Novel Peptide Derived from Gadus morhua Stimulates Osteoblastic Differentiation and Mineralization through Wnt/β-Catenin and BMP Signaling Pathways

Marine biodiversity offers a wide array of active ingredient resources. Gadus morhua peptides (GMPs) showed excellent osteoprotective effects in ovariectomized mice. However, the potential osteogenesis mechanisms of key osteogenic peptides in GMP were seldom reported. In this study, a novel osteogenic peptide (GETNPADSKPGSIR, P-GM-2) was screened from GMP. P-GM-2 has a high stability coefficient and a strong interaction with epidermal growth factor receptor. Cell culture experiments showed that P-GM-2 stimulated the expression of osteogenic differentiation markers to promote osteoblast proliferation, differentiation, and mineralization. Additionally, P-GM-2 phosphorylates GSK-3β, leading to the stabilization of β-catenin and its translocation to the nucleus, thus initiating the activation of the Wnt/β-catenin signaling pathway. Meanwhile, P-GM-2 could also regulate the osteogenic differentiation of preosteoblasts by triggering the BMP/Smad and mitogen-activated protein kinase signaling pathways. Further validation with specific inhibitors (ICG001 and Noggin) demonstrated that the osteogenic activity of P-GM-2 was revealed by the activation of the BMP and Wnt/β-catenin pathways. In summary, these results provide theoretical and practical insights into P-GM-2 as an effective antiosteoporosis active ingredient.

Gastrointestinal delivery of codfish Skin-Derived collagen Hydrolysates: Deep eutectic solvent extraction and bioactivity analysis

The fishing industry produces substantial by-products, such as heads, skins, bones, and scales, rich in collagen-a prevalent protein in these materials. However, further application of deep eutectic solvent-based extraction remains unexplored. In this study, we extracted collagen with urea: propanoic acid mixture (U:PA; 1:2) with a 2.2 % yield, followed by enzymatic hydrolysis with alcalase for 120 min. The resulting bioactive peptides demonstrated notable antioxidant activity (961 µmol TE) and antihypertensive properties (39.3 % ACE inhibition). Subsequently, we encapsulated 39.3 % of these hydrolysates in chitosan-TPP capsules, which released about 58 % of their content, primarily in the intestine, as mimicked in the in vitro model of the gastrointestinal tract. Although the digestion process did not significantly alter the size of the non-encapsulated collagen peptides, it did influence their health benefits. The promising results suggest that further research could optimize the use of collagen from fish by-products, potentially offering a sustainable source for health products.

Diverse Transcriptome Responses to Salinity Change in Atlantic Cod Subpopulations

Adaptation to environmental variation caused by global climate change is a significant aspect of fisheries management and ecology. A reduction in ocean salinity is visible in near-shore areas, especially in the Baltic Sea, where it is affecting the Atlantic cod population. Cod is one of the most significant teleost species, with high ecological and economical value worldwide. The population of cod in the Baltic Sea has been traditionally divided into two subpopulations (western and eastern) existing in higher- and lower-salinity waters, respectively. In recent decades, both Baltic cod subpopulations have declined massively. One of the reasons for the poor condition of cod in the Baltic Sea is environmental factors, including salinity. Thus, in this study, an oligonucleotide microarray was applied to explore differences between Baltic cod subpopulations in response to salinity fluctuations. For this purpose, an exposure experiment was conducted consisting of salinity elevation and reduction, and gene expression was measured in gill tissue. We found 400 differentially expressed genes (DEGs) involved in the immune response, metabolism, programmed cell death, cytoskeleton, and extracellular matrix that showed a subpopulation-dependent pattern. These findings indicate that osmoregulation in Baltic cod is a complex process, and that western and eastern Baltic cod subpopulations respond differently to salinity changes.

Climate change dynamics and mercury temporal trends in Northeast Arctic cod (Gadus morhua) from the Barents Sea ecosystem

The Northeast Arctic cod (Gadus morhua) is the world's northernmost stock of Atlantic cod and is of considerable ecological and economic importance. Northeast Arctic cod are widely distributed in the Barents Sea, an environment that supports a high degree of ecosystem resiliency and food web complexity. Here using 121 years of ocean temperature data (1900-2020), 41 years of sea ice extent information (1979-2020) and 27 years of total mercury (Hg) fillet concentration data (1994-2021, n = 1999, ≥71% Methyl Hg, n = 20) from the Barents Sea ecosystem, we evaluate the effects of climate change dynamics on Hg temporal trends in Northeast Arctic cod. We observed low and consistently stable, Hg concentrations (yearly, least-square means range = 0.022-0.037 mg/kg wet wt.) in length-normalized fish, with a slight decline in the most recent sampling periods despite a significant increase in Barents Sea temperature, and a sharp decline in regional sea ice extent. Overall, our data suggest that recent Arctic amplification of ocean temperature, "Atlantification," and other perturbations of the Barents Sea ecosystem, along with rapidly declining sea ice extent over the last ∼30 years did not translate into major increases or decreases in Hg bioaccumulation in Northeast Arctic cod. Our findings are consistent with similar long-term, temporal assessments of Atlantic cod inhabiting Oslofjord, Norway, and with recent investigations and empirical data for other marine apex predators. This demonstrates that Hg bioaccumulation is highly context specific, and some species may not be as sensitive to current climate change-contaminant interactions as currently thought. Fish Hg bioaccumulation-climate change relationships are highly complex and not uniform, and our data suggest that Hg temporal trends in marine apex predators can vary considerably within and among species, and geographically. Hg bioaccumulation regimes in biota are highly nuanced and likely driven by a suite of other factors such as local diets, sources of Hg, bioenergetics, toxicokinetic processing, and growth and metabolic rates of individuals and taxa, and inputs from anthropogenic activities at varying spatiotemporal scales. Collectively, these findings have important policy implications for global food security, the Minamata Convention on Mercury, and several relevant UN Sustainable Development Goals.

Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s)

Range expansions can lead to increased contact of divergent populations, thus increasing the potential of hybridization events. Whether viable hybrids are produced will most likely depend on the level of genomic divergence and associated genomic incompatibilities between the different entities as well as environmental conditions. By taking advantage of historical Baltic cod (Gadus morhua) otolith samples combined with genotyping and whole genome sequencing, we here investigate the genetic impact of the increased spawning stock biomass of the eastern Baltic cod stock in the mid 1980s. The eastern Baltic cod is genetically highly differentiated from the adjacent western Baltic cod and locally adapted to the brackish environmental conditions in the deeper Eastern basins of the Baltic Sea unsuitable for its marine counterparts. Our genotyping results show an increased proportion of eastern Baltic cod in western Baltic areas (Mecklenburg Bay and Arkona Basin)-indicative of a range expansion westwards-during the peak population abundance in the 1980s. Additionally, we detect high frequencies of potential hybrids (including F1, F2 and backcrosses), verified by whole genome sequencing data for a subset of individuals. Analysis of mitochondrial genomes further indicates directional gene flow from eastern Baltic cod males to western Baltic cod females. Our findings unravel that increased overlap in distribution can promote hybridization between highly divergent populations and that the hybrids can be viable and survive under specific and favourable environmental conditions. However, the observed hybridization had seemingly no long-lasting impact on the continuous separation and genetic differentiation between the unique Baltic cod stocks.

