Effect of turbidity on habitat preference of juvenile Atlantic cod, Gadus morhua

We examined the effects of turbidity on habitat preference of juvenile Atlantic cod in the laboratory, using a shuttle box where fish could select between two different habitats. In the first experiment, we compared three turbidity levels of kaolin (3, 8 and 21 beam attenuation m⁻¹). In the second experiment, we looked at the effect of turbidity media (kaolin versus algae), after controlling for spectral differences between turbidity media. Although cod preferred an intermediate turbidity of kaolin over low turbidity water, comparisons between low and high turbidity, and intermediate and high turbidity did not significantly influence habitat preference. Algae did not influence habitat preference by cod. Although other studies have found that turbidity affects both foraging and antipredator behaviour of juvenile cod, this study has shown that gradients in turbidity per se do not have a strong effect on their habitat preference.     

Temperature during early development has long-term effects on microRNA expression in Atlantic cod

Background

Environmental temperature has serious implications in life cycle of aquatic ectotherms. Understanding the molecular mechanisms of temperature acclimation and adaptation of marine organisms is of the uttermost importance for ecology, fisheries, and aquaculture, as it allows modeling the effects of global warming on population dynamics. Regulatory molecules are major modulators of acclimation and adaptation; among them, microRNAs (miRNAs) are versatile and substantial contributors to regulatory networks of development and adaptive plasticity. However, their role in thermal plasticity is poorly known. We have asked whether the temperature and its shift during the early ontogeny (embryonic and larval development) affect the miRNA repertoire of Atlantic cod (Gadus morhua), and if thermal experience has long-term consequences in the miRNA profile.

Results

We characterized miRNA during different developmental stages and in juvenile tissues using next generation sequencing. We identified 389 putative miRNA precursor loci, 120 novel precursor miRNAs, and 281 mature miRNAs. Some miRNAs showed stage- or tissue-enriched expression and miRNAs, such as the miR-17 ~ 92 cluster, myomiRs (miR-206), neuromiRs (miR-9, miR-124), miR-130b, and miR-430 showed differential expression in different temperature regimes. Long-term effect of embryonic incubation temperature was revealed on expression of some miRNAs in juvenile pituitary (miR-449), gonad (miR-27c, miR-30c, and miR-200a), and liver (let-7 h, miR-7a, miR-22, miR-34c, miR-132a, miR-192, miR-221, miR-451, miR-2188, and miR-7550), but not in brain. Some of differentially expressed miRNAs in the liver were confirmed using LNA-based rt-qPCR. The effect of temperature on methylation status of selected miRNA promoter regions was mostly inconclusive.

Conclusions

Temperature elevation by several degrees during embryonic and larval developmental stages significantly alters the miRNA profile, both short-term and long-term. Our results suggest that a further rise in seas temperature might affect life history of Atlantic cod.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1503-7) contains supplementary material, which is available to authorized users.     

Climate and fishing steer ecosystem regeneration to uncertain economic futures

Overfishing of large predatory fish populations has resulted in lasting restructurings of entire marine food webs worldwide, with serious socio-economic consequences. Fortunately, some degraded ecosystems show signs of recovery. A key challenge for ecosystem management is to anticipate the degree to which recovery is possible. By applying a statistical food-web model, using the Baltic Sea as a case study, we show that under current temperature and salinity conditions, complete recovery of this heavily altered ecosystem will be impossible. Instead, the ecosystem regenerates towards a new ecological baseline. This new baseline is characterized by lower and more variable biomass of cod, the commercially most important fish stock in the Baltic Sea, even under very low exploitation pressure. Furthermore, a socio-economic assessment shows that this signal is amplified at the level of societal costs, owing to increased uncertainty in biomass and reduced consumer surplus. Specifically, the combined economic losses amount to approximately 120 million € per year, which equals half of today''s maximum economic yield for the Baltic cod fishery. Our analyses suggest that shifts in ecological and economic baselines can lead to higher economic uncertainty and costs for exploited ecosystems, in particular, under climate change.     

