A 20-year retrospective review of global aquaculture

Uncovering the spatial characteristics of global net anthropogenic nitrogen input at high resolution and across 1.42 million lake basins

Global Net Anthropogenic Nitrogen Input (NANI) at high resolution is crucial for assessing the impact of human activities on aquatic environments. Insufficient global high-resolution data sources and methods have hindered the effective examination of the global characteristics and driving forces of NANI. This study presents a general framework for calculating global NANI, providing estimates at a 5-arc-minute resolution and over 1.42 million lake basins in 2015. The results highlight the region near the Tropic of Cancer as a concentration area for high NANI and an inflection point for latitude-based accumulation variation. It also emphasizes the uneven distribution of NANI among continents, with Asia and Africa having the highest proportions, yet their high and low values are notably lower than those of Europe and South America. A similar pattern is observed in global lakes, where Asia has the smallest quantity and volume, but the highest NANI intensity. In contrast, North America and Europe have larger quantities and volumes but the lowest NANI intensity. The global distribution characteristics reveal a clustering pattern in high and low values, with 1.25 % of the area having a sum of NANI exceeding 20 %. The uncertainty analysis regarding model parameters indicates that continents with the highest NANI do not always exhibit the highest uncertainty. These results bridge the gap between global nitrogen sustainable management and anthropogenic nitrogen input. They support research on spatiotemporal changes and controlling factors of global river nutrient loads, as well as the impact of climatic factors on basin nitrogen loss and its variability.

Restorative function of offshore longline mussel farms with ecological benefits for commercial crustacean species

Offshore ocean aquaculture is expanding globally to meet the growing demand for sustainable food production. At the United Kingdom's largest longline mussel farm, we assessed the potential for the farm to improve the habitat suitability for commercially important crustaceans. Modelled distribution patterns (GAM & GLM) predicted the low complexity seabed beneath the mussel farm was 34-94 % less suitable for European lobster (Homarus gammarus) and brown crab (Cancer pagurus) than nearby rocky reefs. The mussel farm operations, however, contributed large amounts of living mussels and shell material to the seabed. Acoustic telemetry revealed that H.gammarus remained within the farm for between 2 and 283 days using both the farm anchors and areas of seabed dominated by fallen mussels for refuge. In contrast, C. pagurus movements showed no affinity to either the farm infrastructure or benthic habitat under the farm. Stable isotope analysis indicated a high dietary niche overlap in C. pagurus and H. gammarus (67.8 and 84.6 %) between the mussel farm (mixed muddy sediment) and nearby rocky reef. Our mixed-methods suggest that the mussel farm augments structural complexity on the seabed providing refuge and similar feeding opportunities for lobster and crab as their typical habitat on rocky reefs. Longline mussel farms can deliver profound biodiversity-positive effects through biogenic augmentation of degraded habitat for commercial species and potential for co-benefits to local fisheries.

Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture

Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 106 CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.

Shellfish polysaccharides: A comprehensive review of extraction, purification, structural characterization, and beneficial health effects

Global food systems are currently facing great challenges, such as food sources, food safety, and environmental crises. Alternative nutritional resources have been proposed as part of the solution to meeting future global food demand. In the natural resources, shellfish are the major component of global aquatic animals. Although most studies focus on the allergy, toxin, and contamination of shellfish, it is also a delicious food to the human diet rich in proteins, polysaccharides, minerals, and omega-3. Among the functional ingredients, shellfish polysaccharides possess nutritional and medicinal values that arouse the great interest of researchers. The selection of the extraction approach and the experimental condition are the key factors that influence the extraction efficiency of shellfish polysaccharides. Importantly, the purification of crude polysaccharides comprises the enrichment of shellfish polysaccharides and isolation of fractions, also resulting in various structural characteristics and physicochemical properties. Chemical modification is also an efficient method to further improve the biological activities of shellfish polysaccharides. This review summarizes the extraction, purification, structural characterization, and chemical modification methods for shellfish polysaccharides. Additionally, the beneficial health effects of shellfish polysaccharides are highlighted, with an emphasis on their potential mechanism. Finally, current challenges and perspectives on shellfish polysaccharides are also spotlighted.