Seals, fish, humans and parasites in the Baltic: ecology, evolution and history

Evolutionary and ecological processes affecting the interactions between hosts and parasites in the aquatic environment are at display in the Baltic Sea, a young and ecologically unstable marine ecosystem, where fluctuating abiotic and biotic factors affect the parasitofauna in fish. The dynamic infections of Baltic cod, a subpopulation of the Atlantic cod (Gadus morhua Linnaeus), with third stage anisakid nematode larvae of Pseudoterranova decipiens (Krabbe, 1878) and Contracaecum osculatum (Rudolphi, 1802) have increased following a significant increase of the Baltic grey seal Halichoerus grypus (Fabricius) population in the region. Cod serves as a paratenic host and marine mammals, pinnipeds, are definitive hosts releasing parasite eggs, with faeces, to the marine environment, where embryonation and hatching of the third stage larva take place. The parasite has no obligate intermediate hosts, but various invertebrates, smaller fish and cod act as paratenic hosts transmitting the infection to the seal. Contracaecum osculatum has an impact on the physiological performance of the cod, which optimises transmission of the larva from fish to seal. Thus, a muscle mass decrease of nearly 50% may result from heavy C. osculatum infections, probably amplified by a restricted food availability. The muscle atrophy is likely to reduce the escape reactions of the fish when meeting a foraging seal. In certain regions, where fish and seals are restricted in their migration patterns, such as the semi-enclosed Baltic Sea, the predation may contribute to a severe cod stock depletion. The parasites are zoonotic and represent a human health risk, when consumers ingest insufficiently heat- or freeze-treated infected products. Marked infections of the cod were previously reported during periods with elevated seal populations (late 19th and middle 20th century) and various scenarios for management of risk factors are evaluated in an evolutionary context.

Effects of weathered polyethylene microplastic ingestion on sexual maturation, fecundity and egg quality in maturing broodstock Atlantic cod Gadus morhua

Microplastics (MPs) have become a global issue as they are omnipresent in the ocean. Fish ingesting MPs through feed could be affected in their physiological function, e.g., disrupted enzyme production and function, reduction of feeding and reproductive failure. This study assessed the effects of feed containing naturally weathered MPs from the Oslofjord (Norway) on the reproductive physiology of Atlantic cod (Gadus morhua). Farmed cod broodstock were fed either control (C-diet) or feeds containing 1% microplastic (MP-diet) starting nine months prior to spawning, from June until May. No major differences were found between diet groups in overall biometrics or gonad histology. Sex steroid levels (testosterone, 11-ketotestosterone and 17β-estradiol) resulted in expected profiles increasing over time without any significant differences between treatments. Gene expression levels of the steroidogenic enzyme 20β-hydroxysteroid dehydrogenase (20β-hsd) and vitellogenin1 (vtg1) showed significant differences between dietary treatments with lower expression in the control group. This can be a direct effect of MPs, but endocrine disrupting effects of potentially leachable plastic additives cannot be completely ruled out. Thus, these enzymes could be indicators of exposure to contaminants that disrupt sexual maturation by affecting the production of primarily maturation-inducing steroid. Although the concentration of MPs employed in this study may not be high enough to elicit any observable short-term biological effects, the observed gene expression suggests that long-term consequences should be considered caused by an expected increase of MPs in marine environments.

The Effect of the Species and Harvesting Location on Dried Salted Cod Fatty Acid Signatures and Nutritional Quality

The Atlantic cod was listed as 'vulnerable' by the International Union for Conservation of Nature, a condition that persists today. Fishing pressure on the Atlantic cod could be partially transferred to the Pacific cod, since the two cod species share genetic and phenotypic similarities. The aim of this study is to expand knowledge of the composition of dried salted cod obtained from Atlantic and Pacific cod species, with the Atlantic cod being from two different harvesting locations. The comparison of these cod species revealed the existence of nine significant differences among individual FAs (accountable for 63.2% of total FAs), which was at a similar level to that observed between different harvesting locations for the Atlantic cod (ten significant differences among individual FAs, accountable for 61.6% of total FAs). Canonical discriminant analysis and cross-validation achieved full discrimination of the cod's origin and 100% accuracy in the cod's origin classification. The amount of EPA plus DHA in dried salted cod reached its higher value among the Pacific cod (302.3 mg/100 g), while the Atlantic cod averaged 284.1 g/100 g of edible portion. The Pacific cod presented a higher α-tocopherol content than its Atlantic counterpart (8.04 vs. 4.94 µg/g).

Hidden but revealed: After years of genetic studies behavioural monitoring combined with genomics uncover new insight into the population dynamics of Atlantic cod in Icelandic waters

Stock structure is of paramount importance for sustainable management of exploited resources. In that context, genetic markers have been used for more than two decades to resolve spatial structure of marine exploited resources and to fully fathom stock dynamics and interactions. While genetic markers such as allozymes and RFLP dominated the debate in the early era of genetics, technology advances have provided scientists with new tools every decade to better assess stock discrimination and interactions (i.e. gene flow). Here, we provide a review of genetic studies performed to understand stock structure of Atlantic cod in Icelandic waters, from the early allozyme approaches to the genomic work currently carried out. We further highlight the importance of the generation of a chromosome-anchored genome assembly together with whole-genome population data, which drastically changed our perception of the possible management units to consider. After nearly 60 years of genetic investigation of Atlantic cod structure in Icelandic waters, genetic (and later genomic) data combined with behavioural monitoring using Data Storage Tags shifted the attention from geographical population structures to behavioural ecotypes. This review also demonstrates the need for future research to further disentangle the impact of these ecotypes (and gene flow among them) on the population structure of Atlantic cod in Icelandic waters. It also highlights the importance of whole-genome data to unravel unexpected within-species diversity related to chromosomal inversions and associated supergenes, which are important to consider for future development of sustainable management programmes of the species within the North Atlantic.

Evaluating dried salted cod amino acid signature for nutritional quality assessment and discriminant analysis

Aim

Thus, the aim of this study was to answer three scientific questions: (1) Are the protein content and amino acid profile of dried salted cod influenced by species (Gadus morhua and Gadus macrocephalus)? (2) Are the protein content and amino acid profile of dried salted cod influenced by the geographical area of capture (Iceland and Norway)? and (3) Does the amino acid profile have the potential to be used as a discriminator of species and geographical areas of capture?

Methods

A total of 45 dried salted cods (2-3 kg of dry weight; n = 15 samples/origin) were used in this study. The Atlantic cod was fished in the Atlantic northeast (FAO 27 area) within the Exclusive Economic zones (EEZ) of Norway (n = 15) and Iceland (n = 15), while the Pacific cod was caught in the Pacific northeast (FAO 67 area) within the Alaska EEZ (n = 15). Total protein content was determined by the Kjeldahl method, in accordance with the AOAC procedures. The amino acid profile was analyzed by HPLC with fluorescence detection (at excitation and emission wavelengths of 338 and 425 nm, respectively).

