Deep-sequencing of the bacterial microbiota in commercial-scale recirculating and semi-closed aquaculture systems for Atlantic salmon post-smolt production

Rud, Ida; Kolarevic, Jelena; Holan, Astrid Buran; Berget, Ingunn; Calabrese, Sara; Terjesen, Bendik Fyhn

doi:10.1016/j.aquaeng.2016.10.003

Cited by 85 publications

(53 citation statements)

References 65 publications

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“…The dominance of Proteobacteria and Bacteroidetes was congruent to previous high‐throughput sequencing analyses from commercial scale RAS for Atlantic Salmon (Rud et al, ) and experimental RAS for Convict Grouper ( Epinephelus septemfasciatus ) (Lee, Lee, Kim, Myeong, & Kim, ), despite water conditions (e.g. salinity and temperature) of the RAS were quite different from our study.…”

Section: Discussionsupporting

confidence: 91%

Tilapia recirculating aquaculture systems as a source of plant growth promoting bacteria

2019

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A recirculating aquaculture system with farmed tilapia is the most popular combination in aquaponics, an integration of aquaculture and hydroponics. Despite nutrient-rich fish-rearing water being regarded as a valuable resource for aquaponics, the quality and value of inhabitant microorganisms are certainly understudied. Our present research illustrates the feasibility of the tilapia-rearing water as a valuable source of beneficial microorganisms called plant growth promoting bacteria (PGPB).Microbial communities were examined with a combination of culture-independent high-throughput 16S rRNA gene sequencing and cultivation methods. Microbial communities determined using high-throughput sequencing indicated the usefulness of Bacteroidetes and Alphaproteobacteria as beneficial microbial indicators to assess the health condition of recirculating aquaculture systems. Siderophore production, ammonia production and phosphate solubilization assays were used for screening and 41% of isolates were identified as plant growth promoting bacteria. These bacteria were classified as Actinobacteria (eight strains [32% in total], Dietzia, Gordonia, Microbacterium, Mycobacterium and Rhodococcus), Bacilli (six strains [24%], Bacillus and Paenibacillus), Flavobacteriia (one strain [4%], Myroides), Betaproteobacteria (two strains [8%], Acidovorax and Chromobacterium) and Gammaproteobacteria (eight strains [32%], Aeromonas, Plesiomonas and Pseudomonas). We found that the tilapiarearing water naturally contained various lineages of PGPB and could be esteemed as a worthy seed bank of PGPB. Because aquaponics is a difficult system to use pesticides and herbicides, the role of PGPB to prevent plant pathogens and maintain healthy root system may be more important than traditional agricultural settings. K E Y W O R D Saquaponics, plant growth promoting bacteria (PGPB), recirculating aquaculture system (RAS), tilapia

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Section: Discussionsupporting

confidence: 91%

Tilapia recirculating aquaculture systems as a source of plant growth promoting bacteria

2019

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“…This genus is often found in diseased fishes, being considered opportunistic and colonizing already weakened hosts (Bornø and Linaker, 2015). Species from this genus seem to be common in fish farms and have been reported in the water and biofilm of recirculating and semiclosed aquaculture systems rearing Atlantic salmon, turbot and the Senegalese sole (Martins et al, 2013;Rud et al, 2017).…”

Section: Potential Pathogens Detected In the Core Microbiomesmentioning

confidence: 99%

“…Particularly problematic for fish, pathogenic bacteria that naturally reside in the aquatic environment can also form part of their microbiomes (e.g. Borchardt et al, 2003;Califano et al, 2017;Rivas et al, 2011;Rud et al, 2017) and cause disease if there is a shift in abundance (i.e., dysbiosis) (e.g. Hess et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the skin and gill microbiomes of the farmed seabass (Dicentrarchus labrax) and seabream (Sparus aurata)

