Showing papers on "Gadus published in 2019"

Bottom trawl surveys in the northern Bering Sea indicate recent shifts in the distribution of marine species

Abstract: The climate regime in the eastern Bering Sea has recently been dominated by a pattern of multi-year stanzas, in which several successive years of minimal sea-ice formation and warm summer temperatures (e.g., 2002–2005, 2014–2017) alternate with several years of relatively extensive sea-ice formation and cold summer temperatures (e.g., 2006–2013). This emerging climate pattern may be forcing long-term changes in the spatial distributions of the Bering Sea’s marine fauna. The National Marine Fisheries Service’s Alaska Fisheries Science Center recently conducted two bottom trawl surveys covering the entire Bering Sea shelf from the Alaska Peninsula to the Bering Strait. The first, in the summer of 2010, was conducted during a cold year when the majority of the continental shelf was covered by a pool of cold (< 2 °C) water. The second, in the summer of 2017, was during a warmer year with water temperatures above the long-term survey mean. These two surveys recorded significantly different spatial distributions for populations of several commercially important fish species, including walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus), and several flatfish species, as well as jellyfishes. Population shifts included latitudinal displacement as well as variable recruitment success. The large-scale distributional shifts reported here for high-biomass species raise questions about long-term ecosystem impacts, and highlight the need for continued monitoring. They also raise questions about our management strategies for these and other species in Alaska’s large marine ecosystems.

Environmental DNA concentrations are correlated with regional biomass of Atlantic cod in oceanic waters

Abstract: Environmental DNA (eDNA) has emerged as a powerful approach for studying marine fisheries and has the potential to negate some of the drawbacks of trawl surveys. However, successful applications in oceanic waters have to date been largely focused on qualitative descriptions of species inventories. Here we conducted a quantitative eDNA survey of Atlantic cod (Gadus morhua) in oceanic waters and compared it with results obtained from a standardized demersal trawl survey. Detection of eDNA originating from Atlantic cod was highly concordant (80%) with trawl catches. We observed significantly positive correlations between the regional integrals of Atlantic cod biomass (kg) and eDNA quantities (copies) (R2 = 0.79, P = 0.003) and between sampling effort-normalised Catch Per Unit Effort (kg hr−1) and eDNA concentrations (copies L−1) (R2 = 0.71, P = 0.008). These findings extend the potential application of environmental DNA to regional biomass assessments of commercially important fish stocks in the ocean. Ian Salter et al. report a quantitative comparison of environmental DNA (eDNA) and demersal trawl surveys for detecting Atlantic cod in oceanic waters. Their results suggest that this approach could contribute to regional assessments of commercially important fish species.

Disentangling structural genomic and behavioural barriers in a sea of connectivity.

Abstract: Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole-genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord-type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord-type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.

Catastrophic dynamics limit Atlantic cod recovery.

Abstract: Collapses and regime changes are pervasive in complex systems (such as marine ecosystems) governed by multiple stressors. The demise of Atlantic cod (Gadus morhua) stocks constitutes a text book ex...

Field metabolic rates of teleost fishes are recorded in otolith carbonate.

Abstract: Field metabolic rate (FMR) is key to understanding individual and population-level responses to environmental changes, but is challenging to measure in field conditions, particularly in aquatic environments. Here we show that FMR can be estimated directly from the isotopic composition of carbon in fish otoliths (δ13Coto). We describe the relationship between δ13Coto values and oxygen consumption rate, and report results from laboratory experiments relating individual-level measurements of oxygen consumption rates to δ13Coto values in Atlantic cod (Gadus morhua). We apply our new δ13Coto metabolic proxy to existing δ13Coto data from wild cod and four deepwater fish species to test the validity of inferred FMR estimates. The δ13Coto metabolic proxy offers a new approach to study physiological ecology in free-ranging wild fishes. Otolith-based proxies for FMR are particularly promising as they allow retrospective assessment of time-integrated, individual-level FMR throughout an individual fish's life history.

Continued decline of a collapsed population of Atlantic cod (Gadus morhua) due to predation-driven Allee effects1

Abstract: Most stocks of Atlantic cod (Gadus morhua) in the Northwest Atlantic collapsed in the early 1990s, with little sign of recovery since then. In the southern Gulf of St. Lawrence (sGSL), the failed r...

