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Abstract A major expense in the operation of bivalve nurseries is the culture of high‐quality live microalgae feeds, and efforts to develop effective alternative feeds have had limited success. Juvenile bivalves are known to be able to absorb dissolved nutrients, but this ability has received minimal attention as a route for supplementary feeding. This study assessed the capacity of juvenile green‐lipped mussels (GLMs) (Perna canaliculus) to uptake and assimilate dissolved glucose at five experimental concentrations (i.e. 10 µg mL−1, 100 µg mL−1, 1 mg mL−1, 10 mg mL−1 and 30 mg mL−1) as a supplement to cultured microalgae. Growth and survival of the mussels were measured over 3 weeks. Although all glucose concentrations improved the performance of mussel spat compared to the control, the best performing was a concentration of 1 mg mL−1 of dissolved glucose which enhanced daily spat growth 2.7 times that of the control live microalgal diet without glucose. Survival was high (i.e. >95%) for all treatments except for the highest experimental concentration of glucose, for which a concentration of 30 mg mL−1 resulted in mean mortality of 24%. Mussel spat supplemented with dissolved glucose accumulated up to 30% greater lipid and improved the carbohydrate content per mg g−1 of ash‐free dry weight as much as 3.5 times compared to those in the control treatment, indicating that they were in greater nutritional condition. This demonstration that dissolved glucose can be used to fuel growth by GLM spat at concentrations as low as 10 µg mL−1 suggests that other soluble nutrients may also act as a supplemental feed for cultured juvenile molluscs. Dissolved nutrients have the potential to improve the performance of spat in nursery systems while simultaneously reducing the reliance of cultured microalgae as a sole feed input.

Abstract Dynamic models of sugar kelp (Saccharina latissima) growth are used to estimate the production potential of seaweed aquaculture in many regions around the world. These models do not currently account for the existence of S. latissima ecotypes that are adapted to regional environmental conditions, particularly temperature. We tested the hypothesis that recalibrating the temperature parameters of a dynamic energy budget model using literature data for S. latissima from regions with a similar climate to the region of interest would result in more accurate predictions than using a general species‐wide temperature response curve. Calibrating the model using data from warm regions significantly improved model accuracy for kelp cultivation at the southern end of the species range (Rhode Island, USA) in cases where the original parameters underestimated growth but resulted in drastic overestimates when heavy frond erosion occurred. In Trømso, Norway, a cold parameterization produced extremely accurate predictions: the model predicted a final frond length of 88.2 cm, compared with the observed length of 87.5 (±4.70) cm. Our results demonstrate that recalibrating temperature response curves allows one model to be applied to kelp aquaculture in different regions, an important step toward the prediction of S. latissima productivity over large areas.

ABSTRACT Salmonid aquaculture, a major component of the Northern European, North American, and Chilean coastal economies, is under threat from challenges to gill health, many of which originate from plankton communities. A first step toward mitigating losses is to characterize the biological drivers of poor gill health. Numerous planktonic taxa have been implicated, including toxic and siliceous microalgae, hydrozoans, and scyphozoans; however, rigorous longitudinal surveys of plankton diversity and gill health have been lacking. In the current study, we present and assess an exhaustive identification approach combining both morphological and molecular methods together with robust statistical models to identify the planktonic drivers of proliferative gill disease (PGD) and fish mortality. We undertook longitudinal evaluation at two marine aquaculture facilities on the west coast of Scotland using daily data collected during the 2021 growing season (March–October). Examining these two different sites, one sheltered and one exposed to the open sea, we identified potentially new, important, and unexpected planktonic drivers of PGD and mortality (e.g., doliolids and appendicularians) and confirmed the significance of some established threats (e.g., hydrozoans and diatoms). We also explored delayed or “lagged” effects of plankton abundances on gill health and undertook a comparison of environmental DNA (eDNA) metabarcoding and microscopy in their ability to identify and quantify planktonic species. Our data highlight the diversity of planktonic threats to salmonid aquaculture as well as the importance of using both molecular and morphological approaches to detect these. There is now an urgent need to expand systematic longitudinal molecular and morphological approaches across multiple sites and over multiple years. The resultant catalogue of main biological drivers will enable early warning systems, new treatments, and, ultimately, a sustainable platform for future salmonid aquaculture in the marine environment.

Abstract Sentiment analysis, a form of data analytics, utilises information from online discussions, reviews, and social media posts to assess consumer sentiments. This study utilised data collected from social media using online listening procedures to assess online sentiments on oysters from January 2019 through December 2022. The analysis utilises machine learning algorithms to extract consumer sentiments, opinions, and demands from online chatter from different online domains. The online sentiments are determined as positive, negative, or neutral based on their word choice, tone, and context. The information provided gives insights into perception, which is valuable information for oyster producers, seafood industry stakeholders, and marketers to identify consumer preferences and formulate appropriate strategies accordingly. The results suggest that while farmed oysters are gaining popularity, there are still some concerns and criticisms around the industry. Positive words associated with mentions of oysters in general include ‘great’, ‘love’, ‘delicious’, ‘enjoyed’, and ‘oyster bar’, while negative words associated with oysters include ‘water’, ‘raw oyster’, ‘bad’, and ‘not eat’. The overall percentage net sentiment associated with all oysters in the United States is positive at 63%. The net sentiment associated with wild oysters is positive, at 51%, and that of farmed oysters is 58%. The oyster industry could invest more in public education, sustainability, and water‐cleaning initiatives to improve its image. Utilising social media to monitor and shape public perception can help the industry address concerns and enhance oyster‐related sentiments, offering valuable insights for marketing and sales strategies.

Abstract The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices. In a commercial setting, we explore the genetic structure of growth characteristics, measure genotype–environment interactions (GxE) in salmon smolts, and examine genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net‐pens and RAS. After an 8‐week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re‐ranking for whole‐body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented.

Abstract The European Commission requested scientific and technical assistance in the preparation of a EU‐wide baseline survey of antimicrobial resistance (AMR) in bacteria from aquaculture animals. It is recommended that the survey would aim at estimating the occurrence of AMR in Aeromonas spp. isolated from Atlantic Salmon (Salmo salar), European seabass (Dicentrarchus labrax) and trout (Salmo trutta, Salvelinus fontinalis, Oncorhynchus mykiss) intended to consumption, at harvesting (at farm/slaughter), at the EU level and in addition, at estimating the occurrence and diversity of AMR of Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Vibrio parahaemolyticus and Vibrio alginolyticus in blue mussel (Mytilus edulis) and Mediterranean mussel (Mytilus galloprovincialis) from production areas and at dispatch centres at the EU level. These technical specifications define the target populations, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic analysis of some of the bacteria targeted) and the data reporting requirements. The data to be reported by the EU Member States to support this baseline survey are presented in three data models. The results of the survey should be reported using the EFSA reporting system.