Inclusion of oil from transgenic Camelina sativa in feed effectively supplies EPA and DHA to Atlantic salmon (Salmo salar) grown to market size in seawater pens

Atlantic salmon were fed either a diet reflecting current commercial feeds with added oil supplied by a blend of fish oil and rapeseed oil (COM), or a diet formulated with oil from transgenic Camelina sativa containing 20% EPA + DHA (TCO). Salmon were grown from smolt to market size (>3 kg) in sea pens under semi-commercial conditions. There were no differences in growth, feed efficiency or survival between fish fed the TCO or COM diets at the end of the trial. Levels of EPA + DHA in flesh of salmon fed TCO were significantly higher than in fish fed COM. A 140 g fillet from TCO-fed salmon delivered 2.3 g of EPA + DHA, 67% of the weekly requirement level recommended by many health agencies, and 1.5-fold more than the 1.5 g of EPA + DHA for COM-fed fish. Oil from transgenic Camelina supported growth and improved the nutritional quality of farmed salmon in terms of increased "omega-3" supply for human consumers.

c-Jun N-terminal kinase 1/P53 signaling mediates intrinsic apoptosis of largemouth bass (Micropterus salmoides) hepatocytes under heat stress

The increasing frequency of high-temperature extremes threatens largemouth bass Micropterus salmoides, a significant fish for freshwater ecosystems and aquaculture. Our previous studies at the transcript level suggested that heat stress induces hepatic apoptosis in largemouth bass. In the current study, we sought to validate these findings and further investigate the role of the c-Jun N-terminal kinase (JNK)/P53 signaling in hepatic apoptosis under heat stress. First, heat treatments were conducted in vivo and in vitro under different temperatures: 28 °C, 32 °C, and 37 °C. In primary hepatocytes subjected to heat treatment, cell viability was evaluated via the Cell Counting Kit-8, while mitochondrial membrane potential and nuclear morphology were assessed through JC-1 and Hoechst 33258 staining, respectively. We observed reductions in both cell viability and mitochondrial membrane potential (ΔΨm), along with alterations in nuclear morphology, in primary hepatocytes exposed to heat stress at temperatures of 32 °C and 37 °C. Quantitative real-time PCR revealed significant alterations in the expression profiles of intrinsic apoptosis-related genes within liver tissues under heat stress. Immunohistochemistry analysis revealed that JNK1 signaling increased as the temperature increased, JNK2 expression increased only at 37 °C, and JNK3 expression did not change with temperature. We speculate that JNK1 and JNK2 have pro- and anti-apoptotic effects, respectively. Western blot analysis conducted on cultured hepatocytes further validated these findings. JNK inhibition reduced hepatocyte apoptosis, improved nuclear morphology, and maintained ΔΨm even after 37 °C treatment. These results not only confirm that heat stress led to intrinsic apoptosis of hepatocytes but also indicated that JNK1 could mediate P53 expression and activate caspase-dependent intrinsic apoptosis in largemouth bass hepatocytes under such conditions. This study illuminates the physiological responses of largemouth bass to acute heat stress, offering valuable insights into the potential impacts of climate change on freshwater fishes and the sustainability of aquaculture.

The perfect match between macroalgae and eutectic solvents as a sustainable gateway to ready-to-use extracts towards a (blue + green) economy ─ A perspective review

The article discusses how aligning with the Sustainable Development Goals (SDGs) can foster a sustainable economy, mainly through the (green + blue) economy, which involves valorizing macroalgae to produce ready-to-use extracts. It focuses on the potential of eutectic solvents (commonly known as deep eutectic solvents - DES) as promising candidates for this purpose. Traditional methods for extracting bioactive compounds from macroalgae, which rely on organic solvents and aqueous buffers, often involve harsh conditions and extensive processing. These factors can lead to reduced extract quality and/or low yields. In contrast, if properly designed, DES presents a green and sustainable alternative. They offer advantages such as low volatility, adjustable polarity, and negligible toxicity, making them a more environmentally friendly and efficient option for extraction processes. They can be customized to enhance both biological and technological properties, resulting in extracts with unique characteristics such as increased antioxidant activity, antiproliferative and anti-inflammatory effects, as well as improving the viscoelasticity of polysaccharides (fucoidans, alginates, and κ-carrageenan) from macroalgae. In this sense, the tunable nature of DES enables the optimization of extraction conditions to maximize yield, purity, and bioactivity, making it a smart alternative for producing bio-based products. Despite limited literature on DES for this purpose, the article highlights their potential and outlines the main advantages and challenges needed for macroalgae valorization.