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

Abstract: Chromosome structural variation may underpin ecologically important intraspecific diversity by reducing recombination within supergenes containing linked, coadapted alleles. Here, we confirm that an ancient chromosomal rearrangement is strongly associated with migratory phenotype and individual genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. We reconstruct trends in effective population size over the last century and reveal declines in effective population size matching onset of industrialized harvest (after 1950). We find different demographic trajectories between individuals homozygous for the chromosomal rearrangement relative to heterozygous or homozygous individuals for the noninverted haplotype, suggesting different selective histories across the past 150 years. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic, phenotypic, and demographic variation in a highly connected marine species and show how overfishing may have led to loss of biocomplexity within Northern cod stock.

Barents Sea cod (Gadus morhua) diet composition: long-term interannual, seasonal, and ontogenetic patterns

Abstract: Atlantic cod (Gadus morhua) is an ecologically and commercially important species in the North-Atlantic region. Cod is a top predator and information on its trophic ecology is integral for understanding predator–prey relationships and food-web dynamics. We present an analysis of the trophic patterns of Barents Sea (BS) cod using a unique 33-year time-series of stomach-content data from 1984 to 2016. We assessed patterns in diet (prey) composition across years, between seasons, as well as ontogenetic trends in diet, including predator–prey size relationships. Ontogenetic shifts in diet were observed, with fish becoming more important prey with increasing cod size. A very early onset of piscivory was found in <20 cm cod. Cannibalism was found in cod > 20 cm and increased with size. Juvenile cod exhibit a tendency towards consuming prey up to 33% of their body length, whereas larger cod feed on all prey sizes, resulting in asymmetric predator–prey size distributions. Diet varied significantly during 1984–2016, consistent with changes in both prey, cod abundance, and distribution. Seasonal differences were observed; capelin dominated the winter diet, whereas cod, polar cod, and other fish species were prevalent in summer/autumn months. This work represents an important step towards understanding trophic linkages that determine BS ecosystem dynamics.

Habitat suitability models for groundfish in the Gulf of Alaska

Abstract: Identifying and quantifying the major ecosystem processes that regulate recruitment strength of commercially and ecologically important fish species is a central goal of fisheries management research. In the Gulf of Alaska (GOA) five groundfish species are of particular interest: sablefish (Anoplopoma fimbria), Pacific cod (Gadus macrocephalus), walleye pollock (Gadus chalcogrammus), arrowtooth flounder (Atheresthes stomias), and Pacific ocean perch (Sebastes alutus). Habitat suitability models (HSM) were developed for the demersal early juvenile stage to inform survival to recruitment for these species, using catch data and seafloor habitat metrics with presence-only models. Regional-scale maps were produced that predict the probability of suitable habitat available in the GOA from settlement through residency in nursery areas. For example, the HSM for sablefish (150–399 mm) described suitable habitat as bathymetrically low-lying areas with low rocky structure within 25–300 m depth. In contrast, the HSM for Pacific ocean perch (50–200 mm) described suitable habitat as bathymetry rises with rocky structure present on north-south facing slopes within 85–270 m depth. These habitat covariates are useful to refine population estimates for North Pacific groundfish species and to inform life stage-specific definitions of Essential Fish Habitat. This application of MaxEnt models should be applicable for species with low occurrence of spatial data in other marine ecosystems globally.

Characterization of a male specific region containing a candidate sex determining gene in Atlantic cod

Abstract: The genetic mechanisms determining sex in teleost fishes are highly variable and the master sex determining gene has only been identified in few species. Here we characterize a male-specific region of 9 kb on linkage group 11 in Atlantic cod (Gadus morhua) harboring a single gene named zkY for zinc knuckle on the Y chromosome. Diagnostic PCR test of phenotypically sexed males and females confirm the sex-specific nature of the Y-sequence. We identified twelve highly similar autosomal gene copies of zkY, of which eight code for proteins containing the zinc knuckle motif. 3D modeling suggests that the amino acid changes observed in six copies might influence the putative RNA-binding specificity. Cod zkY and the autosomal proteins zk1 and zk2 possess an identical zinc knuckle structure, but only the Y-specific gene zkY was expressed at high levels in the developing larvae before the onset of sex differentiation. Collectively these data suggest zkY as a candidate master masculinization gene in Atlantic cod. PCR amplification of Y-sequences in Arctic cod (Arctogadus glacialis) and Greenland cod (Gadus macrocephalus ogac) suggests that the male-specific region emerged in codfishes more than 7.5 million years ago.