Abstract DNA cytosine methylation is an important epigenetic mechanism in genomic DNA. In most land plants, it is absent in the chloroplast DNA. We detected methylation in the chloroplast DNA of the kelp Saccharina latissima, a non‐model macroalgal species of high ecological and economic importance. Since the functional role of the chloroplast methylome is yet largely unknown, this fundamental research assessed the chloroplast DNA cytosine methylation in wild and laboratory raised kelp from different climatic origins (High‐Arctic at 79° N, and temperate at 54° N), and in laboratory samples from these origins raised at different temperatures (5, 10 and 15°C). Results suggest genome‐wide differences in methylated sites and methylation level between the origins, while rearing temperature had only weak effects on the chloroplast methylome. Our findings point at the importance of matching conditions to origin in restoration and cultivation processes to be valid even on plastid level.

Abstract Selective breeding for production traits has yielded relatively rapid successes with high‐fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1–17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild − wild]

Abstract Microalgae offer a sustainable source of omega − 3 fatty acids that can replace fish oil in aquafeeds, but the nutritional benefits are not always clear, particularly when microalgae are used as complete oil replacements in starter feeds. We compared the survival, growth, omega − 3 deposition and composition of the gut microbiota of juvenile mixed‐sex Nile tilapia (Oreochromis niloticus) that had been fed over a 3‐month period on six isonitrogenous, isolipidic and isocaloric aquafeeds that varied only on the contribution of fish oil, soya oil and microalgae (Schizochytrium) oil as lipid sources. Survival was not affected by diet, but fish fed a diet where the entire oil component (5%) was replaced by microalgae oil grew twice as fast as fish fed plant oil or a mixture of plant and fish oil. Dietary omega − 3 content was strongly correlated with omega − 3 deposition in the fish fillet. Complete replacement of fish oil by plant oil caused a significant decrease in the abundance of Peptostreptococcaceae and an increase in the abundance of Aeromonadaceae which is often associated with an inflammatory response in the fish gut. In contrast, when fish and soya oil in the reference diet were replaced by 100% microalgae oil, an increase in Mycobacteriaceae was observed. Our study indicates that Schizochytrium oil can be used to improve the growth of Nile tilapia and increase its omega − 3 content without any of the detrimental effects on the gut microbiome typically associated with some plant oil replacements.

Abstract This study focuses on the structural integrity analyses of a submersible cage with dimensions of 20 m in diameter and 10 m depth under extreme oceanographic conditions, including current speed of 0.5 and 1 m/s, combined with waves ranging from 2 to 5 m in height and a period of 7 s. Employing a dynamic simulation model based on finite elements, The study examines the stresses in the cage's pipes, as well as the tension in the bridle lines and mooring lines. Results indicate that submerging the cage leads to a reduction in peak tensions, with mooring lines experiencing a decrease of up to 32% and bridle lines experiencing a decrease of up to 59%. Furthermore, the stresses in the pipes exhibit a significant decline of up to 71.4%. These findings demonstrate that the submersible cage, when submerged, significantly reduces peak stresses, thereby decreasing the risk of structural loss or damage when the system is submerged.

Abstract Regulatory changes to the Lacey Act and recent petitions to add aquaculture species in trade to the list of injurious wildlife could lead to prohibitions of interstate movement of live aquatic organisms with the potential for unintended, negative economic consequences. In this analysis, the economic impact of the potential federal prohibition of interstate transport of seven aquaculture species (blue catfish, tilapia, red swamp crawfish, grass carp, koi, guppy, and goldfish) currently in trade was assessed. Total economic impact was estimated to be $452 million (USD) annually, with a loss of 4819 jobs and a loss of $35 million in tax revenue. Effects could potentially occur on the largest sectors of U.S. aquaculture in as many as 80% of U.S. states and result in negative economic effects on as much as 21% of U.S. aquaculture farms.

Abstract Aquaculture is one of the most prominent sectors of Bangladesh regarding nutrition, livelihood, and revenues. Although this nation has made promising improvements in aquaculture, several existing and imminent challenges can disrupt further development. Until now, no studies have extensively reviewed the existing aquaculture practices of this nation. Thus, this article elucidates the prospects, production, and problems of common aquaculture practices for the establishment of sustainable aquaculture in Bangladesh. The culture units are mainly natural bodies of water including earthen ponds, seasonal floodplains, baor, and gher. Although pond farming is the oldest and most dominant practice in this nation, the use of pen and cage cultures has also been intensified in the last decade. Regarding farmed fish species, indigenous major carps, exotic carps, tilapia, pangas catfish, and climbing perch are the major runners. Among crustaceans, giant freshwater prawns and tiger shrimp are the leading farmed species. Mud crab, biofloc, and seaweed farming are a growing focus that can evolve as artisanal and commercial‐scale farming practices in the near future. Major challenges that are potent enough to impede the establishment of viable aquaculture practices in Bangladesh are inadequate seed production, disease outbreaks, climate change, mediocre management practices, and limited mariculture propagations.

Abstract In the United States, catfish are primarily farmed in earthen ponds, resulting in an aquatic environment influenced both by management practices and natural ecological processes. Profiling pond water microbiota can be useful for understanding what conditions may lead to microbial communities associated with production issues and could inform management practices. The aim of this study was to identify appropriate methods for bacterial community profiling of catfish pond water with nanopore sequencing of the 16S rRNA gene. To this end, two forward primers, two reverse primers, and three different polymerase chain reaction (PCR) cycle numbers were tested on a mock community consisting of aquaculture‐relevant bacteria. The optimized protocol was applied to water samples obtained from three experimental catfish ponds sampled in May, June, August, and September 2020. Applying these methods to pond samples allowed for the identification of 1488 genera, primarily within four dominating phyla: Actinobacteriota, Bacteroidota, Cyanobacteria, and Firmicutes. High variation was observed between individual ponds and sampling timepoints; only 18 of the 1488 genera were found in relative abundances ≥1% in all ponds from at least one sampling point. Despite this variation, consistent results could be observed. Samples obtained from the month of September had the highest number of observed genera, and samples from June had the lowest. Overall, these data demonstrated individual ponds represent distinct microcosms composed of unique bacterial communities, although this pond effect was secondary to the influence of sampling month on pond community composition.

Abstract Pacific bluefin tuna (PBT), Thunnus orientalis, is one of the most important species for aquaculture worldwide. For the conservation of this species and sustainable development of the tuna farming industry, production based on closed‐cycle aquaculture should be promoted. In this study, to develop an efficient method for transporting PBT eggs, we simulated egg transportation to optimize stocking density and shipping duration, which are the two variables critical to the transportation procedure of PBT. Based on the findings of this study, we concluded that PBT eggs should be transported at a density of 1 × 104 eggs/L within 12 h in the field. Furthermore, we showed that collisions between eggs during transportation negatively affected the normal hatching rates of eggs, and polyethylene glycol (PEG) treatment (at 1000 μg/mL for 12 h) could reduce such damage. Our results suggest that PEG treatment is a practical approach that contributes to the stable transportation of PBT eggs, particularly in cases where the effects of physical shock damage is considerably increased.