Global climate change impacts on the potential distribution of typical Trachinotus fishes and early warning assessment of invasions

Marine habitats and ecosystems are increasingly being impacted by global climate change and the global spread of captive breeding. In this study, we focused on five typical Trachinotus species (Trachinotus anak, Trachinotus blochii, Trachinotus mookalee, Trachinotus goreenisi, Trachinotus ovatus) as research subjects. We utilized species distribution models and ecological niche models to predict the present and future potential distribution of these species, as well as to assess ecological niche overlap and evaluate the early warning of invasion by Trachinotus species. T. ovatus stands out with its broad distribution range and high adaptability to different environments. It occupies 1.114% of medium-high suitable areas, spanning 100,147 km2. Our predictions also suggest that T. ovatus would undergo a significant expansion (approximately 55% of the total area) under both past and future environmental scenarios, demonstrating a higher tolerance and adaptability to changes in ambient temperatures. It can be discerned that T. ovatus exhibits strong environmental adaptability, which may potentially lead to biological invasion along the southeastern coast of China. The T. anak, on the other hand, showed a higher expansion trend under high carbon dioxide concentrations (RCP8.5), indicating a certain convergence with carbon dioxide concentration. Our models showed that under future climatic conditions, T. ovatus would become the dominant species, with increased competition with T. mookalee and decreased competition with T. goreenisi, T. mookalee, and T. anak. Based on our findings and the net-pen culture mode of T. ovatus, we identified the hotspot habitat of T. ovatus to be located in the Indo-Pacific convergence zone. However, there is a possibility of an expansion trend towards the southeast coast of China in the future. Therefore, it is crucial to provide an early warning for the potential biological invasion of T. ovatus.

Effects of stress-associated odor on ventilation rate and feeding performance in Nile tilapia

In this study, we described immediate/acute reactions to stress-related chemical cues (SC - Stress Cue) in fish. Specifically, we evaluated the effects of SC on ventilation rate (VR) and feeding behavior in Nile tilapia (Oreochromis niloticus), a highly relevant species for world aquaculture, therefore, to understand the diversity of stressful contexts and stress responses in this species have important practical applications (stress reduction). Stress cue was obtained from conspecifics exposed to a handling stressor. Stress was confirmed by measuring plasma cortisol levels. The responses to SC were contrasted to chemical control cues: a cue originated from non-stressed conspecifics and pure water (vehicle control). We observed that Nile tilapia exposed to SC had an increase in VR, but without effects on feeding behavior (feeding latency and ingestion). Thus, the SC is a stressor that induces readily stress response (VR increase), suggesting sympathetic activation, but did not change feeding performance. In practical terms, it is positive because although social propagation of stress via SC elicits a stress response, it did not harm appetite.

In vitro efficacy of aquaculture antimicrobials and genetic determinants of resistance in bacterial isolates from tropical aquaculture disease outbreaks

Understanding the efficacy of antimicrobials against pathogens from clinical samples is critical for their responsible use. The manuscript presents in vitro efficacy and antimicrobial resistance (AMR) genes in seven species of fish pathogens from the disease outbreaks of Indian aquaculture against oxytetracycline, florfenicol, oxolinic acid, and enrofloxacin. In vitro efficacy was evaluated by minimum inhibitory concentration and minimum bactericidal concentration. The gene-specific PCR screened AMR genes against quinolones (qnrA, qnrB, and qnrS) and tetracyclines (tetM, tetS, tetA, tetC, tetB, tetD, tetE, tetH, tetJ, tetG, and tetY). The results showed that Aeromonas veronii (45%) showed the maximum resistance phenotype, followed by Streptococcus agalactiae (40%), Photobacterium damselae (15%), Vibrio parahaemolyticus (10%), and Vibrio vulnificus (5%). There was no resistance among Vibrio harveyi and Vibrio alginolyticus against the tested antimicrobials. The positive association between tetA, tetB, tetC, tetM, or a combination of these genes to oxytetracycline resistance and qnrS to quinolone resistance indicated their potential in surveillance studies. The prevalence of resistance phenotypes (16.43%) and evaluated AMR genes (2.65%) against aquaculture antimicrobials was low. The resistance phenotype pattern abundance was 0.143. All the isolates showed susceptibility to florfenicol. The results help with the appropriate drug selection against each species in aquaculture practices.

