Illumina™ adapters: Forward IlumF-Bakt_341F and Reverse IlumR-Bakt_805R [42]. For lettuce roots microbiota, the V1-V3 region was targeted using the Forward 27F and Reverse 534R Illumina primers used in a previous study of aquaponic systems [43].…”