Abstract Evaluation of viability of new marine species in aquaculture systems is important to reduce negative social and environmental externalities, offering sustainable options for supply to fish markets. The objective was to describe the performance indicators of late juvenile yellowtail snapper (243.2 ± 57.1 mean weight of total fish) in an experimental recirculating aquaculture system (RAS) system supplied by seawater to determine its pre‐feasibility. Two densities were stocked, D1: 10 fish/tank (2.6 kg/m3, mean weight 258.3 ± 57 g) and D2: 20 fish/tank (4.7 kg/m3, mean weight 235.6 ± 55.9 g). Fish were fed to satiety with an extruded diet containing 46% crude protein and 12% crude lipid. After 238 days, survival rate was 93% for both densities, and mean weight and biomass were 534.5 ± 19.4 g and 5.7 kg/m3 for D1, and 606.9 ± 34.5 g and 10 kg/m3 for D2. Final feed conversion rate (3.13 for D1 and 3.03 for D2) did not differ significantly between densities. The exponents (b) of the length–weight relationship calculated for D1 (3.15) versus D2 (3.10) and condition factor (2.12 ± 0.07 for D1, and 2.03 ± 0.04 for D2) demonstrated a higher condition factor than those of their wild counterparts. This study is one of the few reports on this species’ performance in late juvenile stage in RAS.

Abstract Although small‐scale fisheries and aquaculture provide opportunities to increase fish yield to supplement rural food and income, they remain undeveloped in Ghana. To contribute towards the development of the sectors, this study sought to assess the biology and ecology of Oreochromis niloticus and Sarotherodon melanotheron in the Brimsu reservoir to provide the requisite information for their management. From the results, mean temperature, dissolved oxygen, pH and transparency of the reservoir were 30.03 ± 0.27°C, 3.78 ± 0.38 mg/L, 8.30 ± 0.21 and 69.79 ± 1.76 cm, respectively. S. melanotheron had a sex ratio of 1:1.36; with mean condition factors of 2.177 ± 0.089 and 2.06 ± 0.029 (p = 0.08) for males and females, respectively. The sex ratio of O. niloticus was 1.45: 1; with mean condition factors of 2.208 ± 0.012 and 2.257 ± 0.014 (p = 0.07) for males and females, respectively. Both species exhibited positive allometric growth with no significant differences between the condition factors for males and females. In addition, there was no significant difference between the sex ratios for S. melanotheron but the number of males of O. niloticus was significantly higher than the females (p ˂ 0.05). Size at sexual maturity (Lm), form factor (a3.0), growth coefficient (K), asymptotic length (L∞) and natural mortality (M) of S. melanotheron were 18.00 cm, 0.020, 0.42 year−1, 30.32 cm and 0.64 year−1, respectively. For O. niloticus Lm, a3.0, K, L∞ and M were 18.57 cm, 0.0223, 0.26 year−1, 38.42 cm and 0.41 year−1, respectively. However, the catch per unit effort for O. niloticus was higher than that of S. melanotheron throughout the study period. The conditions of the reservoir were favourable for the growth of these cichlids. It is recommended that measures should be put in place for the sustainable management and exploitation of fish stocks.

Abstract Fish aquaculture potentially affects the local ecosystem through feed (leftovers) and feces. However, evaluation of its impacts on biodiversity, especially those of mobile organisms such as fish, is not straightforward. Here, we report a case study in which environmental DNA (eDNA) metabarcoding with MiFish universal primers for the 12S rRNA region of fish is used to detect and assess the impact of aquaculture on local fish communities. In Shizugawa Bay, Minamisanriku Town, Miyagi Prefecture, Japan, Oncorhynchus kisutch (coho salmon) is aquacultured in sea cages from November to July, but is absent from August to October. We conducted eDNA surveys in June, August, October, and December 2021 of water at depths of 5 m and 1 m above the bottom obtained from two sites, one approximately 100 m and the other approximately 2500 m from the nearest aquaculture site. The total number of operational taxonomic units (OTUs) detected was 122, with a maximum of 50 and a minimum of 10. With distance‐based redundancy analysis (dbRDA) and PERMANOVA applied to the eDNA‐based community compositional data, we detected a significant effect of the presence of O. kisutch aquaculture on fish biodiversity. The generalized linear model (GLM) applied to each detected OTUs indicated that the aquaculture was associated positively with Leucopsarion petersii (ice goby), and Oncorhynchus spp. and negatively with Chaenogobius annularis (forktongue goby). Environmental DNA metabarcoding surveys, combined with multivariate statics, are a promising tool to identify the dimension of biodiversity that human activity affects and would serve as a basic survey for sustainable use of the sea.

Abstract Surveillance data published since 2010, although limited, showed that there is no evidence of zoonotic parasite infection in market quality Atlantic salmon, marine rainbow trout, gilthead seabream, turbot, meagre, Atlantic halibut, common carp and European catfish. No studies were found for greater amberjack, brown trout, African catfish, European eel and pikeperch. Anisakis pegreffii, A. simplex (s. s.) and Cryptocotyle lingua were found in European seabass, Atlantic bluefin tuna and/or cod, and Pseudamphistomum truncatum and Paracoenogonimus ovatus in tench, produced in open offshore cages or flow‐through ponds or tanks. It is almost certain that fish produced in closed recirculating aquaculture systems (RAS) or flow‐through facilities with filtered water intake and exclusively fed heat‐treated feed are free of zoonotic parasites. Since the last EFSA opinion, the UV‐press and artificial digestion methods have been developed into ISO standards to detect parasites in fish, while new UV‐scanning, optical, molecular and OMICs technologies and methodologies have been developed for the detection, visualisation, isolation and/or identification of zoonotic parasites in fish. Freezing and heating continue to be the most efficient methods to kill parasites in fishery products. High‐pressure processing may be suitable for some specific products. Pulsed electric field is a promising technology although further development is needed. Ultrasound treatments were not effective. Traditional dry salting of anchovies successfully inactivated Anisakis. Studies on other traditional processes – air‐drying and double salting (brine salting plus dry salting) – suggest that anisakids are successfully inactivated, but more data covering these and other parasites in more fish species and products is required to determine if these processes are always effective. Marinade combinations with anchovies have not effectively inactivated anisakids. Natural products, essential oils and plant extracts, may kill parasites but safety and organoleptic data are lacking. Advanced processing techniques for intelligent gutting and trimming are being developed to remove parasites from fish.

