Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

Background: Aquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod (Gadus morhua) is just 2.5% of total market production. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. Results: The results demonstrated there was no significant difference in fish condition, gut morphology or hindgut microbiota between the U. rigida supplemented fish group and the control group at any time-point. This trend was not observed with the A. nodosum treatment. Fish within this group were further categorised as either ‘Normal’ or ‘Lower Growth’. ‘Lower Growth’ individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota was largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales (Lachnoclostridium). Conclusions: Our study indicates that U. rigida macroalgae can be supplemented at 10% inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. nodosum is not a suitable feed supplement in a farmed cod diet

Genetic and phenotypic differentiation of lumpfish (Cyclopterus lumpus) across the North Atlantic: implications for conservation and aquaculture

Demand for lumpfish (Cyclopterus lumpus) has increased exponentially over the last decade, both for their roe, which is used as a caviar substitute, and increasingly also as cleaner fish to control sea lice in salmon farming. The species is classified as Near Threatened by the IUCN and there are growing concerns that over-exploitation of wild stocks and translocation of hatchery-reared lumpfish may compromise the genetic diversity of native populations. We carried out a comparative analysis of genetic and phenotypic variation across the species’ range to estimate the level of genetic and phenotypic differentiation, and determined patterns of gene flow at spatial scales relevant to management. We found five genetically distinct groups located in the West Atlantic (USA and Canada), Mid Atlantic (Iceland), East Atlantic (Faroe Islands, Ireland, Scotland, Norway and Denmark), English Channel (England) and Baltic Sea (Sweden). Significant phenotypic differences were also found, with Baltic lumpfish growing more slowly, attaining a higher condition factor and maturing at a smaller size than North Atlantic lumpfish. Estimates of effective population size were consistently low across the North East Atlantic (Iceland, Faroe Islands and Norway), the area where most wild lumpfish are fished for their roe, and also for the aquaculture industry. Our study suggests that some lumpfish populations are very small and have low genetic diversity, which makes them particularly vulnerable to over-exploitation and genetic introgression. To protect them we advocate curtailing fishing effort, closing the breeding cycle of the species in captivity to reduce dependence on wild stocks, restricting the translocation of genetically distinct populations, and limiting the risk of farm escapes

The Development of Farmed Cod in Ireland

This study is interlinked with the work programme of the EIROCD project. Utilising historical data and empirical experimental approaches, various aspects of development, growth and phenotypic plasticity of North Atlantic cod, particularly the Celtic Sea stock, were examined. An examination of the wild stocks around Ireland revealed differences in population dynamics. The Celtic Sea stock had the highest growth rate of all Irish stocks considered, which prompted its' use as the base population for the development of the national broodstock and breeding programme (EIRCOD). The growth performance of farmed Irish cod was confirmed and benchmarked. Although there was a clear need for the improvement of our larval rearing strategy, growth was remarkably consistent across all year classes. Previously established growth models for more northerly populations were found to be useful within certain constraints for predicting growth of cod under Irish conditions. Comparative modelling of growth in different countries revealed a competitive advantage to Irish cod farmed during the first and second years. The effects of temperature on egg development as well as larval and juvenile growth were examined. Optimum temperatures for growth of Celtic Sea juveniles have been established and are remarkably similar to those estimated for more northerly stocks; however, actual growth rates were lower than those predicted from models. Body shape variation in the head and shoulder region was examined and has the potential to easily discriminate between wild and farmed cod populations. Phenotypic plasticity in body shape was also explored and results suggest that cod are capable of adaptive change in morphological features in response to changing environmental conditions. Finally, it has been demonstrated that the performance of farmed cod in Ireland, prior to selective breeding, is as good as that found in the wild Celtic Sea stock