Effects of Agricultural Pesticides in Aquafeeds on Wild Fish Feeding on Leftover Pellets Near Fish Farms.

Abstract: Screening has revealed that modern-day feeds used in Atlantic salmon aquaculture might contain trace amounts of agricultural pesticides. To reach slaughter size, salmon are produced in open net pens in the sea. Uneaten feed pellets and undigested feces deposited beneath the net pens represent a source of contamination for marine organisms. To examine the impacts of long-term and continuous dietary exposure to an organophosphorus pesticide found in Atlantic salmon feed, we fed juvenile Atlantic cod (Gadus morhua), an abundant species around North Atlantic fish farms, three concentrations (0.5, 4.2, and 23.2 mg/kg) of chlorpyrifos-methyl (CPM) for 30 days. Endpoints included liver and bile bioaccumulation, liver transcriptomics and metabolomics, as well as plasma cholinesterase activity, cortisol, liver 7-ethoxyresor-ufin-O-deethylase activity, and hypoxia tolerance. The results show that Atlantic cod can accumulate relatively high levels of CPM in liver after continuous exposure, which is then metabolized and excreted via the bile. All three exposure concentrations lead to significant inhibition of plasma cholinesterase activity, the primary target of CPM. Transcriptomics profiling pointed to effects on cholesterol and steroid biosynthesis. Metabolite profiling revealed that CPM induced responses reflecting detoxification by glutathione-S-transferase, inhibition of monoacylglycerol lipase, potential inhibition of carboxylesterase, and increased demand for ATP, followed by secondary inflammatory responses. A gradual hypoxia challenge test showed that all groups of exposed fish were less tolerant to low oxygen saturation than the controls. In conclusion, this study suggests that wild fish continuously feeding on leftover pellets near fish farms over time may be vulnerable to organophosphorus pesticides.

Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod ( Gadus morhua )

Abstract: The population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply “skrei,” lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world’s largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or “fjord” cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromso, Norway. Our analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are “Carbohydrates”; “Amino Acids and Derivatives”; “Protein Metabolism”; “Cofactors, Vitamins, Prosthetic, Groups, and Pigments”; and “DNA Metabolism,” which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category “Protein Metabolism” is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol. We present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus (Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes.

Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod.

Abstract: Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdansk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea andO¨ resund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.

The acute and incremental thermal tolerance of Atlantic cod (Gadus morhua) families under normoxia and mild hypoxia.

Abstract: Given climate change projections, the limited ability of fish reared in sea-cages to behaviourally thermoregulate, and that thermal tolerance may be heritable, studies that examine family-related differences in upper thermal tolerance are quite relevant to the aquaculture industry. Thus, we investigated the upper thermal tolerance of 15 Atlantic cod (Gadus morhua L.) families by challenging them with acute (2 °C h-1) and incremental (1 °C every 4 days) temperature increases (CTmax and ITmax tests, respectively) under normoxia (~ 100% air saturation) and mild hypoxia (~ 75% air sat.). The cod's CTmax was 22.5 ± 0.1 °C (mean ± S.E.) during normoxia and 21.8 ± 0.1 °C during hypoxia (P < 0.001); and these two CTmax values were significantly correlated across families. In both the normoxic and hypoxic ITmax tests, feed intake fell by ~50% between 17 and 18 °C, and stopped entirely by 21 °C. No mortalities were observed under 20 °C in the normoxic and hypoxic ITmax tests, and the ITmax value was ~21.7 °C in both groups. Differences in the upper thermal tolerance between families were only observed in the CTmax experiment. No correlation was found between the specific growth rate and the CTmax of the families. Further, no correlation existed between CTmax and ITmax. This study is the first to compare the thermal tolerance of fish families to both CTmax and ITmax challenges, and the data: 1) suggest that the Atlantic cod is quite tolerant of acute (i.e., hours) or short-term (i.e., weeks) exposure to high water temperatures (i.e., up to 20 °C); 2) indicate that it might be difficult to select fish with higher ITmax values; and 3) question the relevance of CTmax for selecting fish that are destined for sea-cages where temperatures slowly warm over the summer.