Abstract Elucidating the effects of domesticated organisms escaping into the natural environment represents a topic of importance in both evolutionary and conservation biology. However, when excluding the abundant data on salmonids, there is a lack of knowledge on this topic for marine fish aquaculture, which continues to expand globally. In order to bridge this empirical gap, we investigated a suspected escape of sexually mature domesticated Atlantic cod from a commercial marine fish farm in northern Norway. This involved genotyping samples of fish from cages on the farm, putatively identified escapees and wild cod captured in the region and samples of recently spawned eggs collected in the sea. Genetic analyses confirmed a farmed ancestry of the suspected escapees, and significantly, 27% of the sampled cod eggs. Furthermore, statistical analyses revealed a strong reduction in genetic variation in all samples of the farmed cod, including low effective population size and high degree of siblingship. These results thus document the escape of sexually mature adult cod and the release of fertilized domesticated cod eggs into the natural environment. Although it is possible that some of the mature escapees spawned post‐escape, the fact that only a single egg of potential hybrid farmed × wild origin was identified, together with the high number of mature cod in the farm, points to within cage spawning as the primary source of these eggs. This suggestion is supported by oceanic particle‐drift modelling, verifying that transport of eggs between the farm and the egg sampling locations was plausible. This study represents a rare documentation of interaction between domesticated and wild populations for a marine fish, pointing towards potential impacts on the local wild population.

Abstract Crustacean feeding morphology and postprandial nutrient processing is a highly size‐selective procedure. The digestive system of lobsters is predicated on grinding feed to a fine particle size before digestion. Therefore, fine pregrinding of raw materials may bypass the need for extensive grinding in the proventriculus and expedite digestive and absorptive processes. Panulirus ornatus juveniles (N = 56) were allocated to four feed groups (n = 14). Groups A, B and C were fed nutritionally identical feeds featuring raw materials ground to 1000 µm (Feed A), 500 µm (Feed B) and 200 µm (Feed C) while the fourth group (Group S) acted as a 24‐h nonfeeding baseline control group. Sequential postprandial haemolymph extractions were performed at 0.5, 1, 1.5, 2, 3.5, 5.5 and 24 h across treatment groups. Haemolymph samples were assessed and analysed for brix (%), total proteins (g L–1), glucose (mmol L–1) and cholesterol (mmol L–1). Brix was found to have significant positive correlations with all the haemolymph biochemical properties while no significant correlations were identified between individual lobster size and haemolymph properties. Analysis of deviance applied to mixed effects models did not identify significant differences in haemolymph properties across feed groups. Trends identified here are indicative of diurnal rhythm patterns, likely orchestrated by the release of the crustacean hyperglycaemic hormone (CHH) when anticipating a meal. Additionally, the use of brix values, may not be optimal for identifying postprandial trends, yet could remain a valid indicator of longer‐term nutritional status.

Abstract The presence of wild fish in and around aquaculture habitats is often assumed a response to food resources within these habitats, either from input feed, the presence of cultured species, and/or the assemblage of biofouling that naturally colonises aquaculture structures. The nutritional quality of the food resources consumed by wild fish in aquaculture habitats is also important in determining their nutritional condition and subsequent productivity. Few studies have investigated the nutritional quality of prey in aquaculture habitats, and these have mostly focused on fed aquaculture by tracking manufactured fish pellets into the diets of wild fish. However, in non‐fed aquaculture, the assemblage of cultured and biofouling species may also provide a nutritional benefit to fish feeding in these habitats. The Australasian snapper, Chrysophrys auratus, are commonly present as adults within coastal mussel farms in New Zealand and tend to become a resident species. This study investigated the nutritional quality of the gut contents of snapper in soft‐sediment habitats within and outside of New Zealand green‐lipped mussel farms. Total lipid, protein, carbohydrate and total calorific content were measured from the gut contents of snapper sampled from mussel farm and natural (i.e. control) habitats. Snapper in mussel farms had double the dietary intake of lipid (16% vs. 8%) from consuming lipid‐rich bivalves and barnacles which are in abundance in mussel farms. Higher lipid intake can contribute to improved nutritional condition, reproduction and growth in snapper. However, the higher dietary lipid intake of snapper in mussel farms did not increase their overall body condition (i.e. Fulton condition index). This may be due to the coarse nature of this measure, or the use of the additional lipid in more rapid somatic growth or reproductive outputs, possibilities that warrant examination through further research. Overall, this study shows for the first time the potential ecosystem benefits of shellfish aquaculture in provisioning nutritionally valuable prey for coastal fish populations.

Abstract The increase in hard artificial structures in the marine environment is contributing to ocean sprawl. As well as adding hard structure to the seabed, mussel aquaculture adds rope droppers and anchor lines to the water column, where such structure would otherwise be absent. This paper aims to monitor the effects of mussel headlines on the pelagic fish community over time, as well as to investigate whether there is an interaction between the age of cultivated mussels with the number of epibiota species and the abundance of pelagic fishes. Two surveys were carried out: a time series monitoring survey to assess whether the mussel headlines change the surrounding fish species relative to control areas over time, and a fish aggregation device effect survey to investigate whether older and larger mussels support greater abundances of pelagic fishes and epibiota. The most abundant fish species was Atlantic horse mackerel, Trachurus trachurus, with significantly greater numbers recorded around ropes growing older mussels. Results from the surveys show that the physical farm infrastructure has provided a substrate for colonisation by a variety of epibiota: A total of 21 species were recorded growing on the mussel ropes. Furthermore, the older and larger the mussels become, the greater the numbers of epibiota taxa that can colonise, coupled with a greater abundance of pelagic fish recorded around the ropes. The sustainable development of offshore Blue Industries is essential to produce renewable resources. This study brings essential evidence for marine managers and regulators that offshore mussel farming can provide benefits for pelagic and benthic species of both conservation and commercial importance while producing sustainable protein to feed a growing population.

Abstract The major carp Rohu (Labeo rohita) is a prime freshwater aquaculture species across the Indian subcontinent that faces various production‐related issues associated with water quality parameters. The present study examined the effects of three different doses of NH3 (T1 = 1 mg/L, T2 = 2 mg/L and T3 = 3 mg/L) on cellular (gill ultrastructure), physiological (growth and oxygen consumption rate), biochemical (blood cell counts, blood cortisol and glucose levels) and genetic (expression of five genes involved in growth, immunity and metabolism) traits of Rohu. The experimental ammonia dose significantly affected the tested biological parameters (p

Abstract Studies investigating microplastics (MPs) in marine species have been published over recent decades, including studies on depuration efficacy on aquaculture products. This preliminary study investigates the depuration efficacy of MPs in two commercial oyster species from Ireland. The innovative aspects are the sampling size (n = 50 per species) and the experiment duration (up to 96 h). The case study organisms are the Pacific oyster (Magallana gigas) and the European flat oyster (Ostrea edulis). Prior to depuration, the mean MP concentration on M. gigas edible tissue was 0.6 MP g−1 while for O. edulis was 0.4 MP g−1. Significant differences in mean MP concentrations were identified after 96‐h for M. gigas 0.2 MP g−1 (p = 0.014) and O. edulis, 0.1 MP g−1 (p = 0.003). Additionally, no significant correlation was established between MP concentrations and edible tissue weight. Polymer identification revealed that 51.6% were fibers of natural origin. Preliminary results show that increasing depuration times beyond 72‐h can significantly reduce MPs in selected oyster species, which is what is being recommended with this baseline study. Further investigation on commercial conditions at adequate depuration facilities is required. Given the relevance of low‐trophic aquaculture species for local economies, this preliminary study provides important baseline information for stakeholders.