Results

The Atlantic cod presented higher contents of total protein (33.90 versus 33.10 g/100 g of cod edible portion; p = 0.017) and total amino acid contents (32.52 versus 32.04 g/100 g of cod edible portion; p = 0.015) but displayed lower percentage of indispensable amino acids (32.16 versus 32.83 g/100 g of protein; p < 0.001) than Pacific cod. Among the Atlantic cod harvesting locations, the Norwegian cod displayed higher total amino acid contents (96.91 versus 96.81 g/100 g of protein; p = 0.012) and higher percentage of indispensable amino acids (35.38 versus 28.94 g/100 g of protein; p = 0.042) than the Icelandic counterpart. A correct classification of 100% was obtained for the Pacific and Icelandic cod varieties, but the classification accuracy in the Norwegian cod was of just 86.67%, since 2 samples out of 15 were incorrectly classified as Icelandic.

Conclusion

The comparison of cod species showed that the Atlantic cod had a significantly lower EAAI than the Pacific cod (p < 0.001; 88.23 versus 88.61). On the other hand, the comparison of the two origins in the Atlantic cod, showed that Norwegian cod displayed a significantly higher EAAI than the Icelandic cod (99.15 versus 77.32). The assessment of the EAAI allows the classification of the protein's nutritional quality, allowing us to classify both cod species as a good protein source to human diet. However, within the Atlantic cod, the Norwegian cod's protein is classified as high quality, while the Icelandic cod attain the classification of useful quality. Regarding the amino acid profile discriminatory potential to classify cod samples. The results show that the AA profile has 100% accuracy in the separation of cod species, but was not globally efficient in the differentiation of the Norwegian from the Icelandic cod.

Effects of changing environmental conditions on plastic ingestion and feeding ecology of a benthopelagic fish (Gadus morhua) in the Southwest Baltic Sea

This study documents how the abundance of microplastics (<5 mm) in the Atlantic cod, Gadus morhua, relates to the changes of the fish diet during years with contrasting levels of anoxia for example following years of low or high major Baltic inflows (MBI). A MultiNet Maxi trawl and CTD were deployed annually to collect microplastic samples alongside oxygen, temperature, and salinity conditions. Microplastics were homogenously distributed both within the water column and across years. Gadus morhua diet shifted from dominantly benthic invertebrates (61 %) under oxygenated conditions to dominantly Sprattus sprattus (81 %) under anoxic conditions. The proportion of G. morhua with microplastics in their digestive tract increased when they fed on pelagic fish (38 %) versus on benthic invertebrates (15 %). The proportion of S. sprattus which ingested microplastics (~18 %) did not vary. As anoxia at depth is expected to increase due to climate change, microplastic ingestion by G. morhua will potentially increase.

Allee effects and the Allee-effect zone in northwest Atlantic cod

According to the theory of compensatory dynamics, depleted populations should recover when the threat responsible for their decline is removed because per capita population growth is assumed to be highest when populations are at their smallest viable sizes. Yet, many seriously depleted fish populations have failed to recover despite threat mitigation. Atlantic cod (Gadus morhua) stocks off Newfoundland, despite 30 years of dramatically reduced fishing mortality and numerous fishery closures, have not recovered, suggesting that drivers other than fishing can regulate the growth of collapsed fish populations, inhibiting or preventing their recovery. Here, using Bayesian inference, we show strong evidence of Allee effects in a south Newfoundland cod population, based on data on recruitment and spawning stock biomass. We infer the Allee-effect threshold, below which recovery is impaired. We demonstrate the necessity of data at low population sizes to make inferences about the nature of low-abundance dynamics. Our work indicates that Allee effects are not negligible in commercially exploited fish populations, as commonly projected, and that they represent an inhibitory force that can effectively prevent recovery from overfishing. Our findings contrast with prevailing fisheries management practices that assume compensatory dynamics at low abundances with potential to seriously overestimate the recovery potential of collapsed populations.

In situ evidence of the role of Crangon crangon in infection of cod Gadus morhua with nematode parasite Hysterothylacium aduncum in the Baltic Sea

Cod was one of the most important fish species in the Baltic Sea, but its condition is deteriorating for several reasons, including an increasing parasite burden. The aim of this study was to determine the source of infection of Baltic cod with parasites by examination of invertebrates found in situ in the cod stomach. A total of 1681 cod were sampled during four research cruises in the southern Baltic Sea in 2012, 2013 and 2014 and the composition of their diet was analysed. Each prey item from cod stomach was identified to the lowest possible taxonomic level and a parasitological analysis of all invertebrates collected was performed. Crangon crangon, Saduria entomon and Mysis mixta were the most commonly represented invertebrates among food items. Hysterothylacium aduncum was found only in C. crangon. This host–parasite system is reported here for the first time in situ in the stomach of cod from the Baltic Sea, confirming the role of C. crangon in cod infection with H. aduncum.

Detection of chemical warfare agent related phenylarsenic compounds and multibiomarker responses in cod (Gadus morhua) from munition dumpsites

Recently, sea-dumped chemical weapons (CWs) containing toxic chemical warfare agents (CWAs) have raised international attention. It is well known that CWAs are leaking from corroded munitions causing a risk to the surrounding marine environment, while the impact on marine biota is still unknown. In this study, cod (Gadus morhua) was used as a model species to study the possible bioaccumulation of phenylarsenic CWAs and their negative effects at multiple levels of biological organization on fish living in the vicinity of a major CWs dumpsite in the Bornholm Basin in the Baltic Sea. In total, 14% of the cod muscle samples collected close to the main dumpsite contained trace levels of phenylarsenic CWAs. However, most of the biomarkers measured did not show clear differences between this area compared with a lesser contaminated reference area. On the other hand, significant changes in some biomarkers were observed in individuals containing trace levels of CWA-related chemicals. The results gained in this study have significant importance for environmental risk assessment and for evaluating the risk of CWA contamination for human seafood consumers.

Effects of seismic airgun playbacks on swimming patterns and behavioural states of Atlantic cod in a net pen

Anthropogenic sound can affect fish behaviour and physiology which may affect their well-being. However, it remains a major challenge to translate such effects to consequences for fitness at an individual and population level. For this, energy budget models have been developed, but suitable data to parametrize these models are lacking. A first step towards such parametrization concerns the objective quantification of behavioural states at high resolution. We experimentally exposed individual Atlantic cod (Gadus morhua) in a net pen to the playback of seismic airgun sounds. We demonstrated that individual cod in the net pen did not change their swimming patterns immediately at the onset of the sound exposure. However, several individuals changed their time spent in three different behavioural states during the 1 h exposure. This may be translated to changes in energy expenditure and provide suitable input for energy budget models that allow predictions about fitness and population consequences.

The pantophysin gene and its relationship with survival in early life stages of Atlantic cod

Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.

