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The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea.

The effect of a pollutant on the base of the food web can have knock-on effects for trophic structure and ecosystem functioning. In this study we assess the effect of microplastic exposure on juveniles of a planktivorous fish (Acanthochromis polyacanthus), a species that is widespread and abundant on Indo-Pacific coral reefs. Under five different plastic concentration treatments, with plastics the same size as the natural food particles (mean 2mm diameter), there was no significant effect of plastic exposure on fish growth, body condition or behaviour. The amount of plastics found in the gastro-intestinal (GI) tract was low, with a range of one to eight particles remaining in the gut of individual fish at the end of a 6-week plastic-exposure period, suggesting that these fish are able to detect and avoid ingesting microplastics in this size range. However, in a second experiment the number of plastics in the GI tract vastly increased when plastic particle size was reduced to approximately one quarter the size of the food particles, with a maximum of 2102 small (< 300μm diameter) particles present in the gut of individual fish after a 1-week plastic exposure period. Under conditions where food was replaced by plastic, there was a negative effect on the growth and body condition of the fish. These results suggest plastics could become more of a problem as they break up into smaller size classes, and that environmental changes that lead to a decrease in plankton concentrations combined with microplastic presence is likely have a greater influence on fish populations than microplastic presence alone.

Ectopic lipid accumulation has been observed in fish fed a high-lipid diet. However, no information is available on the mechanism by which dietary lipid levels comprehensively regulate lipid transport, uptake, synthesis and catabolism in fish. Therefore, the present study aimed to gain further insight into how dietary lipids affect lipid deposition in the liver of large yellow croaker(Larimichthys crocea). Fish (150.00±4.95 g) were fed a diet with a low (6%), moderate (12%, the control diet) or high (18%) crude lipid content for 10 weeks. Growth performance, plasma biochemical indexes, lipid contents and gene expression related to lipid deposition, including lipoprotein assembly and clearance, fatty acid uptake and triacylglycerol synthesis and catabolism, were assessed. Growth performance was not significantly affected. However, the hepato-somatic and viscera-somatic indexes as well as plasma triacylglycerol, non-esterified fatty acids and LDL-cholesterol levels were significantly increased in fish fed the high-lipid diet. In the livers of fish fed the high-lipid diet, the expression of genes related to lipoprotein clearance (LDLR) and fatty acid uptake (FABP11) was significantly up-regulated, whereas the expression of genes involved in lipoprotein assembly (apoB100), triacylglycerol synthesis and catabolism (DGAT2, CPT I) was significantly down-regulated compared with fish fed the control diet, and hepatic lipid deposition increased. In fish fed the low-lipid diet, the expression of genes associated with lipoprotein assembly and clearance (apoB100, LDLR, LRP-1), fatty acid uptake (CD36, FATP1, FABP3) and triacylglycerol synthesis (FAS) was significantly increased, whereas the expression of triacylglycerol catabolism related genes (ATGL, CPT I) was reduced compared with fish fed the control diet. However, hepatic lipid content in fish fed the low-lipid diet decreased mainly due to low dietary lipid intake. In summary, findings of this study provide molecular insight into the role of lipid deposition in the liver in response to different dietary lipid contents.

The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes.

The greater amberjack Seriola dumerili is a large teleost fish with rapid growth and excellent flesh quality, whose domestication represents an ambitious challenge for aquaculture. The occurrence of reproductive dysfunctions in greater amberjack reared in captivity was investigated by comparing reproductive development of wild and captive-reared individuals. Wild and captive-reared breeders were sampled in the Mediterranean Sea during three different phases of the reproductive cycle: early gametogenesis (EARLY, late April-early May), advanced gametogenesis (ADVANCED, late May-early June) and spawning (SPAWNING, late June-July). Fish reproductive state was evaluated using the gonado-somatic index (GSI), histological analysis of the gonads and determination of sex steroid levels in the plasma, and correlated with leptin expression in the liver and gonad biochemical composition. The GSI and sex steroid levels were lower in captive-reared than in wild fish. During the ADVANCED period, when the wild greater amberjack breeders were already in spawning condition, ovaries of captive-reared breeders showed extensive atresia of late vitellogenic oocytes and spermatogenic activity ceased in the testes of half of the examined males. During the SPAWNING period, all captive-reared fish had regressed gonads, while wild breeders still displayed reproductive activity. Liver leptin expression and gonad proximate composition of wild and captive greater amberjack were similar. However, the gonads of captive-reared fish showed different total polar lipid contents, as well as specific lipid classes and fatty acid profiles with respect to wild individuals. This study underlines the need for an improvement in rearing technology for this species, which should include minimum handling during the reproductive season and the formulation of a specific diet to overcome the observed gonadal decrements of phospholipids, DHA (22:6n-3) and ARA (20:4n-6), compared to wild breeders.

