Divergent responses of Atlantic cod to ocean acidification and food limitation

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

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.     

Algal turf scrubber (ATS) floways on the Great Wicomico River,Chesapeake Bay: productivity,algal community structure,substrate and chemistry1

Two Algal Turf Scrubber (ATS) units were deployed on the Great Wicomico River (GWR) for 22 months to examine the role of substrate in increasing algal productivity and nutrient removal. The yearly mean productivity of flat ATS screens was 15.4 g · m^?2 · d^?1. This was elevated to 39.6 g · m^?2 · d^?1 with a three‐dimensional (3‐D) screen, and to 47.7 g · m^?2 · d^?1 by avoiding high summer harvest temperatures. These methods enhanced nutrient removal (N, P) in algal biomass by 3.5 times. Eighty‐six algal taxa (Ochrophyta [diatoms], Chlorophyta [green algae], and Cyan‐obacteria [blue–green algae]) self‐seeded from the GWR and demonstrated yearly cycling. Silica (SiO₂) content of the algal biomass ranged from 30% to 50% of total biomass; phosphorus, nitrogen, and carbon content of the total algal biomass ranged from 0.15% to 0.21%, 2.13% to 2.89%, and 20.0% to 25.7%, respectively. Carbohydrate content (at 10%–25% of AFDM) was dominated by glucose. Lipids (fatty acid methyl ester; FAMEs) ranged widely from 0.5% to 9% AFDM, with Omega‐3 fatty acids a consistent component. Mathematical modeling of algal produ‐ctivity as a function of temperature, light, and substrate showed a proportionality of 4:3:3, resp‐ectively. Under landscape ATS operation, substrate manipulation provides a considerable opportunity to increase ATS productivity, water quality amelioration, and biomass coproduction for fertilizers, fermentation energy, and omega‐3 products. Based on the 3‐D prod‐uctivity and algal chemical composition demonstrated, ATS systems used for nonpoint source water treat‐ment can produce ethanol (butanol) at 5.8× per unit area of corn, and biodiesel at 12.0× per unit area of soy beans (agricultural production US).     

Genetic variation in life-history reaction norms in a marine fish

Neither the scale of adaptive variation nor the genetic basis for differential population responses to the environment is known for broadcast-spawning marine fishes. Using a common-garden experimental protocol, we document how larval growth, survival and their norms of reaction differ genetically among four populations of Atlantic cod (Gadus morhua). These traits, and their plastic responses to food and temperature, differed across spatial scales at which microsatellite DNA failed to detect population structure. Divergent survival reaction norms indicate that warm-water populations are more sensitive to changes in food, whereas cold-water populations are more sensitive to changes in temperature. Our results suggest that neither the direction nor the magnitude of demographic responses to environmental change need be the same among populations. Adaptive phenotypic plasticity, previously undocumented in marine fishes, can significantly influence the probability of recovery and persistence of collapsed populations by affecting their ability to respond to natural and anthropogenic environmental change.     

Real-Time Quantitative PCR Measurement of Ileal Lactobacillus salivarius Populations from Broiler Chickens To Determine the Influence of Farming Practices

A real-time quantitative PCR assay targeting a 16S-23S intergenic spacer region sequence was devised to measure the sizes of populations of Lactobacillus salivarius present in ileal digesta collected from broiler chickens. This species has been associated with deconjugation of bile salts in the small bowel and reduced broiler productivity. The assay was tested as a means of monitoring the sizes of L. salivarius populations from broilers fed diets with different compositions, maintained at different stocking densities, or given the antimicrobial drugs bacitracin and monensin in the feed. Stocking densities did not influence the numbers of L. salivarius cells in the ileum. A diet containing meat and bone meal reduced the size of the L. salivarius population relative to that of chickens given the control diet, as did administration of bacitracin and monensin in the feed. These changes in the target bacterial population were associated with improved broiler weight gain.     