Seeking the true time: Exploring otolith chemistry as an age-determination tool

Fish otoliths' chronometric properties make them useful for age and growth rate estimation in fisheries management. For the Eastern Baltic Sea cod stock (Gadus morhua), unclear seasonal growth zones in otoliths have resulted in unreliable age and growth information. Here, a new age estimation method based on seasonal patterns in trace elemental otolith incorporation was tested for the first time and compared with the traditional method of visually counting growth zones, using otoliths from the Baltic and North seas. Various trace elemental ratios, linked to fish metabolic activity (higher in summer) or external environment (migration to colder, deeper habitats with higher salinity in winter), were tested for age estimation based on assessing their seasonal variations in concentration. Mg:Ca and P:Ca, both proxies for growth and metabolic activity, showed greatest seasonality and therefore have the best potential to be used as chemical clocks. Otolith image readability was significantly lower in the Baltic than in the North Sea. The chemical (novel) method had an overall greater precision and percentage agreement among readers (11.2%, 74.0%) than the visual (traditional) method (23.1%, 51.0%). Visual readers generally selected more highly contrasting zones as annuli whereas the chemical readers identified brighter regions within the first two annuli and darker zones thereafter. Visual estimates produced significantly higher, more variable ages than did the chemical ones. Based on the analyses in our study, we suggest that otolith microchemistry is a promising alternative ageing method for fish populations difficult to age, such as the Eastern Baltic cod.

Contracaecum osculatum (sensu lato) infection of Gadus morhua in the Baltic Sea: inter- and intraspecific interactions

The subpopulation of Atlantic cod, Gadus morhua, in the eastern part of the Baltic Sea has experienced a significant increase in infections with anisakid nematode larvae of the species Contracaecum osculatum sensu lato (s.l.) since the year 2000. The life cycle of the parasite includes seals and especially the grey seal, Halichoerus grypus, as final hosts, carrying the adult nematodes in the stomach, crustaceans (copepods, amphipods) as first intermediate hosts and various fish species (clupeids, sandeel) including cod as second intermediate/paratenic hosts. Cod with a body length below 28 cm are generally non-infected but experience increasing infection levels when they switch to a piscine diet (infected intermediate/paratenic hosts). We present an overall frequency distribution analysis of worms in 166 cod (body length 30-49 cm) collected in the spawning area over the last 5 years. It shows a fit to the negative binomial distribution, a prevalence of infection of 89.8%, a mean intensity of 29.3 parasites per fish (range 1-377) and a variance/mean ratio of 59.2 (≫1), indicating overdispersion. We present measurements of the adult Contracaecum osculatum (s.l.) specimens in the seal stomach and show that the parasites reach a maximum length of 6.6 cm (females) and 5.8 cm (males). L3s in sprat have a total length from 1to 11 mm whereas the larvae in cod liver are 3-27 mm. A decreasing mean worm length associated with high worm densities in cod (number of nematodes per liver) was recorded. Possible explanations might include timing of feeding on infected intermediate/paratenic hosts, intraspecific competition (crowding) between larvae in cod and host responses (indicated by a significant antibody production in cod against C. osculatum (s.l.) antigens). A significant negative correlation between infection intensity and muscle mass of cod was found, suggesting parasite-induced down-regulation of growth factors in cod.

Baltic cod endohelminths reflect recent ecological changes

We suggest helminthological investigations of cod as a supplement to traditional biological and hydrographical methods for elucidation of ecological changes in the Baltic Sea. It is under discussion if oxygen deficit or seal abundance should explain the present critical situation of Baltic cod. A comparative investigation of endoparasitic helminths in Baltic cod (Gadus morhua), captured in the same marine habitat with an interval of 35 years (1983/2018) recorded 11 species of helminths comprising trematodes (Hemiurus luehei, Podocotyle atomon, Lepidapedon elongatum), nematodes (Contracaecum osculatum, Hysterothylacium aduncum, Capillaria gracilis, Cucullanus cirratus), cestodes (Bothriocephalus sp.) and acanthocephalans (Echinorhynchus gadi, Pomphorhynchus laevis, Corynosoma semerme). Significant prevalence and intensity increases were recorded for third-stage larvae of the nematode C. osculatum (liver location) and larvae of C. semerme (encapsulated in viscera). Both parasite species use grey seal as their final host, indicating the recent expansion of the Baltic seal population. A lower E. gadi intensity and an increased prevalence of L. elongatum of small cod (31-40 cm body length) suggest a lowered intake of amphipods (intermediate host) and elevated ingestion of polychaetes, respectively, but no significant changes were seen for other helminths.

Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes

The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.

The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes.

IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.

Microplastic ingestion by fish: Body size, condition factor and gut fullness are not related to the amount of plastics consumed

This study investigates the frequency of microplastic (MP) ingestion and the relationship between microplastics in the guts of two commercial fish species in Iceland (cod; Gadus morhua and saithe; Pollachius virens) and the weight, length, gut fullness, and condition index (CI) of the fish. MPs were found in 20.5% of the cod (n = 39) and 17.4% of the saithe (n = 46). There was no significant correlation between gut fullness nor CI and findings of MPs, indicating that, especially in large individuals, MPs are not retained to a large extent, and if so, the CI is most likely not affected. A difference was found in fish length between fish containing plastic and fish without plastics. Further studies such as this must be conducted in all water ecosystems if we are to fully understand the impact that MP's are having at the individual, population, species, and ecosystem levels.

Otolith chemistry indicates recent worsened Baltic cod condition is linked to hypoxia exposure

Deoxygenation worldwide is increasing in aquatic systems with implications for organisms' biology, communities and ecosystems. Eastern Baltic cod has experienced a strong decline in mean body condition (i.e. weight at a specific length) over the past 20 years with effects on the fishery relying on this resource. The decrease in cod condition has been tentatively linked in the literature to increased hypoxic areas potentially affecting habitat range, but also to benthic prey and/or cod physiology directly. To date, no studies have been performed to test these mechanisms. Using otolith trace element microchemistry and hypoxia-responding metrics based on manganese (Mn) and magnesium (Mg), we investigated the relationship between fish body condition at capture and exposure to hypoxia. Cod individuals collected after 2000 with low body condition had a higher level of Mn/Mg in the last year of life, indicating higher exposure to hypoxic waters than cod with high body condition. Moreover, lifetime exposure to hypoxia was even more strongly correlated to body condition, suggesting that condition may reflect long-term hypoxia status. These results were irrespective of fish age or sex. This implies that as Baltic cod visit poor-oxygen waters, perhaps searching for benthic food, they compromise their own performance. This study specifically sheds light on the mechanisms leading to the low condition of cod and generally points to the impact of deoxygenation on ecosystems and fisheries.

The crystal structure of haemoglobin from Atlantic cod

The isolation of the dominant isoform of haemoglobin from Atlantic cod caught in southwest Norway is reported and its X-ray crystal structure is presented.

The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.