Assessing the effect of therapeutic level of oxytetracycline dihydrate on pharmacokinetics and biosafety in Oncorhynchus mykiss (Walbaum, 1792)

The aim of the experiment was to investigate the pharmacokinetics of oxytetracycline dihydrate after a single oral administration of 80 mg kg-1 day-1 in rainbow trout and assess its biosafety at concentration of 80, 240, 400, and 800 mg kg-1 day-1 over 30 days, focusing on various aspects such as effective feed consumption, physiological responses, drug tolerance, and detection of low drug concentrations in rainbow trout. The pharmacokinetics study spanned a duration of 5 days, while the assessment of biosafety extended for a 30-day safety margin, followed by a subsequent 10-day residual analysis. Pharmacokinetic analysis revealed slow absorption with low-rate constant in tissues. Absorption rates vary among tissues, with the gill showing the highest rate (0.011 h-1) and plasma exhibiting the slowest (0.0002 h-1). According to pharmacokinetic analysis, the highest concentration, Cmax (µg kg-1) was observed in the kidney (9380 µg kg-1) and gill (8710 µg kg-1), and lowest in muscle (2460 µg kg-1). The time (Tmax) to reach peak concentration (Cmax) varied among tissues, ranging from 3 h in the gill to 32 h in the muscle, with 24 h in plasma, 32 h in the kidney, and 16 h in both the liver and skin. The liver and kidney had the highest area under the concentration-time curve (AUC(0-128)), indicating widespread drug distribution. Prolonged elimination occurred at varying rates across tissues, with the gill showing the highest rate. The study found that OTC concentrations exceeded the LOD and LOQ values. Biosafety evaluation showed effective feed consumption, physiological responses, and low drug concentrations in muscle at the recommended dosage of 80 mg kg-1 fish day-1.

Paleolimnological evidence for variable impacts of fish farms on the water quality of Scottish freshwater lochs

Since the 1980s, fish farming (aquaculture) has been an important contributor to Scotland's economy, but there are concerns that nutrient-rich food waste and excreta from these farms are causing eutrophication. Water quality monitoring preceding the arrival and subsequent expansion of the industry is limited. Therefore, to better understand the impacts of in-lake fish farms on the quality of freshwater ecosystems, we examined the diatom records in sediment cores from seven freshwater lochs in Scotland over a timescale of c.100-200 years, spanning the period before and after installation of the fish cages at these sites. At three lochs (A, C, E) we observed marked diatom assemblage shifts indicative of eutrophication, coincident with arrival of the fish farms, at two lochs (B, G) there was evidence of enrichment over a longer timescale although with some further enrichment occurring with the advent of the fish farms, and at the other two lochs (D, F), diatom shifts were subtle and showed no sign of eutrophication. Thus, while marked ecological shifts are shown to occur with the arrival of fish farms in some sites, this is not always the case. The natural background conditions, the scale of operations, the siting of the fish cages in relation to location of inflows and outflows, the role of flushing rate and additional sources of nutrients are discussed as potential factors for the variable impacts observed across the seven lochs. Such factors should be considered when planning future installation and expansion of fish farms to ensure sustainable development of these resources. Our study provides an understanding of baseline conditions and long-term water quality trajectories in freshwater lakes with fish farms and demonstrates the value of paleolimnology in supporting management decisions with respect to fisheries.

