Atlantic Salmon (Salmo salar) Transfer to Seawater by Gradual Salinity Changes Exhibited an Increase in The Intestinal Microbial Abundance and Richness.

The host's physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon's intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.

Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon.

Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies.

Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids.

Early marine survival of juvenile salmon is intimately associated with their physiological condition during smoltification and ocean entry. Smoltification (parr-smolt transformation) is a developmental process that allows salmon to acquire seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+-ATPase (NKA) activity or plasma hormones, but gill gene expression offers the possibility of another method. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as a literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for TaqMan quantitative PCR assay design and their expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt and de-smolt trials from acute seawater transfers from a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt or de-smolt.

Behavioural changes during the parr-smolt transformation in coho salmon Oncorhynchus kisutch: is it better to be cool?

Behavioural changes that occur during the parr-smolt transformation were investigated in juvenile coho salmon Oncorhynchus kisutch. Fish from two populations were examined from the Fraser River catchment in British Columbia, Canada; a short and a long-distance migrating population. Fish showed a significant decrease in condition factor and significant increase in gill Na+ K+ -ATPase activity during the spring indicating that they became competent smolts, but no difference between populations. Temperature preference trials were conducted using a shuttlebox system throughout the spring. Mean temperature preference did not differ between the two populations, but preferred temperature decreased with development from 16.5 ± 0.3°C for parr to 15.5 ± 0.4°C for smolts. Mean swimming velocity was also greater in smolts than parr, but there was no difference between the two populations. The preference for warmer water temperature observed for parr in early spring may be advantageous for stimulating smolt development. Preference for slightly cooler temperatures observed for smolts would sustain elevated seawater tolerance during the smolt window by a short time and may ensure successful transition to the marine environment.

Atlantic salmon (Salmo salar L.) smolts require more than two weeks to recover from acidic water and aluminium exposure.

The detrimental effects of acid rain and aluminium (Al) on salmonids have been extensively studied, yet knowledge about the extent and rate of potential recovery after exposures to acid and Al episodes is limited. Atlantic salmon smolts in freshwater (FW) were exposed for 2 and 7-day episodes (ACID2 and ACID7, respectively) to low pH (5.7±0.2) and inorganic aluminium (Ali; 40±4 µg) and then transferred to good water quality, control water (CW; pH 6.8±0.1; <14±2 µg Ali). Al accumulation on gills after 2 and 7 days of acid/Al exposure was 35.3±14.1 and 26.6±1.8 µg g(-1) dry weight, respectively. These elevated levels decreased 2 days post transfer to CW and remained higher than in control (CON; 5-10 µg Ali) for two weeks. Plasma Na(+) levels in ACID2 and ACID7 smolts decreased to 141±0.8 and 138.6±1.4mM, respectively, and remained significantly lower than CON levels for two weeks post transfer to CW. Similarly, plasma Cl(-) levels in ACID7 smolts (124.3±2.8mM) were significantly lower than in CON, with Cl(-) levels remaining significantly lower in ACID7 (126.2±4.8 mM) and ACID2 (127.6±3.7 mM) than in CON following 9 and 14 days post-transfer to CW, respectively. ACID2 and ACID7 smolts sustained elevated plasma glucose levels post transfer to CW suggesting elevated stress for more than a week following exposure. While gill Na(+), K(+)-ATPase (NKA) activity was only slightly affected in ACID2 and not in ACID7 smolts in FW, acid/Al exposure resulted in a transient decrease in NKA activity following SW exposure in both groups. Acid/Al episodes had limited impact on isoform specific NKA α-subunit mRNA during exposure. However, the transfer of ACID2 and ACID7 smolts to CW showed an increase in NKAα1a mRNA (the FW isoform) and inhibited the up-regulation of NKAα1b (the SW isoform), probably resulting in higher abundance of the enzyme favouring ion uptake. Gill caspase 3B gene transcription did not change in acid/Al treated smolts, indicating no increased apoptosis in gills. ACID2 and ACID7 treatments resulted in lower smolt-related gill transcription of the gene encoding the tight junction protein claudin 10e compared to CON, while the gene encoding claudin 30 showed lower mRNA expression only after 11 days SW exposure in ACID7 fish. Our data suggest that acid/Al conditions affect ion perturbations through a combination of alteration of the preparatory increase in paracellular permeability and negative impact on the SW type NKA α-subunit mRNA transcripts, and raise major concerns regarding the recovery of physiological disruption in smolts following acid/Al exposure. Smolts may require more than two weeks to fully recover from even short moderate episodes of acid/Al exposure. Acid/Al exposure thus probably has greater impact on salmon populations than previously acknowledged.

Aluminum exposure impacts brain plasticity and behavior in Atlantic salmon (Salmo salar).

Aluminum (Al) toxicity occurs frequently in natural aquatic ecosystems as a result of acid deposition and natural weathering processes. Detrimental effects of Al toxicity on aquatic organisms are well known and can have consequences for survival. Fish exposed to Al in low pH waters will experience physiological and neuroendocrine changes that disrupt homeostasis and alter behavior. To investigate the effects of Al exposure on both the brain and behavior, Atlantic salmon (Salmo salar) kept in water treated with Al (pH 5.7, 0.37±0.04 µmol 1(-1) Al) for 2 weeks were compared with fish kept in under control conditions (pH 6.7, <0.04 µmol 1(-1) Al). Fish exposed to Al and acidic conditions had increased Al accumulation in the gills and decreased gill Na(+), K(+)-ATPase activity, which impaired osmoregulatory capacity and caused physiological stress, indicated by elevated plasma cortisol and glucose levels. Here we show for the first time that exposure to Al in acidic conditions also impaired learning performance in a maze task. Al toxicity also reduced the expression of NeuroD1 transcript levels in the forebrain of exposed fish. As in mammals, these data show that exposure to chronic stress, such as acidified Al, can reduce neural plasticity during behavioral challenges in salmon, and may impair the ability to cope with new environments.