Life history and temporal variability of escape events interactively determine the fitness consequences of aquaculture escapees on wild populations

Domesticated individuals are likely to be maladaptive in the wild due to adaptation to captivity. Escaped aquaculture fish can cause unintended fitness and demographic consequences for their wild conspecifics through interbreeding and competition. Escape events from different sources exhibit great heterogeneity in their frequencies and magnitudes, ranging from rare but large spillover during a storm, to continuous low-level leakage caused by operational errors. The timescale of escape events determines the distribution of gene flow from aquaculture to the wild. The evolutionary consequences of this variation in timescale will depend on the degree of generation overlap and the focal species' life history attributes, especially those under selection in aquaculture (e.g., growth rate, which can influence additional demographically important traits such as age at maturity). To evaluate the effects of variable escape both within and across generations, we construct an age-structured model of coupled genetic and demographic dynamics and parameterize it for species with contrasting life history characteristics (Salmo salar and Gadus morhua). Our results are consistent with earlier discrete-generation models that constant, low-level spillover can have a greater impact than rare, large pulses of leakage, even after accounting for the averaging effects of overlapping generations. The age-structured model also allows detailed evaluation of the role of different life history traits, which reveals that species with longer generation times might experience greater fitness consequences of aquaculture spillover but are less sensitive to variability in spillover. Additionally, environment-induced earlier maturity of escapees can increase the fitness effects on wild fish, especially those with shorter generation times. Our results suggest that effective management to minimize the unintended fitness consequences of aquaculture releases might require extensive monitoring efforts on constant, low-level spillover and assessment of the focal species' life history characteristics.

Characterization and Transcript Expression Analyses of Atlantic Cod Viperin

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.

Concomitant Temperature Stress and Immune Activation may Increase Mortality Despite Efficient Clearance of an Intracellular Bacterial Infection in Atlantic Cod

The environmental temperature has profound effects on biological systems of marine aquatic organisms and plays a critical role in species distribution and abundance. Particularly during the warmer seasons, variations in habitat temperature may introduce episodes of stressful temperatures which the organisms must adapt to and compensate for to maintain physiological homeostasis. The marine environment is changing and predicted raises in water temperatures will affect numerous marine species. Translocation of pathogens follow migration of species and alternations in physical environmental parameters may have influence upon the virulence of pathogens, as well as the hosts immune responses. While pathogenicity of many true pathogens is expected to increase following climate induced temperature stress, the impact from environmental stressors on the occurrence and severity of opportunistic infections is unknown. Here we describe how thermal stress in the cold-water species Atlantic cod influenced the fish immune responses against an opportunistic intracellular bacterium. Following experimental infection with Brucella pinnipedialis at normal water temperature (6°C) and sub-optimal temperature (15°C), cod cleared the intracellular bacteria more rapidly at the highest temperature. The overall immune response was faster and of higher amplitude at 15°C, however, a significant number of cod died at this temperature despite efficient clearance of infection. An increased growth rate not affected by infection was observed at 15°C, confirming multiple energy demanding processes taking place. Serum chemistry suggested that general homeostasis was influenced by both infection and increased water temperature, highlighting the cumulative stress responses (allostatic load) generated by simultaneous stressors. Our results suggest a trade-off between resistance and tolerance to survive infection at sub-optimal temperatures and raise questions concerning the impact of increased water temperatures on the energetic costs of immune system activation in aquatic ectotherms.

Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.

Fine-scale population differences in Atlantic cod reproductive success: A potential mechanism for ecological speciation in a marine fish

Successful resource-management and conservation outcomes ideally depend on matching the spatial scales of population demography, local adaptation, and threat mitigation. For marine fish with high dispersal capabilities, this remains a fundamental challenge. Based on daily parentage assignments of more than 4,000 offspring, we document fine-scaled temporal differences in individual reproductive success for two spatially adjacent (<10 km) populations of a broadcast-spawning marine fish. Distinguished by differences in genetics and life history, Atlantic cod (Gadus morhua) from inner- and outer-fjord populations were allowed to compete for mating and reproductive opportunities. After accounting for phenotypic variability in several traits, reproductive success of outer-fjord cod was significantly lower than that of inner-fjord cod. This finding, given that genomically different cod ecotypes inhabit inner- and outer-fjord waters, raises the intriguing hypothesis that the populations might be diverging because of ecological speciation. Individual reproductive success, skewed within both sexes (more so among males), was positively affected by body size, which also influenced the timing of reproduction, larger individuals spawning later among females but earlier among males. Our work suggests that spatial mismatches between management and biological units exist in marine fishes and that studies of reproductive interactions between putative populations or ecotypes can provide an informative basis on which determination of the scale of local adaptation can be ascertained.

Mitochondrial genome variation of Atlantic cod

OBJECTIVE

The objective of this study was to analyse intraspecific sequence variation of Atlantic cod mitochondrial DNA, based on a comprehensive collection of completely sequenced mitochondrial genomes.

RESULTS

We determined the complete mitochondrial DNA sequence of 124 cod specimens from the eastern and western part of the species' distribution range in the North Atlantic Ocean. All specimens harboured a unique mitochondrial DNA haplotype. Nine hundred and fifty-two polymorphic sites were identified, including 109 non-synonymous sites within protein coding regions. Eighteen variable sites were identified as indels, exclusively distributed in structural RNA genes and non-coding regions. Phylogeographic analyses based on 156 available cod mitochondrial genomes did not reveal a clear structure. There was a lack of mitochondrial genetic differentiation between two ecotypes of cod in the eastern North Atlantic, but eastern and western cod were differentiated and mitochondrial genome diversity was higher in the eastern than the western Atlantic, suggesting deviating population histories. The geographic distribution of mitochondrial genome variation seems to be governed by demographic processes and gene flow among ecotypes that are otherwise characterized by localized genomic divergence associated with chromosomal inversions.

Viscoelastic and Functional Properties of Cod-Bone Gelatin in the Presence of Xylitol and Stevioside

The physical, rheological, structural and functional properties of cod bone gelatin (CBG) with various concentrations (0, 2, 4, 6, 10, and 15%) of low-calorie sweeteners [xylitol (X) and stevioside (S)] to form gels were investigated. The gel strength of CBGX increased with increased xylitol due presumably to hydrogen bonds between xylitol and gelatin, but with CBGS the highest gel strength occurred when S concentration was 4%. Viscosity of CBGS samples were higher than CBGX due to S's high molecular mass. The viscoelasticity (G′ and G′′), foaming capacity and fat binding capacity of CBGX were higher while foam stability was lower. The emulsion activity and emulsion stability of CBGX were a little lower than CBGS at the same concentration. The structure of X is linear making it easier to form a dense three-dimensional network structure, while the complex cyclic structure of S had more difficulty forming a network structure with cod bone gelatin. Therefore, X may be a better choice for sweetening gelatin gels.

A Comparison of the Effects of Packaging Containing Nano ZnO or Polylysine on the Microbial Purity and Texture of Cod (Gadus morhua) Fillets

Portions of fresh Baltic cod fillets were packed into cellulose boxes (control samples), which were covered with Methyl Hydroxypropyl Celluloses (MHPC) coating with 2% polylysine. The cellulose boxes had square PE films and were enclosed in MHPC coating containing ZnO nanoparticles. The cod fillets were stored at 5 °C and examined after 72 h and 144 h storage times. Results obtained in this study showed that the textural parameters of the cod fillets increased, with both Springiness and Cohesiveness found greater after 144 h of storage for all analysed packaging materials. The Gumminess of fillets increased after storage, but the lowest increase was noted in cod samples that were stored in boxes containing PE films with ZnO nanoparticles. It was found that water loss from the cod fillets in these boxes was also lowest. The Adhesiveness of the fish samples stored in boxes devoid of active coatings also increased. In contrast to the packaging material devoid of active coatings, the storage of fillets in active coating boxes resulted in a decrease of adhesiveness. Microbial analysis showed that packaging material containing nano-ZnO was found to be more active against mesophilic and psychotropic bacterial cells than the coatings with polylysine after 72 h and 144 h of storage.