Rosado

Pérez‐Losada

Severino³

et al. 2019

Aquaculture

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There is substantial evidence showing that the microbiome of teleosts plays a key role in host health and wellbeing. Aquaculture practices increase the risk of dysbiosis (i.e. microbial imbalance), which is known to facilitate pathogen infections. The skin and gills are the primary defense organs against pathogens, thus, characterizing their microbiome composition in farmed fish is pivotal for detecting potential alterations that may lead to disease susceptibility.Here, we assessed the skin and gill microbiomes of two of the most important adult fish species farmed in southern Europe, the seabass and the seabream, during winter months. We coupled next-generation sequencing (MiSeq) of the 16S rRNA V4 region with the DADA2 bioinformatic pipeline to assess microbial composition and structure. Variation in microbial alpha-diversity (intra-sample) and taxa proportions were assessed using analysis of variance. Differences in beta-diversity (between-sample) were tested using permutational multivariate analysis of variance. Microbiomes of both tissues (n=30 per species) identified 19 bacteria phyla, dominated by the phyla Proteobacteria (44 -68%) andBacteroidetes (15 -37%); the families Flavobacteriaceae (11 -28%), Rhodobacteraeae (4 -8%) and Vibrionaceae (2 -17%); and the genera Rubritalea (4 -13%), Pseudomonas (4 -8%) and the NS3a marine group (4 -12%). Mean relative proportion of these taxa, some alpha-diversity indices and all beta-diversity distances varied significantly between tissues within and between species. ASVs belonging to the genera Polaribacter and Vibrio, which include several species that are pathogenic, were detected in the core microbiomes of seabass or seabream.

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“…Proteobacteria is reported to be very common in aquaculture ponds in the most of the earlier reports (Qin et al 2016;Rud et al 2017;Zhou et al 2017). Due to their role in global carbon, nitrogen and sulphur cycle, abundance of 50-61% Proteobacteria have been described to be appropriate in the wetland ecosystem to ensure the optimum growth of aquatic animals (Ansola et al 2014;Cardona et al 2016).…”

Section: Microbial Diversity In Two Different Conditionsmentioning

confidence: 91%

Biological ball filters regulate bacterial communities in marron ( Cherax cainii ) culture system

Foysal

Fotedar

Gupta

et al. 2019

Lett Appl Microbiol

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This study aimed to characterize the bacterial communities in rearing water treated with commercial plastic biological ball filters named as Bio‐ball in marron culture for 60 days. Inclusion of Bio‐ball in the aquaculture tanks showed improvement in water quality parameters and enrichment of bacterial communities in terms of operational taxonomic units. The water treated with Bio‐ball showed significantly less nitrate, nitrite, ammonia, phosphorus and high dissolved oxygen concentration than untreated control group. At phylum level, Proteobacteria was dominant in both control and treated water, whereas Firmicutes was found to be significantly (P < 0·05) enriched in Bio‐ball treated water. Among the classified genus, Aquabacterium and Polunucleobacter were most dominant in control and Bio‐ball treated water respectively. Linear Discriminant Analysis Effect Size exhibited 31 indicator bacterial genus, 10 in control and 21 in treated condition, suggesting the enrichment of microbial lineages with addition of Bio‐ball. The bacteria Haliscomenobacter, Hypnocyclicus, Pajaroellobacter and Vibrio were found to be significantly (P < 0·001) correlated with higher pH, nitrate, nitrite, phosphorus and ammonia in control tanks, whereas Corynebacterium was linked to higher temperature in treated water. Overall results suggest that Bio‐ball filter media significantly improved the water quality and microbial populations in aquaculture tanks. Significance and Impact of the Study The results of this study revealed the positive impacts of Bio‐ball in enrichment of microbial flora associated with the degradation process of nitrogenous and organic compounds. Bio‐ball also showed the capability to prevent the colonization of harmful bacteria, and favoured the growth of beneficial microbes in aquatic system. This study therefore could pave the ways of increasing the aquaculture production by improving the water quality.

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Deep-sequencing of the bacterial microbiota in commercial-scale recirculating and semi-closed aquaculture systems for Atlantic salmon post-smolt production

Cited by 85 publications

References 65 publications

Tilapia recirculating aquaculture systems as a source of plant growth promoting bacteria

Tilapia recirculating aquaculture systems as a source of plant growth promoting bacteria

Characterization of the skin and gill microbiomes of the farmed seabass (Dicentrarchus labrax) and seabream (Sparus aurata)

Biological ball filters regulate bacterial communities in marron ( Cherax cainii ) culture system

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