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Abstract: Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine-scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway-located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.

Divergent responses of Atlantic cod to ocean acidification and food limitation.

Abstract: In order to understand the effect of global change on marine fishes, it is imperative to quantify the effects on fundamental parameters such as survival and growth. Larval survival and recruitment of the Atlantic cod (Gadus morhua) were found to be heavily impaired by end-of-century levels of ocean acidification. Here, we analysed larval growth among 35-36 days old surviving larvae, along with organ development and ossification of the skeleton. We combined CO2 treatments (ambient: 503 µatm, elevated: 1,179 µatm) with food availability in order to evaluate the effect of energy limitation in addition to the ocean acidification stressor. As expected, larval size (as a proxy for growth) and skeletogenesis were positively affected by high food availability. We found significant interactions between acidification and food availability. Larvae fed ad libitum showed little difference in growth and skeletogenesis due to the CO2 treatment. Larvae under energy limitation were significantly larger and had further developed skeletal structures in the elevated CO2 treatment compared to the ambient CO2 treatment. However, the elevated CO2 group revealed impairments in critically important organs, such as the liver, and had comparatively smaller functional gills indicating a mismatch between size and function. It is therefore likely that individual larvae that had survived acidification treatments will suffer from impairments later during ontogeny. Our study highlights important allocation trade-off between growth and organ development, which is critically important to interpret acidification effects on early life stages of fish.

How effective is freezing at killing Anisakis simplex, Pseudoterranova krabbei, and P. decipiens larvae? An experimental evaluation of time-temperature conditions.

Abstract: The consumption of raw or inadequately cooked marine fish can lead to several disorders caused by the ingestion of viable anisakid nematodes. Although anisakid larvae can be killed by subzero temperatures, making freezing an important control measure for this potential health hazard, these parasites can survive freezing under some conditions. Therefore, the aim of the present study was to experimentally evaluate the time-temperature conditions needed to kill Anisakis simplex and Pseudoterranova spp. The effectiveness of freezing was tested on two species of fish: cod, Gadus morhua from the North Atlantic, and herring, Clupea harengus membras from the southern Baltic Sea. Samples, which comprised skinless fillets of cod (n = 40) with visible parasites and whole herring (n = 240), were separately frozen at − 15, − 18, or − 20 °C for 24 h, or at − 20 °C for 48 h in the single-compressor freezer and at − 20, − 25, or − 35 °C for 24 h in the double-compressor freezer. After thawing, parasites were stained with malachite green and examined under the microscope for viability. All A. simplex and Pseudoterranova spp. larvae in cod fillets died at a temperature of − 15 °C or lower. However, freezing did not kill all the A. simplex larvae in whole herring: spontaneous movement of these parasites was observed in samples stored in the single-compressor freezer at − 15, − 18, and − 20 °C over 24 h. Our results demonstrate that the freezing procedure must consider both the capability of the freezing device and the nature of the fish product to ensure consumer safety.

Ticket to spawn: Combining economic and genetic data to evaluate the effect of climate and demographic structure on spawning distribution in Atlantic cod.

Abstract: Climate warming and harvesting affect the dynamics of species across the globe through a multitude of mechanisms, including distribution changes. In fish, migrations to and distribution on spawning grounds are likely influenced by both climate warming and harvesting. The Northeast Arctic (NEA) cod (Gadus morhua) performs seasonal migrations from its feeding grounds in the Barents Sea to spawning grounds along the Norwegian coast. The distribution of cod between the spawning grounds has historically changed at decadal scales, mainly due to variable use of the northern and southern margins of the spawning area. Based on historical landing records, two major hypotheses have been put forward to explain these changes: climate and harvesting. Climate could affect the distribution through, for example, spatial habitat shifts. Harvesting could affect the distribution through impacting the demographic structure. If demographic structure is important, theory predicts increasing spawner size with migration distance. Here, we evaluate these hypotheses with modern data from a period (2000-2016) of increasing temperature and recovering stock structure. We first analyze economic data from the Norwegian fisheries to investigate geographical differences in size of spawning fish among spawning grounds, as well as interannual differences in mean latitude of spawning in relation to changes in temperature and demographic parameters. Second, we analyze genetically determined fish sampled at the spawning grounds to unambiguously separate between migratory NEA cod and potentially smaller sized coastal cod of local origin. Our results indicate smaller spawners farther away from the feeding grounds, hence not supporting the hypothesis that harvesting is a main driver for the contemporary spawning ground distribution. We find a positive correlation between annual mean spawning latitude and temperature. In conclusion, based on contemporary data, there is more support for climate compared to harvesting in shaping spawning ground distribution in this major fish stock in the North Atlantic Ocean.