Plasticity in activity and latency to explore differs between juvenile Atlantic cod Gadus morhua across a temperature gradient

In the current study activity and latency to explore, as well as the correlation of these traits, were examined in individually marked juvenile Gadus morhua at 7, 10 and 13° C. It was concluded that individual rank order of both traits was maintained across temperature but that the level of change differed between individuals.

Size-dependent social attraction and repulsion explains the decision of Atlantic cod Gadus morhua to enter baited pots

The present study tested whether the presence of already retained fishes inside baited fish pots acted as a social attraction and affected the entrance probability of Atlantic cod Gadus morhua in a fjord in northern Norway. Video analysis revealed that the probability of an entrance initially increased with the presence of low numbers of fishes inside the pot, but subsequently decreased at a critical number of caught fishes. The critical number was dependent on the size of the G. morhua attempting to enter. This demonstrates that social attraction and repulsion play a role in G. morhua pot fishing and has important implications for the capture efficiency of fisheries executed with pots.

Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages

MicroRNAs (miRNAs) are known to play important immunoregulatory roles in teleosts, although miRNAs involved in the antiviral immune response of Atlantic cod (Gadus morhua) were previously uncharacterised. Using deep sequencing and qPCR, the present study was conducted to identify miRNAs responsive to the viral mimic, polyriboinosinic polyribocytidylic acid (pIC) in Atlantic cod macrophages. Macrophage samples isolated from Atlantic cod (n=3) and treated with pIC or phosphate buffered saline (PBS control) for 24 and 72h were used for miRNA profiling. Following deep sequencing, DESeq2 analyses identified four (miR-731-3p, miR-125b-3-3p, miR-150-3p and miR-462-3p) and two (miR-2188-3p and miR-462-3p) significantly differentially expressed miRNAs at 24 and 72h post-stimulation (HPS), respectively. Sequencing-identified miRNAs were subjected to qPCR validation using a larger number of biological replicates (n=6) exposed to pIC or PBS over time (i.e. 12, 24, 48 and 72 HPS). As in sequencing, miR-731-3p, miR-462-3p and miR-2188-3p showed significant up-regulation by pIC. The sequencing results were not qPCR-validated for miR-125b-3-3p and miR-150-3p as up- and down-regulated miRNAs at 24 HPS, respectively; however, qPCR results showed significant up-regulation in response to pIC stimulation at later time points (i.e. 48 and/or 72 HPS). We also used qPCR to assess the expression of other miRNAs that were previously shown as immune responsive in other vertebrates. qPCR results at 48 and/or 72 HPS revealed that miR-128-3-5p, miR-214-1-5p and miR-451-3p were induced by pIC, whereas miR-30b-3p and miR-199-1-3p expression were repressed in response to pIC. The present study identified ten pIC-stimulated miRNAs, suggesting them as important in antiviral immune responses of Atlantic cod macrophages. Some pIC-responsive miRNAs identified in this study were predicted to target putative immune-related genes of Atlantic cod (e.g. miR-30b-3p targeting herc4), although the regulatory functions of these miRNAs need to be validated by future studies.

Making the most of survey data: Incorporating age uncertainty when fitting growth parameters

Individual growth is an important parameter and is linked to a number of other biological processes. It is commonly modeled using the von Bertalanffy growth function (VBGF), which is regularly fitted to age data where the ages of the animals are not known exactly but are binned into yearly age groups, such as fish survey data. Current methods of fitting the VBGF to these data treat all the binned ages as the actual ages. We present a new VBGF model that combines data from multiple surveys and allows the actual age of an animal to be inferred. By fitting to survey data for Atlantic herring (Clupea harengus) and Atlantic cod (Gadus morhua), we compare our model with two other ways of combining data from multiple surveys but where the ages are as reported in the survey data. We use the fitted parameters as inputs into a yield‐per‐recruit model to see what would happen to advice given to management. We found that each of the ways of combining the data leads to different parameter estimates for the VBGF and advice for policymakers. Our model fitted to the data better than either of the other models and also reduced the uncertainty in the parameter estimates and models used to inform management. Our model is a robust way of fitting the VBGF and can be used to combine data from multiple sources. The model is general enough to fit other growth curves for any taxon when the age of individuals is binned into groups.

Mercury concentration trend as a possible result of changes in cod population demography

Mercury (Hg) in Atlantic cod (Gadus morhua) is one of many parameters that are monitored through OSPAR's Joint Assessment and Monitoring Programme. Time series for cod in the Inner Oslofjord (Norway) go back to 1984. Until 2014, annual median Hg-concentrations in cod from the Inner Oslofjord showed both significant upward long-term (whole time series) and short-term (recent 10 years) trends (when 2015 was included, the short-term trend was not significant). However, the median length of the cod sampled also showed upward trends. This may have been caused by low cod recruitment in the area since the start of the 2000s, as indicated by beach seine surveys. To investigate how length would impact the trend analysis, the Hg-concentrations in the cod were normalised to 50 cm. No significant short-term trend in Hg-concentrations could be detected for length-normalised concentrations. The results indicated that most of the upward trend in Hg-concentrations could be attributed to the sampling of larger fish. The reasons for the apparent change in the cod population demography are not conclusive, however, sampling bias must also be considered.

Life on the edge: O2 binding in Atlantic cod red blood cells near their southern distribution limit is not sensitive to temperature or haemoglobin genotype

Atlantic cod are a commercially important species believed to be threatened by warming seas near their southern, equatorward upper thermal edge of distribution. Limitations to circulatory O₂ transport, in particular cardiac output, and the geographic distribution of functionally different haemoglobin (Hb) genotypes have separately been suggested to play a role in setting thermal tolerance in this species. The present study assessed the thermal sensitivity of O₂ binding in Atlantic cod red blood cells with different Hb genotypes near their upper thermal distribution limit and modelled its consequences for the arterio-venous O₂ saturation difference, Sa–v_O2, another major determinant of circulatory O₂ supply rate. The results showed statistically indistinguishable red blood cell O₂ binding between the three HbI genotypes in wild-caught Atlantic cod from the Irish Sea (53° N). Red blood cells had an unusually low O₂ affinity, with reduced or even reversed thermal sensitivity between pH 7.4 and 7.9, and 5.0 and 20.0°C. This was paired with strongly pH-dependent affinity and cooperativity of red blood cell O₂ binding (Bohr and Root effects). Modelling of Sa–v_O2 at physiological pH, temperature and O₂ partial pressures revealed a substantial capacity for increases in Sa–v_O2 to meet rising tissue O₂ demands at 5.0 and 12.5°C, but not at 20°C. Furthermore, there was no evidence for an increase of maximal Sa–v_O2 with temperature. It is suggested that Atlantic cod at such high temperatures may solely depend on increases in cardiac output and blood O₂ capacity, or thermal acclimatisation of metabolic rate, for matching circulatory O₂ supply to tissue demand.