Spatiotemporal mapping of the motility of the isolated chicken caecum

We studied the caecal contractile activity of the chicken (Gallus gallus) using single caeca that had been cannulated at their proximal and distal ends, and in paired caeca, maintained in situ on excised segments of gut that were cannulated at the colonic and small intestinal ends. Longitudinal and circular contractile patterns were characterised using high-definition spatiotemporal mapping. Low amplitude longitudinal contraction waves of frequency 14.1 cycles/min occurred in the absence of major contractile events. These were termed fast phasic and appeared to be mediated by slow waves. The nature of major spontaneous contractions occurring in the single caecum varied with the level of caecal distension. Type A contractions occurred when the caecum was not distended, originated from variable sites and propagated in both directions. Type B or C contractile events occurred when the caecum was moderately or fully distended, originated from a predominantly distal site and propagated proximally. On diameter maps, each type B event comprised a succession of contractions which had similar propagation speeds, frequency and direction to fast phasic contractions. Type C events were comprised of a succession of higher amplitude contractions with no appreciable propagation. Perfusion of saline via the colon resulted in fluid entering both caeca and the onset of aborad contractions in their proximal canals. Saline was also seen to flow between caeca during contractile events however no saline was seen to enter the small intestine as has been postulated by other workers.     

Mapping the transition state for DNA bending by IHF

How DNA-bending proteins recognize their specific sites on DNA remains elusive, particularly for proteins that use indirect readout, which relies on sequence-dependent variations in DNA flexibility/bendability. The question remains as to whether the protein bends the DNA (protein-induced bending) or, alternatively, "prebent" DNA conformations are thermally accessible, which the protein captures to form the specific complex (conformational capture). To distinguish between these mechanisms requires characterization of reaction intermediates and, in particular, snapshots of the transition state along the recognition pathway. We present such a snapshot, from measurements of DNA bending dynamics in complex with Escherichia coli integration host factor (IHF), an architectural protein that bends specific sites on λ-DNA in a U-turn by creating two sharp kinks in DNA. Fluorescence resonance energy transfer measurements in response to laser temperature-jump perturbation monitor DNA bending. We find that nicks or mismatches that enhance DNA flexibility at the site of the kinks show 3- to 4-fold increase in DNA bending rates that reflect a 4- to 11-fold increase in binding affinities, while sequence modifications away from the kink sites, as well as mutations in IHF designed to destabilize the complex, have negligible effect on DNA bending rates despite >250-fold decrease in binding affinities. These results support the scenario that the bottleneck in the recognition step for IHF is spontaneous kinking of cognate DNA to adopt a partially prebent conformation and point to conformational capture as the underlying mechanism of initial recognition, with additional protein-induced bending occurring after the transition state.     

Real-time quantitative PCR measurement of ileal Lactobacillus salivarius populations from broiler chickens to determine the influence of farming practices

A real-time quantitative PCR assay targeting a 16S-23S intergenic spacer region sequence was devised to measure the sizes of populations of Lactobacillus salivarius present in ileal digesta collected from broiler chickens. This species has been associated with deconjugation of bile salts in the small bowel and reduced broiler productivity. The assay was tested as a means of monitoring the sizes of L. salivarius populations from broilers fed diets with different compositions, maintained at different stocking densities, or given the antimicrobial drugs bacitracin and monensin in the feed. Stocking densities did not influence the numbers of L. salivarius cells in the ileum. A diet containing meat and bone meal reduced the size of the L. salivarius population relative to that of chickens given the control diet, as did administration of bacitracin and monensin in the feed. These changes in the target bacterial population were associated with improved broiler weight gain.     

Gut morphology of diploid and triploid Atlantic cod,Gadus morhua

Little is known about the functional consequences of triploidy in Atlantic cod. This study compared the gut morphology of diploid and triploid offspring of wild and selected broodstock. Three‐year‐old triploid offspring of wild cod (mean weight 1695 ± 346 g) had approximately 18% fewer pyloric caeca (125 ± 9 vs 172 ± 14, P < 0.001) and a 23% shorter intestine [Relative Gut Length, (RGL); 1.40 ± 0.17 vs 1.81 ± 0.17, P < 0.05] than their diploid siblings (mean weight: 1820 ± 262 g). Two‐year‐old triploid offspring of selected broodstock (mean weight: 640 ± 64 g) had 20% fewer pyloric caeca (309 ± 17 vs 387 ± 27, P < 0.001) but similar RGL to their diploid siblings (mean weight: 820 ± 69 g). The average number of mucus cells in the columnar epithelium of pyloric caeca was significantly higher in triploid than in diploid cod (54 ± 9 vs 25 ± 5, P < 0.001). There was no correlation between pyloric caeca number and RGL, or between mucus cells and pyloric caeca number, and no significant differences between sexes for any of the measured variables. Overall, the observations highlight some differences in the digestive system of these two ploidy groups that could have an influence on nutrient utilization and performance capacity in triploids compared to diploids.