The Development of Farmed Cod in Ireland

This study is interlinked with the work programme of the EIROCD project. Utilising historical data and empirical experimental approaches, various aspects of development, growth and phenotypic plasticity of North Atlantic cod, particularly the Celtic Sea stock, were examined. An examination of the wild stocks around Ireland revealed differences in population dynamics. The Celtic Sea stock had the highest growth rate of all Irish stocks considered, which prompted its\u27 use as the base population for the development of the national broodstock and breeding programme (EIRCOD). The growth performance of farmed Irish cod was confirmed and benchmarked. Although there was a clear need for the improvement of our larval rearing strategy, growth was remarkably consistent across all year classes. Previously established growth models for more northerly populations were found to be useful within certain constraints for predicting growth of cod under Irish conditions. Comparative modelling of growth in different countries revealed a competitive advantage to Irish cod farmed during the first and second years. The effects of temperature on egg development as well as larval and juvenile growth were examined. Optimum temperatures for growth of Celtic Sea juveniles have been established and are remarkably similar to those estimated for more northerly stocks; however, actual growth rates were lower than those predicted from models. Body shape variation in the head and shoulder region was examined and has the potential to easily discriminate between wild and farmed cod populations. Phenotypic plasticity in body shape was also explored and results suggest that cod are capable of adaptive change in morphological features in response to changing environmental conditions. Finally, it has been demonstrated that the performance of farmed cod in Ireland, prior to selective breeding, is as good as that found in the wild Celtic Sea stock

Barriers in European spiny lobster ( Palinurus elephas ) aquaculture: What we know so far?

Palinurids, also known as spiny lobsters, are high-value seafood, which is economically important for many European and Asian seafood trades. However, the reduction of wild European spiny lobster populations produces a need for developing alternative renewable strategies to meet current and future demands. Aquaculture of spiny lobsters has the potential to become of major economic importance in the coming years with growing markets in Asia, Europe, and America, with Palinurus elephas being a promising candidate species for use in the commercial culture and stock enhancement of natural fisheries. This is due to its shorter larval periods and rapid growth to the critical puerulus stage compared with other spiny lobster species. While we have a basic understanding of the lifecycle and biology of P. elephas, much of this is based on work undertaken on similar species globally. There are many gaps in our knowledge that need to be addressed to make its aquaculture viable with appropriate feeds being an immediate issue as well as many other husbandry-related factors. Previous studies act as a platform providing a baseline for further research and highlighting constraints. Developments in the use of P. elephas are promising due to realistically bridgeable knowledge gaps, the likelihood of producing sustainable food and the high commercial value of spiny lobsters. This review identifies our present state of knowledge and outlines the scope for further research and necessary technological developments to make it a viable contribution towards crustacean aquaculture in Europe

Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet

It is difficult to disentangle the many variables (e.g. internal or external cues and random events) that shape the microbiota in the gastrointestinal tract of any living species. Ecological assembly processes applied to microbial communities can elucidate these drivers. In our study, farmed Atlantic cod (Gadus morhua) were fed a diet of 10% macroalgae supplement (Ulva rigida [ULVA] or Ascophyllum nodosum [ASCO] or a non-supplemented control diet [CTRL]) over 12 weeks. We determined the influence of ecological assembly processes using a suite of null-modelling tools. We observed dissimilarity in the abundance of common OTUs over time, which was driven by deterministic assembly. The CTRL samples showed selection as a critical assembly process. While dispersal limitation was a driver of the gut microbiome for fish fed the macroalgae supplemented diet at Week 12 (i.e., ASCO and ULVA). Fish from the ASCO grouping diverged into ASCO_N (normal) and ASCO_LG (lower growth), where ASCO_LG individuals found the diet unpalatable. The recruitment of new taxa overtime was altered in the ASCO_LG fish, with the gut microbiome showing phylogenetic underdispersion (nepotistic species recruitment). Finally, the gut microbiome (CTRL and ULVA) showed increasing robustness to taxonomic disturbance over time and lower functional redundancy. This study advances our understanding of the ecological assembly and succession in the hindgut of juvenile Atlantic cod across dietary treatments. Understanding the processes driving ecological assembly in the gut microbiome, in fish research specifically, could allow us to manipulate the microbiome for improved health or resilience to disease for improved aquaculture welfare and production