Effects of sound exposure from a seismic airgun on heart rate, acceleration and depth use in free-swimming Atlantic cod and saithe.

Abstract: Airguns used for offshore seismic exploration by the oil and gas industry contribute to globally increasing anthropogenic noise levels in the marine environment. There is concern that the omnidirectional, high intensity sound pulses created by airguns may alter fish physiology and behaviour. A controlled short-term field experiment was performed to investigate the effects of sound exposure from a seismic airgun on the physiology and behaviour of two socioeconomically and ecologically important marine fishes: the Atlantic cod (Gadus morhua) and saithe (Pollachius virens). Biologgers recording heart rate and body temperature and acoustic transmitters recording locomotory activity (i.e. acceleration) and depth were used to monitor free-swimming individuals during experimental sound exposures (18-60 dB above ambient). Fish were held in a large sea cage (50 m diameter; 25 m depth) and exposed to sound exposure trials over a 3-day period. Concurrently, the behaviour of untagged cod and saithe was monitored using video recording. The cod exhibited reduced heart rate (bradycardia) in response to the particle motion component of the sound from the airgun, indicative of an initial flight response. No behavioural startle response to the airgun was observed; both cod and saithe changed both swimming depth and horizontal position more frequently during sound production. The saithe became more dispersed in response to the elevated sound levels. The fish seemed to habituate both physiologically and behaviourally with repeated exposure. In conclusion, the sound exposures induced over the time frames used in this study appear unlikely to be associated with long-term alterations in physiology or behaviour. However, additional research is needed to fully understand the ecological consequences of airgun use in marine ecosystems.

Characterization and Transcript Expression Analyses of Atlantic Cod Viperin.

Abstract: Viperin is a key antiviral effector in immune responses of vertebrates including the Atlantic cod (Gadus morhua). Using cloning, sequencing and gene expression analyses, we characterized the Atlantic cod viperin at the nucleotide and hypothetical amino acid levels, and its regulating factors were investigated. Atlantic cod viperin cDNA is 1,342 bp long, and its predicted protein contains 347 amino acids. Using in silico analyses, we showed that Atlantic cod viperin is composed of 5 exons, as in other vertebrate orthologs. In addition, the radical SAM domain and C-terminal sequences of the predicted Viperin protein are highly conserved among various species. As expected, Atlantic cod Viperin was most closely related to other teleost orthologs. Using computational modeling, we show that the Atlantic cod Viperin forms similar overall protein architecture compared to mammalian Viperins. qPCR revealed that viperin is a weakly expressed transcript during embryonic development of Atlantic cod. In adults, the highest constitutive expression of viperin transcript was found in blood compared with 18 other tissues. Using isolated macrophages and synthetic dsRNA (pIC) stimulation, we tested various immune inhibitors to determine the possible regulating pathways of Atlantic cod viperin. Atlantic cod viperin showed a comparable pIC induction to other well-known antiviral genes (e.g., interferon gamma and interferon-stimulated gene 15-1) in response to various immune inhibitors. The pIC induction of Atlantic cod viperin was significantly inhibited with 2-Aminopurine, Chloroquine, SB202190, and Ruxolitinib. Therefore, endosomal-TLR-mediated pIC recognition and signal transducers (i.e., PKR and p38 MAPK) downstream of the TLR-dependent pathway may activate the gene expression response of Atlantic cod viperin. Also, these results suggest that antiviral responses of Atlantic cod viperin may be transcriptionally regulated through the interferon-activated pathway.

Aeromonas salmonicida subsp. salmonicida Early Infection and Immune Response of Atlantic Cod (Gadus morhua L.) Primary Macrophages.