Abstract The red snapper (Lutjanus campechanus) has one of the most valued fisheries in the southeastern United States and has been largely studied for its aquaculture potential with varied results that revealed production challenges. This study focused on addressing challenges in larval rearing and juvenile production of this species. Broodstock fish were acclimated in a 60 m3 tank equipped with recirculating aquaculture system (RAS) and temperature control. After 1 year in captivity, fish volitionally spawned and larval rearing trials were conducted in replicated flow‐through seawater tanks ranging from 0.4 to 2.4 m3, at a temperature range of 24–26°C. Enriched s‐strain rotifers, Brachionus rotundiformis (lorica length of 100–210 μm), were used for first feeding. Enriched Artemia sp. were gradually introduced after 18 days post hatch (DPH). The survival rate before metamorphosis (12 DPH) averaged 66.09 ± 0.08%. Survival rate from yolk‐sac larvae to post‐metamorphic early juvenile averaged 4.43 ± 0.01%. At 40 DPH, early red snapper juveniles averaged 0.35 ± 0.02 g in weight and 28.83 ± 0.60 mm in standard length. A total of 31,849 fully weaned juveniles were harvested. This study demonstrates that small strain rotifers can be used exclusively as first feeding prey organism for red snapper larvae, representing a significant advancement for red snapper juvenile production.

Abstract We investigated the possible conditions to cryopreserve six marine microalgae that are frequently used in Taiwanese aquaculture: Amphora exigua, Isochrysis galbana, Nannochloropsis oculata, Seminavis gracilenta, Skeletonema costatum, and Tetraselmis elliptica. The approaches for microalgae cryopreservation with cooling from room temperature to −40°C, a rate of approximately −1°C/min, and final storage in liquid nitrogen at −196°C are described. We subsequently assessed the viability of cultures of these microalgae after thawing in a 40°C water bath and evaluated the relative survival rates to compare the suitability of cryoprotectant and cryopreservation conditions. We used four concentrations (5%, 10%, 15%, and 20%) of five cryoprotectants, dimethyl sulfoxide (DMSO), methanol (MeOH), glycerine (GLY), ethylene glycol (EG), and propylene glycol (PG), and found that the individual microalgae required distinct cryoprotectant and concentrations. Only S. costatum was not viable after cryopreservation under any of the conditions tested. Relative survival rates were 87.6% (A. exigua), 70.73% (I. galbana), 87.48% (N. oculata), 91.0% (S. gracilenta), and 57.8% (T. elliptica), when using 20% DMSO, 15% Gly, 20% EG, 20% DMSO, and 20% PG as cryoprotectants, respectively. In summary, we established suitable conditions to cryopreserve these five microalgae that will facilitate conserving their genetic diversity.

Abstract Bolbophorus damnificus is a digenetic trematode causing significant economic losses within the United States commercial catfish industry. The indirect life cycle is complex, requiring piscivorous birds, aquatic snails, and fish to complete. With federal protections on many piscivorous birds and no FDA‐approved therapeutic treatment for trematode infections in fish, management within the catfish industry is primarily limited to controlling the snail host. Planorbella trivolvis and Biomphalaria havanensis are snails commonly found in commercial catfish ponds and known to transmit B. damnificus. This study evaluated a low‐cost snail trap prototype for monitoring populations of these snails in efforts to better inform treatment regimes. Snail traps were deployed into ponds on a commercial catfish farm and checked weekly throughout the production season. All snails were identified and counted to evaluate trap efficacy. Traps captured significantly more snails in foodfish ponds than in fingerling ponds; however, this trend was not present in monthly box samples. B. havanensis was rarely collected and was only found consistently within one pond, while P. trivolvis was routinely collected from all ponds, although abundance varied widely among ponds. Snail traps could be a useful, low‐cost method to monitor snail populations within ponds and better inform control treatments.

Abstract Fish aquaculture has become the fastest growing sector in global food production. Thus, ensuring the sustainability of aquaculture practices is of the utmost importance. Studies in higher vertebrates (i.e. mammals) have demonstrated the role of the host microbiome in physiological processes from nutrient acquisition to pathogen protection. Therefore, analysis of fish microbiomes is an important factor to consider with regard to overall animal health and welfare. Rainbow trout (Oncorhynchus mykiss) are an economically valued fish cultured worldwide. Several studies have identified microbial constituents inhabiting the intestinal tract of rainbow trout. To better elucidate some of the core constituents of the rainbow trout intestinal microbiome, this systematic literature review analysed the relative abundance results from 25 articles published on the rainbow trout intestinal microbiome from 2017 to 2021. Bacteria classified within the phyla Firmicutes and Proteobacteria were observed in every study. At the family level, Lactobacillaceae was consistently observed. Additionally, bacteria in the Actinobacteria, Bacteroides, and Tenericutes phyla were identified in at least 50% of the studies. Interestingly, Mycoplasma spp. were occasionally the most dominant organisms present in the microbiome. Overall, the results here identify bacteria that are commonly found members of the rainbow trout intestinal microbiome.

Abstract Bivalve mollusc meat—that from mussels, clams, and oysters—offers a highly sustainable and nutritious alternative to meat from other shellfish, fish, or livestock. However, bivalves are an unpopular mass market food relative to these other meat items, limiting our ability to reap potential environmental and health benefits. Hence, this study aimed to assess current barriers to and drivers for bivalve consumption and investigated whether offering bivalves in a highly transformed (i.e., more processed) product format might help to drive consumption. The United Kingdom was used as a case study, and the study was performed via an online survey. Nutrition and quality of ingredients were key drivers, and price and convenience key barriers to bivalve consumption, with views on taste/smell/texture mixed. The more regularly individuals consumed meat, the more willing they were to try bivalves, and those who thought bivalves were healthier or more environmentally friendly than livestock were more likely to substitute bivalves for meat. Importantly, individuals were more willing to substitute highly transformed than minimally transformed (i.e., unprocessed) meats for bivalves. They were also willing to pay more for highly transformed bivalves than any other highly transformed meat product. We suggest that greater publicity regarding the health and environmental benefits of bivalve meat, and industry engagement to develop and pilot a greater range of appealing, affordable, and convenient bivalve products, are key actions that can help drive growth in the bivalve sector for planetary benefit.

Abstract Resistance toward the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (Lepeophtheirus salmonis salmonis), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000–2002 “pre‐resistance”) and contemporary (2014–2017 “post‐resistance”) samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as “neutral” controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000–2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes, respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual. No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and that long‐distance dispersion of resistance is rapid due to high level of genetic connectivity that is observed in this species.