Mandarin fish (Siniperca chuatsi) is an important cultured fish in East Asia that shows sexual size dimorphism (SSD), with females growing faster than males when reaching marketable size. However, the regulatory mechanism of SSD is not clear. To characterize SSD of mandarin fish and its association with gh/igf1/igfbp-5 expression, gonadal developmental atlas of the females and the males were described, and growth parameters and serum levels of E2 and T, as well as the relative expression levels of gh, igf1, and igfbp-5a/b mRNAs, were determined. The results showed that the logistic growth equation of body mass and total length of female and male were W(♀) = 667.57/(1 + e^(4.19 − 1.24*t)), W(♂) = 582.71/(1 + e^(4.07 − 1.27*t)), L(♀) = 31.47/(1 + e^1.95 − 1.08*t)), L(♂) = 26.20/(1 + e^(2.56 − 1.5*t)). The month of inflection points for body mass for females and males were 3.37 mph and 3.20 mph, respectively, when the body mass were 333.79 g and 291.36 g. The month of inflection points for total length growth were 1.80 mph and 1.70 mph, respectively, when the total length were 18.52 cm and 16.28 cm. At 1.5–2.0 mph, SSD was not clearly demonstrated. At 3.0 mph, the body mass of the females was significantly higher than that of the males (P < 0.05), Serum E2, brain gh, and liver igf1 expression of the females was significantly higher than that of the males (P < 0.05); T content of the males was significantly higher than that of the females (P < 0.05). At 4.0 months of age, the body mass of the females was highly significantly higher than that of the males (P < 0.01), Serum E2, brain gh, and liver igf1 expression of the females was highly significantly higher than that of the males (P < 0.05); T content of the males was significantly higher than that of the females (P < 0.05). With the continuous development of gonads, muscle and liver igfbp-5a and -5b expression generally tend to increase in females and males, while igfbp-5a showed a gradual increasing trend, and igfbp-5b expression showed a trend of decreasing and then increasing. Male igfbp-5a/b expression was significantly higher than female at the age of 3.0–4.0 months (P < 0.05). This work verified that the females had faster growth rate since 3.0 mph compared to the males, which may be related to higher E2 levels in females leading to higher igf1 level, through inhibition of igfbp-5a/b expression.

Using fish meal (FM) as the predominant protein source in fish feeds for aquaculture operations poses considerable economic costs and ecological concerns. Therefore, feed nutritionists are looking for inexpensive and supply-stable alternatives to FM in fish feeds. This study aimed to assess the impacts of substituting FM with corn protein concentrate (CPC) in the diet of rockfish ( Sebastes schlegeli ) on the growth, feed availability, biochemical composition, and blood chemistry. Five hundred forty juvenile rockfish were uniformly dispersed into 18 tanks. Six isonitrogenous and isolipidic diets were prepared. The control (Con) diet contained 55% FM. The CPC 10 , CPC 20 , CPC 30 , CPC 40 , and CPC 50 diets were prepared to substitute 10%, 20%, 30%, 40%, and 50% FM with CPC in the Con diet, respectively. Triplicate groups of rockfish received the experimental diets twice daily for 56 days. The weight gain (WG) of rockfish fed the Con and CPC 10 diets was significantly ( P < 0.001) greater than that of rockfish fed all other diets. Rockfish fed the Con and CPC 10 diets exhibited a comparable specific growth rate (SGR) to that of fish fed the CPC 20 diet. Feed consumption (FC) of rockfish fed the Con diet was significantly ( P < 0.0001) higher than that of rockfish fed all other diets, with the exception of the CPC 10 diet. Rockfish fed the Con, CPC 10 , and CPC 20 diets exhibited significantly ( P < 0.0001) higher feed efficiency (FE) compared to rockfish fed all other diets. Protein efficiency ratio of rockfish fed the Con diet was significantly ( P < 0.001) higher than that of fish fed the CPC 40 and CPC 50 diets. Rockfish fed the Con diet exhibited significantly ( P < 0.01) greater protein retention than rockfish fed the CPC 50 diet. However, the biological indices except for hepatosomatic index, biochemical composition, and blood chemistry of rockfish were not significantly ( P > 0.05) influenced by FM substitution with CPC in diets. Conclusively, up to 10% and 20% of FM can be substituted with CPC in the rockfish diet without significantly lowering WG and FC, and SGR and FE, respectively.

