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Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation.

ABSTRACT: The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability. To test this hypothesis, the stability of the microbiota community composition in a freshwater RAS with (RAS+A) or without algae (RAS-A) was challenged by introducing an acute pH drop (from pH 7 to 4 during three hours) to the system. Stigeoclonium nanum, a periphytic freshwater microalga was used in this study. No significant effect of the algae presence was found on the resistance to the acute pH drop on ammonia conversion to nitrite and nitrite conversion to nitrate. Also the resilience of the ammonia conversion to the pH drop disruption was not affected by the addition of algae. This could be due to the low biomass of algae achieved in the RAS. However, with regard to the conversion step of nitrite to nitrate, RAS+A was significantly more resilient than RAS-A. In terms of overall bacterial communities, the composition and predictive function of the bacterial communities was significantly different between RAS+A and RAS-A.

SUBMITTER: Mohamed Ramli N

PROVIDER: S-EPMC5901992 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:A marine aquaculture recycling system (RAS) for the production of post-smolt was monitored for microbial community structures during the first year of operation. Sample material was obtained monthly from the biofilter biofilm carriers, the production water (tank 3), the fish skin (tank 3) and the tank 3 wall biofilm. Additional samples were taken during outbreaks of fish skin wounds, washing of the plant, UV filtration of the inlet water and from various wall biofilms. Samples for depth profiles from all fish tanks were also collected. The sampling tools were a ladle for capturing biofilter biofilm carriers, toothbrushes for wall biofilm capture, filters for capture of water microbes and scalpels for skin tissue slicing. The sampling times were indicated by the production cycle number (cycle 2-5) and the week number within the cycle (W). Prior to bacterial community analysis, the stored samples were exposed to cell lysis and extraction of environmental DNA by commercial kits. All samples were subjected for PCR amplification of 16S rDNA sequences for library formations and prepared for Ion Torrent technology, which sequences 250 bp fragments. A total of 1.1 million reads were obtained from the 100 RAS samples analysed. The process from Ion Torren analysis to library involved bioinformatics steps with sorting, filtering, adjustment and taxonomic identification, and the final output was shown in a table as operational taxonomic units (OTUs) and relative abundance at different sampling sites and sampling time points. Of a total of 450 taxonomically assigned OTUs, 45% were classified at genus level. The 16S library raw data are deposited in the Mendeley data repository and cited in this Data in Brief article co-submitted with the article "Microbial colonization and stability in a marine post-smolt RAS inoculated with a commercial starter culture." [1]. So far, the raw data are referenced in four more publications in progress. These cover microbial shifts and enrichments between sampling times, sulfur cycling, "in vivo biofilm" and identification of relatives of fish pathogens in RAS. All library sequences are available in GenBank with accession numbers MN890148-MN891672.

Project description: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.

Project description:BackgroundMicrobial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems.ResultsWe compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria.ConclusionThe different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.

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Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation.

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