Abstract Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole‐genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (FST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle‐related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP‐EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.

Abstract The aim of this work was to run an economic assessment of investment in automatic feeding systems for grow‐out farms of different sizes producing European sea bass in the Mediterranean Sea. For this, we have used an economic model to simulate the annual income statement of a typical farm with different production volumes: a small‐sized farm with a production of 413 tons/year, a medium‐sized farm of 1122 tons/year, and a large‐sized farm of 2539 tons/year. With the values obtained in the simulation, we have carried out partial budget and investment analyses to estimate the economic value of this investment decision. To complement our economic assessment, a sensitivity analysis has also been run to include risk in the investment decision. Our findings show that the implementation of automatic feeding systems in sea bass grow‐out farms would be a good economic decision, regardless of the farm size, since there are technological options suitable for different farm sizes and capital investment capacities. Consequently, innovation and investment in feeding management should not be impeded or limited by the farm size.

Abstract Wild fish utilise aquaculture habitats for shelter and/or food resources. It is often assumed that fish respond to feed input, the abundance of the farmed species or the associated assemblage of biofouling which naturally colonises the structural habitats. However, few studies have directly analysed the composition of the diet of fish within aquaculture habitats, and of these most have focused on fed finfish aquaculture. Snapper are commonly present as adults within coastal mussel farms and tend to become a resident species of these farms. Therefore, they are a suitable case study species for exploring differences in diet between natural and aquaculture habitats. This study investigated the gut contents of snapper in soft‐sediment habitats within and outside of New Zealand green‐lipped mussel farms. Visual gut analysis and DNA metabarcoding methods were used to provide complementary analyses on the composition of gut contents between the mussel farm and natural (i.e., control) sites. Snapper within mussel farms were consistently found to have consumed different prey groups compared to the control snapper. Prey groups identified from mussel farm snapper gut contents could be directly linked to species commonly present in the farms, that is cultured green‐lipped mussels, blue mussels and barnacle biofouling. There was good alignment between the visual gut and genetic analyses for the key species identified. Overall, the results show that the highly abundant prey groups consumed by snapper in mussel farm habitats are likely to be beneficial to the snapper population, reducing foraging effort and potentially supplying more nutritious prey. These findings provide evidence towards the supporting services of mussel farm habitats through the provision of food resources.

Abstract The growth of aquaculture sector in Kenya has been anchored on farmed Nile tilapia Oreochromis niloticus. Different strains of the species exist in Kenya with unknown quality due to lack of stock improvement programmes coupled by variations in breeding and management practices in different hatcheries. The seeds supplied to farmers have not exhibited good performance and resilience to changing climate. There is need to validate the quality of strains supplied to fish farmers in Kenya. This study sought to compare the growth performance of three strains of farmed Nile tilapia; Sagana strain (SAG‐F8) produced through selective breeding, super YY strain (KAM‐YY) from Kamuthanga fish farm and the local strain (LOC‐T) obtained from Siaya County. The fish were stocked in fertilised earthen ponds measuring 300 m2 in triplicates at 3 fish/m2. The fish were fed on 35% crude protein diet for 180 days at Bukani Aquapark located in Busia County, Kenya. There was no significant difference in mean weight gain (MWG) between SAG‐F8 and LOC‐T strain exhibiting 159.786 ± 6.76 g and 158.623 ± 4.67 g, respectively. However, under similar conditions, the KAM‐YY strain had a significantly lower MWG (131.74 ± 4.75 g) compared to the two strains. Food conversion ratio (FCR), specific growth rate (SGR) did not demonstrate any significant difference among the different strains. The body protein content in the SAG‐F8 fish strain was higher (65.40 ± 0.20%) followed by LOC‐T strain (61.23 ± 2.34%) and lastly KAM‐YY strain had the lowest (60.37 ± 0.89%). In this study, the impact of genetic improvement has been demonstrated to influence growth and feed efficiency as well as body composition. These improved strains will substantially increase fish production and productivity, hence, a positive impact on the fish farmers' livelihoods when supplied to the farmers and seed multipliers.

Abstract Ongoing global changes are expected to affect the worldwide production of many fisheries and aquaculture systems. Because invertebrates represent a relevant industry, it is crucial to anticipate challenges that are resulting from the current environmental alterations. In this review, we rely on the estimated physiological limits of six commercialised species of sea urchins (Loxechinus albus, Mesocentrotus franciscanus, Paracentrotus lividus, Strongylocentrotus droebachiensis, Strongylocentrotus intermedius and Strongylocentrotus purpuratus) to define the vulnerability (or resilience) of their populations facing ocean warming and acidification (OW&A). Considering that coastal systems do not change uniformly and that the populations’ response to stressors varies depending on their origin, we investigate the effects of OW&A by including studies that estimate future environmental mutations within their distribution areas. Cross‐referencing 79 studies, we find that several sea urchin populations are potentially vulnerable to the predicted OW&A as environmental conditions in certain regions are expected to shift beyond their estimated physiological limit of tolerance. Specifically, while upper thermal thresholds seem to be respected for L. albus along the SW American coast, M. franciscanus and S. purpuratus southern populations appear to be vulnerable in NW America. Moreover, as a result of the strong warming expected in the Arctic and sub‐Arctic regions, the local productivity of S. droebachiensis is also potentially largely affected. Finally, populations of S. intermedius and P. lividus found in northern Japan and eastern Mediterranean respectively, are supposed to decline due to large environmental changes brought about by OW&A. This review highlights the status and the potential of local adaptation of a number of sea urchin populations in response to changing environmental conditions, revealing possible future challenges for various local fishing industries.

Abstract Evaluating salmon hatchery supplementation programs requires assessing not only program objectives but identifying potential risks to wild populations as well. Such evaluations can be hampered by difficulty in distinguishing between hatchery‐ and wild‐born returning adults. Here, we conducted 3 years (2011–2013) of experimental hatchery supplementation of sockeye salmon in Auke Lake, Juneau, Alaska where a permanent weir allows sampling and genotyping of every returning adult (2008–2019). We identified both hatchery‐ and wild‐born returning adults with parentage assignment, quantified the productivity (adult offspring/spawner) of hatchery spawners relative to that of wild spawners, and compared run timing, age, and size at age between hatchery‐ and wild‐born adults. Hatchery‐spawning females produced from approximately six to 50 times more returning adults than did naturally spawning females. Supplementation had no discernable effect on run timing and limited consequences for size at age, but we observed a distinct shift to younger age at maturity in the hatchery‐born individuals in all three brood years. The shift appeared to be driven by hatchery‐born fish being more likely to emigrate after one, rather than two, years in the lake but the cause is unknown. In cases when spawning or incubation habitat is limiting sockeye salmon production, hatchery supplementation can be effective for enhancing the number of returning adult fish but not without the risk of phenotypic change in the recipient population, which can be an undesired outcome of hatchery supplementation. This study adds to a growing body of evidence suggesting that phenotypic change within a single generation of captive spawning might be widespread in salmon hatchery programs.

