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

Abstract

Flowthrough and pond aquaculture system microbiome management practices aim to mitigate fish disease and stress. However, the operational success of recirculating aquaculture systems (RAS) depends directly on system microbial community activities. In RAS, each component environment is engineered for a specific microbial niche for waste management, as the water continuously flowing through the system must be processed before returning to the rearing tank. In this study, we compared waste management component microbiomes (rearing tank water, pH correction tank, solid-waste clarifier, biofilter, and degassing tower) within a commercial-scale freshwater RAS by high-throughput 16S rRNA gene sequencing. To assess consistency among freshwater RAS microbiomes, we also compared the microbial community compositions of six aquaculture and aquaponic farms. Community assemblages reflected site and source water relationships, and the presence of a hydroponic subsystem was a major community determinant. In contrast to the facility-specific community composition, some sequence variants, mainly classified into Flavobacterium, Cetobacterium, the family Sphingomonadaceae, and nitrifying guilds of ammonia-oxidizing archaea and Nitrospira, were common across all facilities. The findings of this study suggest that, independently of system design, core taxa exist across RAS rearing similar fish species but that system design informs the individual aquatic microbiome assemblages. Future RAS design would benefit from understanding the roles of these core taxa and then capitalizing on their activities to further reduce system waste/added operational controls. IMPORTANCE Recirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and AP rely on microbial consortia for maintaining water quality and promoting fish/plant health, but little is known about the microorganisms actually present. This lack of knowledge prevents optimization of designs and operational controls to target the growth of beneficial microbial species or consortia. The significance of our research is in identifying the common microorganisms that inhabit production RAS and AP and the operational factors that influence which microorganisms colonize and become abundant. Identifying these organisms is a first step toward advanced control of microbial activities that improve reproducibility and reduce costs.

Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments

“…2 ) as determined by amplicon sequencing before [ 21 , 39 ], acknowledging that for T-RFLP, it is known that only the most abundant part of the community can be assessed [ 37 , 40 , 41 ]. However, the currently available studies that used amplicon sequencing only sampled a limited number of compartments [ 6 , 21 , 39 ], or even mainly focused on the biofilter only [ 42 ].…”

Planktonic and sediment bacterial communities in an integrated mariculture system

“…Planktonic bacteria in recirculating aquaculture systems have been widely reported (Zhao et al 2018; Bartelme et al 2019;Duarte et al 2019;Jiang et al 2019), and some species are likely to influence fish health (Xue et al 2017;Ben Hamed et al 2018). Some bacteria strains have been used to control water quality or planktonic bacterial community (Stabili et al 2010;Kandel et al 2014;Cui et al 2017;Gao et al 2018), but only in enclosed water bodies.…”

“…Bacteria play a crucial role in the transformation and circulation of components of seawater. The community structure of bacteria in the plankton and in the sediment in aquaculture systems has been reported by many researchers (Robinson et al 2016;Bartelme et al 2019;Duarte et al 2019), although most of these studies were conducted in laboratories or enclosed systems. Knowledge of the relationship between sea-based open aquaculture systems and bacterial communities, which could be used for the improvement of aquaculture operations, is lacking.…”

The complex microbiome in aquaponics: significance of the bacterial ecosystem

“…These more complex systems potentially have more diverse microbial communities, with the microbiome in the different compartments likely to differ. Knowledge of the microbial diversity and functional distribution of these microorganisms in aquaponics systems is key to understanding microbial community dynamics and to enhance system performance (Bartelme et al 2018(Bartelme et al , 2019Munguia-Fragozo et al 2015;Schmautz et al 2017).…”