Life-stage-dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod,Gadus morhua,from Canada's Northern cod stock region and adjacent areas

Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada's Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using double-digest restriction site-associated DNA sequencing–derived single nucleotide polymorphisms. A reduced proportion of homozygotes with a chromosomal inversion located in linkage group 1 (LG1) was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No selectively neutral genetic differences were found between samples from the Northern cod stock; nevertheless, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: (a) the Newfoundland Atlantic Coast, (b) eastern and southern Gulf of St. Lawrence and Burgeo Bank and (c) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote demographic rebuilding of the stock.     

The forgotten feeding ground: patterns in seasonal and depth-specific food intake of adult cod Gadus morhua in the western Baltic Sea

This study presents the diet composition of western Baltic cod Gadus morhua based on 3150 stomachs sampled year-round between 2016 and 2017 using angling, gillnetting and bottom trawling, which enhanced the spatio-temporal coverage of cod habitats. Cod diet composition in shallow areas (<20 m depth) was dominated by benthic invertebrate species, mainly the common shore crab Carcinus maneas. Compared to historic diet data from the 1960s and 1980s (limited to depth >20 m), the contribution of herring Clupea harengus decreased and round goby Neogobius melanostomus occurred as a new prey species. Statistical modelling revealed significant relationships between diet composition, catch depth, fish length and season. Generalized additive modelling identified a negative relationship between catch depth and stomach content weight, suggesting reduced food intake in winter when cod use deeper areas for spawning and during peak summer when cod tend to avoid high water temperatures. The results of this study highlight the importance of shallow coastal areas as major feeding habitats of adult cod in the western Baltic Sea, which were previously unknown because samples were restricted to deeper trawlable areas. The results strongly suggest that historic stomach analyses overestimated the role of forage fish and underestimated the role of invertebrate prey. Eventually, this study shows the importance of a comprehensive habitat coverage for unbiased stomach sampling programmes to provide a more reliable estimation of top predator diet, a key information for food web analyses and multispecies models.     

It’s a wormy world: Meta‐analysis reveals several decades of change in the global abundance of the parasitic nematodes Anisakis spp. and Pseudoterranova spp. in marine fishes and invertebrates

The Anthropocene has brought substantial change to ocean ecosystems, but whether this age will bring more or less marine disease is unknown. In recent years, the accelerating tempo of epizootic and zoonotic disease events has made it seem as if disease is on the rise. Is this apparent increase in disease due to increased observation and sampling effort, or to an actual rise in the abundance of parasites and pathogens? We examined the literature to track long‐term change in the abundance of two parasitic nematode genera with zoonotic potential: Anisakis spp. and Pseudoterranova spp. These anisakid nematodes cause the disease anisakidosis and are transmitted to humans in undercooked and raw marine seafood. A total of 123 papers published between 1967 and 2017 met our criteria for inclusion, from which we extracted 755 host–parasite–location–year combinations. Of these, 69.7% concerned Anisakis spp. and 30.3% focused on Pseudoterranova spp. Meta‐regression revealed an increase in Anisakis spp. abundance (average number of worms/fish) over a 53 year period from 1962 to 2015 and no significant change in Pseudoterranova spp. abundance over a 37 year period from 1978 to 2015. Standardizing changes to the period of 1978–2015, so that results are comparable between genera, we detected a significant 283‐fold increase in Anisakis spp. abundance and no change in the abundance of Pseudoterranova spp. This increase in Anisakis spp. abundance may have implications for human health, marine mammal health, and fisheries profitability.     

Semen characteristics and their ability to predict sperm cryopreservation potential of Atlantic cod, Gadus morhua L

