Research Article: Characterization of bacterioplankton communities from a hatchery recirculating aquaculture system (RAS) for juvenile sole (Solea senegalensis) production

Date Published: January 25, 2019

Publisher: Public Library of Science

Author(s): Letícia N. Duarte, Francisco J. R. C. Coelho, Vanessa Oliveira, Daniel F. R. Cleary, Patrícia Martins, Newton C. M. Gomes, Silvia Martínez-Llorens.


There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs (≥50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.

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The world population is expected to reach approximately 9.7 billion in 2050 [1]. As population increases, so will the demand for food, which will have to increase by 70% over the period from 2005–2050 [2]. The increase in demand will require substantial technological advances in food production. At present, aquaculture is undergoing rapid technological development and is emerging as a major food production sector. The demand for higher sustainability, reduced production costs and food safety has continuously driven the development of new and innovative aquaculture systems. Technologies such as recirculating aquaculture systems (RAS) with shallow raceway systems (SRS) allow more controlled and cost-effective production conditions, while having a reduced environmental impact. RAS is an advanced approach that reuses water in the production system with mechanical and biological filters [3]. SRS contribute for an optimized hydrodynamic performance over common raceways, allowing a lower water level and plug-flow pattern that enables high fish stocking densities, improving overall productivity [4]. RAS technology with shallow raceways continuously processes and recycles water, reducing water pump requirements while maintaining optimal environmental conditions for fish production [4]. However, the use of high fish densities during production may result in more rapid and severe disease outbreaks [5]. In fact, currently, there is a growing understanding that improvements in the prevention and management of disease outbreaks requires a deeper knowledge of the ecology of microbial communities in aquaculture systems. Outbreaks of parasitic, bacterial, and fungal diseases are among the most important limiting factors for the success of aquaculture production, leading to high mortality rates and important economic losses [6]. For example, the production of Senegalese sole (Solea senegalensis), a species of considerable commercial value, is strongly limited by its sensitivity to infectious diseases such as pasteurellosis (caused by Photobacterium damselae subsp piscicida), vibriosis (caused by various species of the genus Vibrio, especially Vibrio anguillarum) and flexibacteriose (caused by Tenacibaculum maritimum) [7]. However, despite the deleterious effects of fish pathogens, the aquaculture water microbiome is essential for maintaining water quality (nutrient recycling) and fish health during intensive fish production [8, 9]. For example, nitrogen and phosphorus are recycled through the activity of heterotrophic decomposers [10]. The presence of beneficial microbes was also shown to reduce colony-forming units (CFU) of pathogenic bacterial species [11]. Naturally occurring or introduced beneficial bacteria (probiotics) may contribute to improve water quality, inhibit the development of fish pathogens, improve the fish immune system and promote the balance of the fish bacterial flora [8, 12, 13].

The physicochemical characteristics of the water in each compartment are summarized in Table 1. The most notable differences were between Sup and the hatchery RAS compartments. There was a slight increase in pH and fairly low levels of nutrients in the Sup compartment when compared to RAS compartments (Table 1).

Exploring the potential of naturally occurring microorganisms as biocontrol agents in aquacultures is not a new concept [46, 53, 71, 72]. The development of microbial management or modulation approaches should be based on a fundamental knowledge about the aquaculture microbiome. This study provides baseline information about the bacterioplankton community composition and diversity of a commercial hatchery RAS for the production of juvenile Senegalese sole. Our results showed that despite the differences in relative abundance, the most abundant orders detected in the hatchery RAS (Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales and Flavobacteriales) were also the most abundant detected in the sole grow-out RAS characterized in our previous study [12]. Curiously, in contrast to our findings for grow-out RAS, our results indicated that the bacterial assemblage of the water supply played an important role for the colonization of bacterial populations (e.g. Pseudoalteromonas sp., members of the Roseobacter clade, Phaeobacter arcticus and Sedimentitalea todarodis and Sulfidobacteria) in the hatchery RAS. Most remarkable, here water supply seems to contribute for a strong colonization of Pseudoalteromonas sp. in the tanks, which in turn may play a role in suppressing the development of potential fish pathogens in the aquaculture system [36–40]. Our findings suggest that the bacterial community of the water supply may influence the bacterioplankton community structure of sole hatchery RAS. However, taking in consideration the results obtained for sole grow out RAS [12], the contribution of water supply to shape RAS bacterioplankton communities may vary between different RAS. Further studies are needed to investigate the effect of reared fish species and aquaculture practices for identification of the key drivers of RAS bacterioplankton communities.




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