Siglec7 functions as an inhibitory receptor of non-specific cytotoxic cells and can regulate the innate immune responses in a primitive vertebrate (Oreochromis niloticus)

In mammals, siglec7, an integral component of the siglecs, is principally found on the surface of natural killer (NK) cells, macrophages, and monocytes, where it interacts with various pathogens to perform immunological regulatory activities. Nonetheless, the immune defense and mechanism of siglec7 in early vertebrates remain unknown. In this study, we identified siglec7 from Oreochromis niloticus (OnSiglec7) and revealed its immune functions. Specifically, OnSiglec7 was abundantly expressed in immune-related tissues of healthy tilapia and its transcription level was strongly activated after being challenged with A. hydrophila, S. agalactiae, and Poly: IC. Meanwhile, OnSiglec7 protein was purified and analyzed, which could recognize multiple pathogens through binding and agglutinating activity. Moreover, OnSiglec7-positive cells were mainly distributed in non-specific cytotoxic cells (NCC) of tilapia HKLs and showed cell membrane localization. Furthermore, OnSiglec7 blockage affected multiple innate immune responses (inflammation, apoptosis, and pyroptosis process) by regulating the activation of MAPK, NF-κB, TLR, and JAK-STAT pathways. Finally, OnSiglec7 blockage also greatly enhanced the cytotoxic effect of tilapia NCC. Summarily, this study uncovers immune functions and mechanisms of siglec7 in primitive vertebrates, thereby enhancing our understanding of the systemic evolution and ancient functions of other siglecs within the host's innate immune system (to our knowledge).

Governance hurdles for expansion of low trophic mariculture production in Sweden

The study examines the governance of low trophic species mariculture (LTM) using Sweden as a case study. LTM, involving species such as seaweeds and mollusks, offers ecosystem services and nutritious foods. Despite its potential to contribute to blue growth and Sustainable Development Goals, LTM development in the EU and OECD countries has stagnated. A framework for mapping governance elements (institutions, structures, and processes) and analyzing governance objective (effective, equitable, responsive, and robust) was combined with surveys addressed to the private entrepreneurs in the sector. Analysis reveals ineffective institutions due to lack of updated legislation and guidance, resulting in ambiguous interpretations. Governance structures include multiple decision-making bodies without a clear coordination agency. Licensing processes were lengthy and costly for the private entrepreneurs, and the outcomes were uncertain. To support Sweden's blue bioeconomy, LTM governance requires policy integration, clearer direction, coordinated decision-making, and mechanisms for conflict resolution and learning.

The role of HMGB2 in the immune response of Nile tilapia (Oreochromis niloticus) to streptococcal infection

High mobility group protein B2 (HMGB2) is an abundant chromatin-associated protein with pivotal roles in transcription, cell proliferation, differentiation, inflammation, and tumorigenesis. However, its immune function in Nile tilapia (Oreochromis niloticus) remains unclear. In this study, we identified a homologue of HMGB2 from Nile tilapia (On-HMGB2) and investigated its functions in the immune response against streptococcus infection. The open reading frame (ORF) of On-HMGB2 spans 642 bp, encoding 213 amino acids, and contains two conserved HMG domains. On-HMGB2 shares over 80 % homology with other fish species and 74%-76 % homology with mammals. On-HMGB2 was widely distributed in various tissues, with its highest transcript levels in the liver and the lowest in the intestine. Knockdown of On-HMGB2 promoted the inflammatory response in Nile tilapia, increased the bacterial load in the tissues, and led to elevated mortality in Nile tilapia following Streptococcus agalactiae infection. Taken together, On-HMGB2 significantly influences the immune system of Nile tilapia in response to streptococcus infection.