An 8-week feeding trial was conducted to evaluate the effects of dietary lipid sources on growth performance, fatty acid composition, rate-limiting enzyme activities and gene expression related to lipid metabolism in large yellow croaker (Larmichthys crocea). Five iso-nitrogenous and iso-lipidic experimental diets were formulated to contain different lipid sources, such as fish oil (FO), soybean oil (SO), linseed oil (LO), rapeseed oil (RO) and peanut oil (PO), respectively. Triplicate groups of 50 fish (initial weight 13.77±0.07g) were stocked in 15 floating net cages (1.5m×1.5m×2.0m). Fish fed the diets containing RO and LO had lower weight gain and specific growth rates than those fed the FO, SO and PO diets. Survival, feed efficiency, protein efficiency ratio, hepatosomatic index, viscerasomatic index and condition factor were not significantly affected by different dietary lipid sources. Fish fed the diet containing FO had higher lipid content in whole body compared with the other groups, whereas fish fed the SO diet had the lowest muscle lipid content. Fatty acid profiles of muscle and liver reflected the fatty acid composition of the diets. Plasma glucose, triglyceride, and the enzymatic activity of aspartate aminotransferase and alanine aminotransferase were significantly influenced by different dietary lipid sources, while total protein, cholesterol, superoxide dismutase or malondialdehyde in plasma were not affected by the different dietary lipid sources. Fish fed the LO diet had lower adipose triglyceride lipase and fatty acid synthase activities in liver than those fed the diets containing FO and RO, while the LO diet resulted in the highest hepatic carnitine palmitoultransferase-1 activity. Hepatic gene relative expression of adipose triglyceride lipase and carnitine palmitoyltransferase-1 in fish fed PO diet was significantly higher than all other groups, whereas fish fed the SO and LO diets had lower relative expression levels of lipoprotein lipase than the other groups. The highest relative expression levels of fatty acid synthase and acyl-CoA diacylglycerol acyltransferase-2 were observed in the FO group, while the highest relative expression of glucose 6-phosphate dehydrogenase occurred in fish fed the FO and RO diets. In summary, based on the growth performance, FO and SO appear to be suitable lipid sources for large yellow croaker, with the findings of this study also providing a molecular insight into the role of lipid metabolic mechanism in response to different dietary lipid sources.

The search for suitable fish meal replacements in aqua-diets is a salient agenda in the constant effort of making aquaculture practices more sustainable. In this study, we tested four customised diets composed by systematic inclusion of pre-selected fish meal substitutes, lupin kernel meal, BSF meal, TH and PBM on growth, metabolism, cytokine profile, gut morphology and microbiota of juvenile Lates calcarifer . Five isoproteic and isoenergetic diets were prepared viz. FM100 as a control (without fish meal substitute), while FM75, FM50, FM25 and FM0 indicates replacement of fish meal (FM) at 25%, 50%, 75%, and 100%, respectively by a mixture of four different pre-selected non-fish meal (NFM) ingredients. Fish fed FM100, FM75, FM50, FM25 exhibited consistent growth and haematological response, while the fish fed no fishmeal (FM0) showed significant decline in final body weight (FBW) and specific growth rate (SGR). The poor growth performance was correlated with a decrease in villous width, microvilli height and goblet cells density. A significant shift in abundance profile of Psychrobacter in the gut microbial profile of fish fed FM50 was noticed compared to fish fed FM100. The results of qRT-PCR showed up-regulated expression of innate immune responsive genes in the FM50 group. The adverse impacts on growth performance and gut health of fish fed FM0 suggest that the complete substitution of fishmeal is not advisable and the inclusion range of these alternatives should be decided for a species only after examining their effect on maximal physiological performance.

The average surface pH of the ocean is dropping at a rapid rate due to the dissolution of anthropogenic CO2, raising concerns for marine life. Additionally, some coastal areas periodically experience upwelling of CO2-enriched water with reduced pH. Previous research has demonstrated ocean acidification (OA)-induced changes in behavioural and sensory systems including olfaction, which is due to altered function of neural gamma-aminobutyric acid type A (GABAA) receptors. Here, we used a camera-based tracking software system to examine whether OA-dependent changes in GABAA receptors affect anxiety in juvenile Californian rockfish (Sebastes diploproa). Anxiety was estimated using behavioural tests that measure light/dark preference (scototaxis) and proximity to an object. After one week in OA conditions projected for the next century in the California shore (1125 ± 100 µatm, pH 7.75), anxiety was significantly increased relative to controls (483 ± 40 µatm CO2, pH 8.1). The GABAA-receptor agonist muscimol, but not the antagonist gabazine, caused a significant increase in anxiety consistent with altered Cl− flux in OA-exposed fish. OA-exposed fish remained more anxious even after 7 days back in control seawater; however, they resumed their normal behaviour by day 12. These results show that OA could severely alter rockfish behaviour; however, this effect is reversible.