Abstract Rainbow trout (Oncorhynchus mykiss) is among the most widely translocated fish species in the world. The current study evaluated the spawning interactions between naturalized and wild rainbow trout from two high‐altitude second‐order streams, in Kenya. Data on total length, weight, condition factor, fecundity, fertilization, egg diameter and fry survival were collected on spawning rainbow trout between March and December 2021. Length–weight relationship showed parabolic equations as W = 0.0144L2.900, W = 0.0069L3.0285 and W = 0.00027L3.175 for wild fish stock, hatchery‐reared and wild × hatchery‐reared rainbow trout, respectively. Total fecundity differed significantly among the hatchery‐reared, wild fish and the cross of the two (p

Abstract Freshwater aquaculture can have negative impacts on chemical, physical and biological water quality. To contextualise the impact that these activities may have, a case study site in Ireland was monitored for 1 year. The study aims were to investigate the impact of freshwater aquaculture on water quality (biological, physical, and chemical) and the degree of the impact and recovery in water quality, within 1000 m downstream of a salmon smolt hatchery. The hatchery was monitored, at four locations (upstream, 10, 100, and 1,000 m downstream of the discharge point). Data on macroinvertebrate, macrophyte, hydromorphology and chemical characteristics were collected. Results for the physical monitoring indicated no significant changes in hydromorphology between up and downstream sites. Chemical water quality did decrease downstream in terms of nitrogen (N) and phosphorus (P). The greatest concentrations in N and P were found at 1000 m though it is likely additional contributions from agriculture impacted this site. Dissolved oxygen was steady throughout the monitoring campaign with a 13% variance between upstream and downstream locations. Changes in biological indices were statistically significant for taxa at all downstream sites. There were positive trends which indicated a degree of recovery in biotic indices.

Abstract Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium‐density 60 K SNP‐array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole‐genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.

Abstract Compared with other aquaculture issues, attention to human and social dimensions is lagging behind. Sectoral development, policy, and programmatic factors have created inequities and sub‐optimal social outcomes, which are jeopardizing the broader contribution the sector could make to human well‐being. Human rights in aquaculture are at the core of this article, which argues that aquaculture development, as a major economic and food producing sector, needs to be about human development. The article reviews: the application of human rights in aquaculture, and the related right to decent work; the notions of justice and equity including the idea of Blue Justice and its relevance in aquaculture; and ethics and social license to operate with the challenges that business ethics and public acceptance pose to the sector. It also reviews how these issues affect people: women, along with slow progress in gender equality in the sector; youth and their engagement in aquaculture, while noting that ‘youth’ does not equate to “jobs” and requires the lifting of many more societal hurdles for their full participation in the sector; indigenous people and local ecological knowledge—a precious asset for future aquaculture as well as the survival and enhancement of the cultural value of aquaculture; and people with disabilities and other minorities who have yet to become fully visible and accounted for in aquaculture development. Redressing human and social issues in aquaculture, and placing people at the center of aquaculture development requires a fundamental change from business as usual. To humanize aquaculture development, a renewed human relationship with aquaculture is proposed, which is founded on recognizing substantive equality and agency, embracing intersectionality, that is, the multiple social dimensions of identity and interaction, and valuing cross‐disciplinary knowledge systems. It would be implemented through new, inclusive, business models, social provisioning approaches, and procedural justice and governance mechanisms for overcoming inequalities. Public, private, and non‐state actors will need to be involved, inclusive of small‐scale farmers, women, youth, people with disabilities, and indigenous communities as key groups. Six key messages conclude the article.

Abstract Effective genetic management of the ~700 aquatic species cultured globally should be addressed for aquaculture to make a significant contribution towards meeting the UN's Sustainable Development Goals. This article aims to identify the current status and challenges relating to the management of farmed aquatic genetic resources (AqGR) and to make recommendations for its improvement. The lack of information on the genetic status of many farmed species is a critical constraint and there is a need to characterize these resources and develop information systems and tools to monitor farmed types used for aquaculture and their wild counterparts. Risk assessment is needed when introducing non‐native species and when managing native species including developed farmed types; policies need to be improved and increased awareness and training in risk assessment are required. To increase the uptake of selective breeding in aquaculture, there is a need for the development and adoption of better and more sustainable business models, including long‐term financial instruments such as public–private partnerships. Training and technology transfer between aquaculture sectors can have significant impact, especially for lower‐value species. Nationally and globally applicable instruments and regulations need to be adapted to AqGR and become operational and be effectively implemented by countries.

Abstract Good water quality in recirculating aquaculture systems (RAS) is crucial for ensuring the successful growth and survival of reared species. So far, there are no regulations for which parameters should be measured in RAS, and each farmer decides which parameters to follow. Traditionally, water quality parameters have been measured at certain intervals with handheld sensors and laboratory analyses, which can be labour intensive. Currently, a variety of sensors and monitoring equipment is available, even for the real‐time monitoring of water quality parameters. Internet of Things‐based systems and artificial intelligence can be applied for the monitoring purposes which allows real‐time measurements and warnings of critical situations. However, many of the modern systems need competent users and require regular maintenance and calibration. Changes in water quality also induces changes in fish behaviour, such as swimming activity, depth, acceleration and water quality can be assessed also based on these changes. In this review, water quality parameters, variety of sensors and monitoring technologies have been summarised to provide an overview of the current monitoring systems for water quality. Additionally, analytical methods for more advanced analyses have also been briefly summarised. Although there are several advanced options available for monitoring the basic water quality parameters, real‐time measurements of more advanced parameters still required require further development.

Abstract Indigenous knowledge is critical in the conservation of wild fish genetic resources and consequent development of fish seed for improved aquaculture production. Local fisher communities rely on aquatic resources mainly for livelihood and subsistence and have therefore come up with systems to manage these resources for sustainable use. This study aimed at identifying the role of indigenous people's knowledge in fish conservation as a way of improving aquaculture, with a specific focus on the conservation of aquaculture fish species in Kenya. Data was collected from individual fisherfolk through semi‐structured questionnaires and field observations. Pearson's chi‐square test was performed on variables that were predicted to influence indigenous knowledge. The chi‐square tests revealed a significant relationship between age and indigenous knowledge (χ2 = 15.153, p = 0.004). Results also revealed a significant relationship between an individual's years of residence in the area and indigenous knowledge (χ2 = 17.767, p = 0.003). It was found that the indigenous people use various concepts and strategies for fish conservation and fish production. From the findings of the study, it is recommended that scientists and policy actors should adopt the indigenous people's knowledge as a source of baseline information for fisheries and aquaculture research, and as additional or alternative strategies for the management of fish genetic resources.