Path2Green: introducing 12 green extraction principles and a novel metric for assessing sustainability in biomass valorization

We propose an innovative approach to address the pressing need for efficient and transparent evaluation techniques to assess extraction processes' sustainability. In response to society's growing demand for natural products and the consequent surge in biomass exploration, a critical imperative arises to ensure that these processes are genuinely environmentally friendly. Extracting natural compounds has traditionally been regarded as a benign activity rooted in ancient practices. However, contemporary extraction methods can also significantly harm the environment if not carefully managed. Recognizing this, we developed a novel metric, Path2Green, tailored specifically and rooted in 12 new principles of a green extraction process. Path2Green seeks to provide a comprehensive framework beyond conventional metrics, offering a nuanced understanding of the environmental impact of extraction activities from biomass collection/production until the end of the process. By integrating factors such as resource depletion, energy consumption, waste generation, and biodiversity preservation, Path2Green aims to offer a holistic assessment of sustainability of an extraction approach. The significance of Path2Green lies in its ability to distill complex environmental data into a simple, accessible metric. This facilitates informed decision-making for stakeholders across industries, enabling them to prioritize greener extraction practices. Moreover, by setting clear benchmarks and standards, Path2Green incentivizes innovation and drives continuous improvement in sustainability efforts, being a new user-friendly methodology.

Ameliorating effects of natural herbal supplements against water-borne induced toxicity of heavy metals on Nile tilapia, (Oreochromis niloticus)

The efficacy of herbal supplements in mitigating heavy metals (HMs) toxicity was investigated using a widely grown fish, the Nile tilapia (Oreochromis niloticus). The experiment was conducted over two phases: during the stress phase, the experimental fishes were exposed to sub-lethal concentrations of HMs, including lead, cadmium, zinc, and copper for 15 days; following which during the feeding phase, herbal supplements were given for 70 days to ameliorate their effects. Seven groups were established: the control negative group (CON-ve), control positive group (CON+ve, without any treatment), and five groups with supplementation of 1% turmeric (TUR), cinnamon (CIN), ginger (GIN), garlic (GAR), and their mixture (MIX), respectively. A total of 315 fishes were distributed evenly in experimental tanks (15 fishes per tank, in triplicates). The results revealed that exposure to HMs led to significant (p < 0.05) alterations in all the tested parameters, i.e., liver damage and growth reduction. The herbal supplements, especially the MIX groups, ameliorated the harmful effects of HMs and restored fish growth, digestibility, carcass composition, and liver health. In conclusion, the study demonstrated that the herbal supplements were effective in reducing the HMs-linked toxicity in Nile tilapia. Future studies pertaining to the mechanisms facilitated by the various herbal bioactive substances-linked tolerance to HMs in fishes are warranted.

Anaerobic degradation of excess protein-rich fish feed drives CH4 ebullition in a freshwater aquaculture pond

Aquaculture is a climate-relevant source of greenhouse gases like methane. Methane emissions depend on various parameters, with organic matter playing a crucial role. Nevertheless, little is known about the composition of organic matter in aquaculture. We investigated the effects of excessive loading of high-protein fish feed on the quality of sediment organic matter in a fishpond to explain extremely high methane ebullition rates (bubble flux). Analysing the molecular composition of water-extractable organic matter using liquid chromatography Fourier-transform ion cyclotron resonance mass spectroscopy, we found strong differences between the feeding area and open water area: low-molecular weight nitrogen and sulphur-rich organic compounds were highly enriched at the feeding area. In addition, methane ebullition correlated well with sediment protein content and total bound nitrogen in pore water. Our results indicate that feed proteins in the sediments are hydrolysed into oligopeptides (CHNO) and subsequently converted to CHOS and CHNOS components during anaerobic deamination of protein and peptide fragments in the presence of inorganic sulphides. These metabolites accumulate at the feeding area due to continuous feed supply. Our findings illustrate the adverse effects of excessive feeding leading to bioreactor-like methane emissions at the feeding area. Improving feed management has the potential to make aquaculture more climate-friendly.

Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production

Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.

Genetic and phenotypic diversity of Flavobacterium psychrophilum isolates from Czech salmonid fish farms

BACKGROUND

The salmonid pathogen Flavobacterium psychrophilum poses a significant economic threat to global aquaculture, yet our understanding of its genetic and phenotypic diversity remains incomplete across much of its geographic range. In this study, we characterise the genetic and phenotypic diversity of 70 isolates collected from rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta m. fario) from fish farms in the Czech Republic between 2012 and 2019 to compare their genomic content with all draft or complete genomes present in the NCBI database (n = 187).