Abstract: In contrast to other teleosts, Atlantic cod (Gadus morhua) has an expanded repertoire of MHC-I and TLR components, but lacks the MHC-II, the invariant chain/CD74, and CD4+ T cell response, essential for production of antibodies and prevention of bacterial infectious diseases. The mechanisms by which G. morhua fight bacterial infections are not well understood. Aeromonas salmonicida subsp. salmonicida is a recurrent pathogen in cultured and wild fish, and has been reported in Atlantic cod. Macrophages are some of the first responders to bacterial infection and the link between innate and adaptive immune response. Here, we evaluated the viability, reactive oxygen species (ROS) production, cell morphology, and gene expression of cod primary macrophages in response to A. salmonicida infection. We found that A. salmonicida infects cod primary macrophages without killing the cod cells. Likewise, infected Atlantic cod macrophages up-regulated key genes involved in the inflammatory response (e.g., IL-1β and IL-8) and bacterial recognition (e.g., BPI/LBP). Nevertheless, our results showed a down-regulation of genes related to antimicrobial peptide and ROS production, suggesting that A. salmonicida utilizes its virulence mechanisms to control and prevent macrophage anti-bacterial activity. Our results also indicate that Atlantic cod has a basal ROS production in non-infected cells, and this was not increased after contact with A. salmonicida. Transmission electron microscopy results showed that A. salmonicida was able to infect the macrophages in a high number, and release outer membrane vesicles (OMV) during intracellular infection. These results suggest that Atlantic cod macrophage innate immunity is able to detect A. salmonicida and trigger an anti-inflammatory response, however A. salmonicida controls the cell immune response to prevent bacterial clearance, during early infection.

Early life history ecology for five commercially and ecologically important fish species in the eastern and western Gulf of Alaska

Abstract: The Gulf of Alaska Integrated Ecosystem Research Program is a multi-disciplinary study examining interactions between physical and biological oceanography to understand how the environment influences the survival and recruitment of early life stages of select commercially and ecologically important groundfish species. Biological and oceanographic surveys in the eastern and western Gulf of Alaska were conducted during spring and summer of 2011 and 2013; we present a synthesis of ichthyoplankton data. The results describe seasonal (spring vs. summer), regional (eastern vs. western Gulf of Alaska), and interannual (2011 vs. 2013) variation in distribution, abundance, and larval sizes of the focal species. In spring, Pacific Cod (Gadus macrocephalus) larvae were more abundant in 2013 than 2011 and occurred primarily in the western Gulf of Alaska near Kodiak Island, over the shelf, and over the continental slope. Walleye Pollock (Gadus chalcogrammus) larvae were also more abundant in the western Gulf of Alaska, with substantially higher abundance in 2013. Larval rockfish (predominantly Pacific Ocean Perch; Sebastes alutus) were collected in deep water or were associated with the slope, troughs and canyons intersecting the slope, and the outer shelf. Rockfish larvae were collected throughout the study region in spring, with no significant differences in abundance between regions or years. In summer, rockfish (predominantly species other than Pacific Ocean Perch) were more widely distributed over the shelf and were more abundant in the eastern Gulf of Alaska both within and across years, indicating species-specific spawning events. Sablefish (Anoplopoma fimbria) larvae, however, were more abundant in the eastern Gulf of Alaska and in 2011 and were predominantly collected near areas of deep water such as Yakutat Canyon. In 2011, Arrowtooth Flounder (Atheresthes stomias) abundances of larvae were higher in the western Gulf of Alaska, whereas in 2013 abundances were higher in the eastern Gulf of Alaska. Arrowtooth Flounder larvae were collected primarily along the slope and near canyons and troughs. The results from individual years presented here can be used in individual-based model validation of connectivity matrices, delineating transport patterns to suitable nursery habitat, and evaluating recruitment bottlenecks for these focal species in the Gulf of Alaska. Future research will examine patterns of community structure and assemblage diversity using the comprehensive ichthyoplankton dataset. The observed ecological patterns provide insight into how environmental forcing may influence early life history aspects of recruitment.

Growth of cod (Gadus morhua) in the western Baltic Sea: estimating improved growth parameters from tag–recapture data

Abstract: Tag–recapture data contain valuable information about individual fish growth, which can enhance the estimation of growth parameters. Tag–recapture data are especially useful when age-determination ...