Highlighted Article: Red blood cell oxygen binding affinity in Atlantic cod near their southern, warmer limit of distribution is largely temperature independent and not affected by functional differences between their major haemoglobin genotypes.

Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine

BACKGROUND

Atlantic cod (Gadus morhua), is known to vary genetically across the North Atlantic, Greenland, and Newfoundland. This genetic variation occurs both spatially and temporally through decades of heavy fishing, and is concentrated in three linkage disequilibrium blocks, previously defined by pedigreed linkage mapping analysis. Variation within these genomic regions is correlated with both seawater temperature and behavioral ecotype. The full extent and nature of these linkage groups is important information for interpreting cod genetic structure as a tool for future fisheries management.

RESULTS

We conducted whole genome sequencing for 31 individual cod from three sub-populations in the Gulf of Maine. Across the genome, we found 3,390,654 intermediate to high frequency Single Nucleotide Polymorphisms (SNPs). We show that pairwise linkage analysis among these SNPs is a powerful tool to detect linkage disequilibrium clusters by recovering the three previously detected linkage groups and identifying the 1031 genes contained therein. Across these genes, we found significant population differentiation among spawning groups in the Gulf of Maine and between Georges Bank and Gulf of Maine. Coordinated divergence among these genes and their differentiation at both short and long spatial scales suggests that they are acting as linked supergenes in local adaptation of cod populations.

CONCLUSIONS

Differentiation between SNPs in linkage disequilibrium blocks is the major signal of genetic differentiation between all groups tested within the Gulf of Maine. Our data provide a map of genes contained in these blocks, allowing an enhanced search for neutral genetic structure for demographic inference and fisheries modeling. Patterns of selection and the history of populations may be possible to identify in cod using this description of linkage disequilibrium blocks and future data sets to robustly separate neutral and selected genetic markers.

Effect of a fish stock's demographic structure on offspring survival and sensitivity to climate

Commercial fishing generally removes large and old individuals from fish stocks, reducing mean age and age diversity among spawners. It is feared that these demographic changes lead to lower and more variable recruitment to the stocks. A key proposed pathway is that juvenation and reduced size distribution causes reduced ranges in spawning period, spawning location, and egg buoyancy; this is proposed to lead to reduced spatial distribution of fish eggs and larvae, more homogeneous ambient environmental conditions within each year-class, and reduced buffering against negative environmental influences. However, few, if any, studies have confirmed a causal link from spawning stock demographic structure through egg and larval distribution to year class strength at recruitment. We here show that high mean age and size in the spawning stock of Barents Sea cod (Gadus morhua) is positively associated with high abundance and wide spatiotemporal distribution of cod eggs. We find, however, no support for the hypothesis that a wide egg distribution leads to higher recruitment or a weaker recruitment-temperature correlation. These results are based on statistical analyses of a spatially resolved data set on cod eggs covering a period (1959-1993) with large changes in biomass and demographic structure of spawners. The analyses also account for significant effects of spawning stock biomass and a liver condition index on egg abundance and distribution. Our results suggest that the buffering effect of a geographically wide distribution of eggs and larvae on fish recruitment may be insignificant compared with other impacts.

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

BACKGROUND

The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.

RESULTS

By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual.

CONCLUSIONS

The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

Host condition and accumulation of metals by acanthocephalan parasite Echinorhynchus gadi in cod Gadus morhua from the southern Baltic Sea

In this study, we analyzed the relationship between concentration of metals in the host-parasite system (cod - acanthocephalan Echinorhynchus gadi) and Fulton's condition factor (FCF) of the host. The relationship between metal (Ca, Cd, Cr, Cu, Fe, Hg, K, Mg, Mn, Na, Pb, Sr, Zn) concentrations in E. gadi and cod tissues was expressed as a bioconcentration factor (BCF), the ratio of the concentration in the parasite tissue to that in host tissues. Acanthocephalans accumulated mainly toxic metals (Cd, Pb), as well as Sr, Ca, Na. Cadmium showed the highest bioconcentration in parasites (BCF >200) compared to fish muscle. Significant negative correlation was detected between FCF and the concentration of Cd and Hg in cod liver. In contrast, FCF was positively correlated with the concentration of Hg in acanthocephalan tissues.

Skeletal muscle growth dynamics and the influence of first-feeding diet in Atlantic cod larvae (Gadus morhua L.)

Dynamics between hypertrophy (increase in cell size) and hyperplasia (increase in cell numbers) of white and red muscle in relation to body size [standard length (SL)], and the influence of the first-feeding diets on muscle growth were investigated in Atlantic cod larvae (Gadus morhua). Cod larvae were fed copepod nauplii or rotifers of different nutritional qualities from 4 to 29 days post hatching (dph), Artemia nauplii from 20 to 40 dph and a formulated diet from 36 to 60 dph. The short period of feeding with cultivated copepod nauplii had a positive effect on both muscle hyperplasia and hypertrophy after the copepod/rotifer phase (19 dph), and a positive long term effect on muscle hypertrophy (60 dph). The different nutritional qualities of rotifers did not significantly affect muscle growth. We suggest here a model of the dynamics between hyperplasia and hypertrophy of red and white muscle fibre cells in relation to cod SL (4 to 30 mm), where the different red and white muscle growth phases clearly coincided with different metamorphosis stages in cod larvae. These shifts could be included as biomarkers for the different stages of development during metamorphosis. The main dietary muscle effect was that hypertrophic growth of red muscle fibres was stronger in cod larvae that were fed copepods than in larvae that were fed rotifers, both in relation to larval age and size. Red muscle fibres are directly involved in larval locomotory performance, but may also play an important role in the larval myogenesis. This can have a long term effect on growth potential and fish performance.

Summary: Hyperplastic and hypertrophic growth dynamics of red and white muscle were strongly related to cod larval size and corresponded with the metamorphosis process. First-feeding diet quality can prolong effects on muscle growth potential in cod larvae.

Tetracycline marks visible in Baltic cod Gadus morhua otoliths stored for 40 years

Baltic cod Gadus morhua otoliths marked with oxytetracycline (OTC) in 1974-1975 had been sectioned and the sections stored in paper envelopes at room temperature in dry, dark conditions. After 40 years of storage, the historic OTC marks were still clearly visible showing that OTC is suitable for long-term chemical marking of otoliths. They were, however, noticeably paler than marks in recently recaptured and archived Baltic G. morhua otoliths, chemically tagged with tetracycline at similar dosage to the historic otoliths.