There is a lack of biomarkers or indices that can be used to predict the quality of fish semen samples following the freezing and thawing cycle. In the present study, a series of semen indices were tested to assess if they could accurately forecast the cryopreservation potential of Atlantic cod (Gadus morhua) semen. Fresh and frozen-thawed sperm activity variables were compared, and relationships between frozen-thawed sperm activity and fertilization success were examined. In comparison with fresh sperm, activity variables of frozen-thawed spermatozoa were reduced. Of the 18 males examined, mean (± SEM) spermatocrit of fresh sperm was 40.72 ± 4.23%, osmolality of the seminal plasma 366.32 ± 4.95 mOsmol/kg, pH 8.32 ± 0.04, protein concentration 1.05 ± 0.08 mg/mL, anti-trypsin activity 153.83 ± 19.25 U/L, and total antioxidant capacity 0.15 ± 0.03 μmol Trolox equivalents/mL. Frozen-thawed fertilization success was highly variable among males with values ranging from 18.5 to 90.2%. Regressions yielded significant positive relationships between frozen-thawed motility, velocity, track crossing frequency, and subsequent fertilization success. Sequential multiple regressions explained up to 95% of the variation in frozen-thawed sperm activity. Spermatocrit and pH of fresh semen were negatively related, whereas osmolality and antioxidant capacity were positively related to frozen-thawed motility and velocity. Each of these indices can be measured within minutes of collecting a fresh sample of semen and are thus early indicators of the capacity of semen samples to withstand cryopreservation. These results have many benefits for conservation of wild stocks, aquaculture production, and for understanding semen biology and cryobiology of fishes.     

Automated sperm head morphology analyzer for open-source software

Sperm head morphology has been identified as a characteristic that can be used to predict a male's semen quality. In the present study, we have developed an automated sperm head morphology analysis (ASMA) plug-in for open-source ImageJ software (http://rsbweb.nih.gov/ij/). We describe the plug-in's functionality, and confirm its validity for sperm head morphology analysis using fish sperm. Sperm head morphological measurements (length and width) made with the ASMA plug-in did not differ from manual measurements. Using the plug-in to measure sperm head-shaped objects of known size, the associated plug-in error rate was < 0.5%. Brightness and contrast ratios influenced sperm head measurements, suggesting the need for standardized protocols. This plug-in was effective at measuring elliptical (i.e., Atlantic cod) as well as slightly irregular (i.e., Chinook salmon) shaped sperm heads. In conclusion, our ASMA plug-in represents a versatile alternative to costly sperm morphology software.     

Are low but statistically significant levels of genetic differentiation in marine fishes ‘biologically meaningful’? A case study of coastal Atlantic cod

A key question in many genetic studies on marine organisms is how to interpret a low but statistically significant level of genetic differentiation. Do such observations reflect a real phenomenon, or are they caused by confounding factors such as unrepresentative sampling or selective forces acting on the marker loci? Further, are low levels of differentiation biologically trivial, or can they represent a meaningful and perhaps important finding? We explored these issues in an empirical study on coastal Atlantic cod, combining temporally replicated genetic samples over a 10‐year period with an extensive capture–mark–recapture study of individual mobility and population size. The genetic analyses revealed a pattern of differentiation between the inner part of the fjord and the open skerries area at the fjord entrance. Overall, genetic differentiation was weak (average F_ST = 0.0037), but nevertheless highly statistical significant and did not depend on particular loci that could be subject to selection. This spatial component dominated over temporal change, and temporal replicates clustered together throughout the 10‐year period. Consistent with genetic results, the majority of the recaptured fish were found close to the point of release, with <1% of recaptured individuals dispersing between the inner fjord and outer skerries. We conclude that low levels of genetic differentiation in this marine fish can indeed be biologically meaningful, corresponding to separate, temporally persistent, local populations. We estimated the genetically effective sizes (N_e) of the two coastal cod populations to 198 and 542 and found a N_e/N (spawner) ratio of 0.14.     

The influence of temperature on the stage at hatch of laboratory reared Gadus morhua and implications for comparisons of length and morphology

A staging table for yolk‐sac larvae of Atlantic cod Gadus morhua was developed and applied to determine the development stage at hatch. Larvae ( n  = 20) were sampled during the period from 50% hatch to first‐feeding from four temperature treatments ( c . 2, 4, 8 and 12° C). Data recorded included standard length, development stage, yolk‐sac area and evidence of feeding by larvae. The results indicated that the stage of development at hatch was positively correlated to larval size. Furthermore, developmentally based changes in morphology shortly after hatch reduced much of the initial difference in size, although some difference still existed. No relationship between size at hatch and the incidence of first‐feeding larvae was found. Based on these observations, it is recommended that the development stage of hatching larvae be reported in studies investigating size and morphological differences when observing individual larval fish that originate from different populations, batches or species.