Abstract Aquaculture in Taiwan is characterised by high breeding densities of up to five times higher than the normal breeding densities. Pollution in the breeding environment and its adjacent waters have exacerbated the occurrence of disease outbreaks in fish, shrimp and shellfish, which greatly impacted the economy. Therefore, the parameters pertaining to water quality status, especially dissolved oxygen are particularly important. In addition to the rising cost of labour, land, infrastructure and other materials, the capital needed to engage in aquaculture has risen, whereas the profits have decreased. This limits the growth of aquaculture and fisheries. To overcome this problem, it is essential to shift towards efficient and ecologically precise smart aquaculture. The application of industrialised and smart systems in the vertical diffusion and in‐depth integration of aquaculture facilitates decision‐making, improves the level of intelligence in breeding, and enhance aquaculture's contribution to Taiwan's economy.

Abstract Most kelp species are of high ecological and economic importance worldwide, but are highly susceptible to rising ocean temperatures due to their sessile lifestyle. Due to interference with reproduction, development and growth, natural kelp forests have vanished in multiple regions after extreme summer heat waves. Furthermore, increasing temperatures are likely to decrease biomass production and, thus, reduce production security of farmed kelp. Epigenetic variation, and cytosine methylation as a heritable epigenetic trait, is a rapid means of acclimation and adaptation to environmental conditions, including temperature. While the first methylome of brown macroalgae has been recently described in the kelp Saccharina japonica, its functional relevance and contribution to environmental acclimation is currently unknown. The main objective of our study was to identify the importance of the methylome in the congener kelp species Saccharina latissima for temperature acclimation. Our study is the first to compare DNA methylation in kelp between wild populations of different latitudinal origin, and the first to investigate the effect of cultivation and rearing temperature on genome‐wide cytosine methylation. Origin appears to determine many traits in kelp, but it is unknown to what extent the effects of thermal acclimation may be overruled by lab‐related acclimation. Our results suggest that seaweed hatchery conditions have strong effects on the methylome and, thus, putatively on the epigenetically controlled characteristics of young kelp sporophytes. However, culture origin could best explain epigenetic differences in our samples suggesting that epigenetic mechanisms contribute to local adaptation of eco‐phenotypes. Our study is a first step to understand whether DNA methylation marks (via their effect on gene regulation) may be used as biological regulators to enhance production security and kelp restoration success under rising temperatures, and highlights the importance to match hatchery conditions to origin.

Abstract The European flat oyster (Ostrea edulis L.) is a bivalve naturally distributed across Europe, which was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite a growing interest in genetic applications to support population management and aquaculture, a reference genome for this species is lacking to date. Here, we report a chromosome‐level assembly and annotation for the European Flat oyster genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation and RNA sequencing. A contig assembly (N50: 2.38 Mb) was scaffolded into the expected karyotype of 10 pseudochromosomes. The final assembly is 935.13 Mb, with a scaffold‐N50 of 95.56 Mb, with a predicted repeat landscape dominated by unclassified elements specific to O. edulis. The assembly was verified for accuracy and completeness using multiple approaches, including a novel linkage map built with ddRAD‐Seq technology, comprising 4016 SNPs from four full‐sib families (eight parents and 163 F1 offspring). Annotation of the genome integrating multitissue transcriptome data, comparative protein evidence and ab‐initio gene prediction identified 35,699 protein‐coding genes. Chromosome‐level synteny was demonstrated against multiple high‐quality bivalve genome assemblies, including an O. edulis genome generated independently for a French O. edulis individual. Comparative genomics was used to characterize gene family expansions during Ostrea evolution that potentially facilitated adaptation. This new reference genome for European flat oyster will enable high‐resolution genomics in support of conservation and aquaculture initiatives, and improves our understanding of bivalve genome evolution.

Abstract The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome‐level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi‐C sequencing. The finished assembly is 887.2 Mb with a scaffold‐N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein‐coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.

Abstract This volume of Evolutionary Applications sees the publication of two genomes for the European native flat oyster Ostrea edulis, a species of significant evolutionary, ecological and commercial value. Each is a highly contiguous chromosome‐level assembly from individuals of different genetic backgrounds, which have been benchmarked against one another. This situation has resulted from the serendipitous discovery that two independent research groups were both deep into the process of building, annotating and investigating separately produced assemblies. Due to constraints with funder requirements and the need to recognize early career researchers for their work, alongside the technical challenge of integrating assemblies from two very different genomes, there was limited capacity to merge the sequences into one publication at the stage of discovery. This issue is likely to become very common over the next few years until the technologies for working with multiple genomes at once, for example, graph genomes, become commonplace in nonmodel species. Consequently, both of our teams have decided to collaborate rather than compete, recognizing the benefit to copublishing two separate genome resources for the research community, each with distinct scientific investigations, and working collaboratively to benchmark the assemblies.

Abstract Water spinach, Ipomoea aquatica, is a common semi‐aquatic weed that is used as an ingredient in fish feed to support its growth and defence system. The present study aimed to identify and quantify bioactive polyphenols through HPLC‐DAD (High Performance Liquid Chromatograpgy ‐ Diode Array Detector) analysis and to evaluate the antioxidant activity of the aquatic weed I. aquatica available in Bangladesh. Different bioactive phytochemical groups were qualitatively appraised in crude ethanol extract, aqueous and n‐hexane fractions of water spinach. The total polyphenol and flavonoids content were spectrophotometrically discerned using Folin–Chiocalteu and aluminium chloride, respectively. Bioactive compounds of the extracts were identified by the HPLC‐DAD method. Furthermore, 2,2‐diphenyl‐1‐picryldydrazyl (DPPH) and hydroxyl‐radical scavenging and reducing power assays were followed to assess antioxidant activity. The experimental extracts confirmed the presence of different bioactive phytochemical groups. The crude extract contained the highest content of both polyphenol (94.93 mg gallic acid (GA) equivalent per gram dry extract) and flavonoids (373.30 mg quercetin equivalent per gram dry extract). Besides, in HPLC (High Performance Liquid Chromatogrphy) analysis, ellagic acid was present at the highest concentration both in crude (337.26 mg/100 g dry extract) and aqueous (280.06 mg/100 g dry extract) extracts. However, the n‐hexane fraction only contained GA (13.91 mg/100 g dry extract). Also, some other bioactive polyphenols were identified in crude and aqueous fraction extracts. The crude extract revealed superior antioxidant activity in DPPH (Half maximal inhibitory Concentration (IC50) = 149.30 ± 1.43 μg/ml) and hydroxyl radical scavenging assays (IC50 = 327.257 ± 1.36 μg/ml) in comparison to the rest of the extracts. Furthermore, all of the extracts showed dose‐dependent reducing power activity. HPLC‐identified bioactive compounds may be responsible for antioxidant activity. Because of these identified compounds, I. aquatica holds the potential feed ingredient in aquaculture.