Transcriptome profiling of the antiviral immune response in Atlantic cod macrophages

A study was conducted to determine the transcriptome response of Atlantic cod (Gadus morhua) macrophages to the viral mimic, polyriboinosinic polyribocytidylic acid (pIC), using a 20K Atlantic cod microarray platform and qPCR. We identified 285 significantly up-regulated and 161 significantly down-regulated probes in cod macrophages 24 h after pIC stimulation. A subset of 26 microarray-identified transcripts was subjected to qPCR validation using samples treated with pIC or phosphate-buffered saline (control) over time (3, 6, 12, 24, 48 h), and 77% of them showed a significant response to pIC. The microarray and qPCR analyses in this study showed that pIC induced the expression of cod macrophage transcripts involved in RLR- and TLR-dependent pathogen recognition (e.g. tlr3, tlr7, mda5 and lgp2), as well as signal transducers (e.g. stat1 and nfkbia) and transcription activators (e.g. irf7 and irf10) in the MyD88-independent and dependent signalling pathways. Several immune effectors (e.g. isg15s, viperin, herc4, mip2 and ccl13) were significantly up-regulated in pIC-stimulated cod macrophages. The expression of some transcripts (e.g. irf7, irf10, viperin) was significantly up-regulated by pIC as early as 12 h. All pIC-induced transcripts had peak expression at either 24 h (e.g. tlr7, irf7, mip2) or 48 h (e.g. tlr3, lgp2, stat1). This study suggests possible roles of both vertebrate-conserved (e.g. tlr3 as an up-regulated gene) and fish-specific (tlr22g as a down-regulated gene) receptors in dsRNA recognition, and the importance of conserved and potentially fish-specific interferon stimulated genes in cod macrophages.

Influence of temperature and fish thickness on the mass transfer kinetics during the cod (Gadus morhua) desalting process

BACKGROUND

The aim of this study was to analyse the influence of desalting temperature, fish thickness and desalting time on the mass transfer kinetics during the cod desalting process by physico-chemical analyses.

RESULTS

Both water uptake and salt loss increased with increasing temperature (15 °C > 10 °C > 5 °C) up to 24 h in 'thicker' pieces. The equilibrium achievement was faster in 'thinner' pieces and also with increasing temperature. Longer desalting times at 10 °C can be a good practice to be used during cod desalting at an industrial scale in order to obtain commercial products with higher yields. The faster mass transfer during desalting of 'thinner' pieces appears to follow three periods as a result of diffusion of the components (water, NaCl, and soluble proteins) because of the concentration differences, and pressure gradients due to expansion/shrinkage of the protein matrix, which is dependent on the NaCl content. The refractive index can be used by industry as an indirect measurement to determine the moment at which the 'thicker' samples are near the Z(NaCl) = Y(NaCl) equilibrium.

CONCLUSION

Optimum combinations between the process variables analysed are essential in order to speed up the mass transfer kinetics during cod desalting at an industrial scale. © 2016 Society of Chemical Industry.

Marine ecosystem connectivity mediated by migrant-resident interactions and the concomitant cross-system flux of lipids

Accumulating research argues that migrants influence the functioning and productivity of local habitats and ecosystems along migration routes and potentially drive cross-system energy fluxes of considerable magnitude, yet empirical documentation of local ecological effects and descriptions of the underlying mechanisms are surprisingly rare. In this study, we discovered migrant-resident interactions and substantial cross-system lipid transportation in the transition zone between the Baltic Sea and the North Sea where a resident cod population (predators) was found to interact with a herring population (prey) on a seasonal basis. We traced the lipids, using fatty acid trophic markers (FATM), from the herring feeding grounds in the North Sea to the cod livers in the Western Baltic Sea. Time series analysis of population dynamics indicated that population-level production of cod is positively affected by the herring subsidies. However, the underlying mechanisms were more complicated than anticipated. During the herring season, large cod received most of its dietary lipids from the herring, whereas smaller cod were prevented from accessing the lipid pool due to a mismatch in predator-prey size ratio. Furthermore, while the herring were extremely rich in bulk energy, they were surprisingly poor in a specific functional fatty acid. Hence, our study was the first to illustrate how the magnitude cross-system fluxes of subsidies in migrant-resident systems are potentially constrained by the size structure of the resident predator population and the nutritional quality of the migrants.

Extracellular glucose supports lactate production but not aerobic metabolism in cardiomyocytes from both normoglycemic Atlantic cod and low glycemic short-horned sculpin

Fish exhibit a wide range of species-specific blood glucose levels. How this relates to glucose utilization is yet to be fully realized. Here, we assessed glucose transport and metabolism in myocytes isolated from Atlantic cod (Gadus morhua) and short-horned sculpin (Myoxocephalus scorpius), species with blood glucose levels of 3.7 and 0.57 mmol l(-1), respectively. Glucose metabolism was assessed by the production of (3)H2O from [2-(3)H]glucose. Glucose metabolism was 3.5- to 6-fold higher by myocytes from Atlantic cod than by those from short-horned sculpin at the same level of extracellular glucose. In Atlantic cod myocytes, glucose metabolism displayed what appears to be a saturable component with respect to extracellular glucose, and cytochalasin B inhibited glucose metabolism. These features revealed a facilitated glucose diffusion mechanism that accounts for between 30% and 55% of glucose entry at physiological levels of extracellular glucose. Facilitated glucose diffusion appears to be minimal in myocytes for short-horned sculpin. Glucose entry by simple diffusion occurs in both cell types with the same linear relationship between glucose metabolism and extracellular glucose concentration, presumably due to similarities in membrane composition. Oxygen consumption by myocytes incubated in medium containing physiological levels of extracellular glucose (Atlantic cod 5 mmol l(-1), short-horned sculpin 0.5 mmol l(-1)) was similar in the two species and was not decreased by cytochalasin B, suggesting that these cells have the capability of oxidizing alternative on-board metabolic fuels. Cells produced lactate at low rates but glycogen levels did not change during the incubation period. In cells from both species, glucose utilization assessed by both simple chemical analysis of glucose disappearance from the medium and (3)H2O production was half the rate of lactate production and as such extracellular glucose was not available for oxidative metabolism. Overall, extracellular glucose makes only a minor contribution to ATP production but a sustained glycolysis may be necessary to support Ca(2+) transport mechanisms at either the sarcoplasmic reticulum or the sarcolemmal membrane.

Measuring abnormal movements in free-swimming fish with accelerometers: implications for quantifying tag and parasite load

Animal-borne data loggers allow movement, associated behaviours and energy expenditure in fish to be quantified without direct observations. As with any tagging, tags that are attached externally may adversely affect fish behaviour, swimming efficiency and survival. We report on free-swimming wild Atlantic cod (Gadus morhua) held in a large mesocosm that exhibited distinctly aberrant rotational swimming (scouring) when externally tagged with accelerometer data loggers. To quantify the phenomenon, the cod were tagged with two sizes of loggers (18 and 6 g; <2% body mass) that measured tri-axial acceleration at 50 Hz. An automated algorithm, based on body angular rotation, was designed to extract the scouring movements from the acceleration signal (98% accuracy). The algorithm also identified the frequency pattern and associated energy expenditure of scouring in relation to tag load (% body weight). The average per cent time spent scouring (5%) was independent of tag load. The vector of the dynamic body acceleration (VeDBA), used as a proxy for energy expenditure, increased with tag load (r(2)=0.51), and suggests that fish with large tags spent more energy when scouring than fish with small tags. The information allowed us to determine potential detrimental effects of an external tag on fish behaviour and how these effects may be mitigated by tag size. The algorithm can potentially identify similar rotational movements associated with spawning, courtship, feeding and parasite-load shedding in the wild. The results infer a more careful interpretation of data derived from external tags and the careful consideration of tag type, drag, buoyancy and placement, as well as animal buoyancy and species.

A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.