RESULTS

The Czech isolates underwent comprehensive evaluation, including multiplex PCR-based serotyping, genetic analysis, antimicrobial resistance testing, and assessment of selected virulence factors. Multiplex PCR serotyping revealed 43 isolates as Type 1, 23 as Type 2, with sporadic cases of Types 3 and 4. Multi-locus sequence typing unveiled 12 sequence types (ST), including seven newly described ones. Notably, 24 isolates were identified as ST329, a novel sequence type, while 22 were classified as the globally-distributed ST2. Phylogenetic analysis demonstrated clonal distribution of ST329 in the Czech Republic, with these isolates lacking a phage sequence in their genomes. Antimicrobial susceptibility testing revealed a high proportion of isolates classified as non-wild type with reduced susceptibility to oxolinic acid, oxytetracycline, flumequine, and enrofloxacin, while most isolates were classified as wild type for florfenicol, sulfamethoxazole-trimethoprim, and erythromycin. However, 31 isolates classified as wild type for florfenicol exhibited minimum inhibitory concentrations at the susceptibility breakpoint.

CONCLUSION

The prevalence of the Czech F. psychrophilum serotypes has evolved over time, likely influenced by the introduction of new isolates through international trade. Thus, it is crucial to monitor F. psychrophilum clones within and across countries using advanced methods such as MLST, serotyping, and genome sequencing. Given the open nature of the pan-genome, further sequencing of strains promises exciting discoveries in F. psychrophilum genomics.

Microplastic pollution in aquafeed of diverse aquaculture animals

Microplastics have emerged as pervasive contaminants, and determining their occurrence in aquafeed is key for evaluating their risks to farmed animals and, by extension, humans. However, knowledge about microplastic in aquafeed is still limited. Herein, we determined microplastic characteristics in aquafeed for five important aquaculture animals with different feeding habits. Aquafeed samples were collected for spotted sea bass, shrimp, grass carp, Tilapia, and frogs from main companies in China. The samples were digested using chemical digestion, and the residuals were subjected to a density separation. Microplastics were identified under the microscope and characterized by their shape, color, size, and polymer type. The results showed that microplastics are highly abundant in the feed of frogs, followed by spotted sea bass, Tilapia, grass carp, and shrimp. We found that feed size contributes to the total microplastic abundance in the feed. Further, microplastics were mainly in microfiber form, and the dominant polymer type was propylene, suggesting that packaging and processing are the main sources of pollution. Additionally, the most abundant size of microplastics was 100-1000 μm. Calculating microplastic ingestion risk, the spotted sea bass had the greatest recorded risk of microplastic ingestion, followed by grass carp, frogs, Tilapia, and shrimp. This study lays a foundational step toward understanding microplastic effects on aquaculture animals and calls for further environmentally relevant laboratory experiments to assess the risk of microplastic ingestion on animals and potential transfer to humans.

Localization and Tissue Tropism of Ostreid Herpesvirus 1 in Blood Clam Anadara broughtonii

OsHV-1 caused detrimental infections in a variety of bivalve species of major importance to aquaculture worldwide. Since 2012, there has been a notable increase in the frequency of mass mortality events of the blood clam associated with OsHV-1 infection. The pathological characteristics, tissue and cellular tropisms of OsHV-1 in A. broughtonii remain unknown. In this study, we sought to investigate the distribution of OsHV-1 in five different organs (mantle, hepatopancreas, gill, foot, and adductor muscle) of A. broughtonii by quantitative PCR, histopathology and in situ hybridization (ISH), to obtain insight into the progression of the viral infection. Our results indicated a continuous increase in viral loads with the progression of OsHV-1 infection, reaching a peak at 48 h or 72 h post-infection according to different tissues. Tissue damage and necrosis, as well as colocalized OsHV-1 ISH signals, were observed primarily in the connective tissues of various organs and gills. Additionally, minor tissue damage accompanied by relatively weak ISH signals was detected in the foot and adductor muscle, which were filled with muscle tissue. The predominant cell types labeled by ISH signals were infiltrated hemocytes, fibroblastic-like cells, and flat cells in the gill filaments. These results collectively illustrated the progressive alterations in pathological confusion and OsHV-1 distribution in A. broughtonii, which represent most of the possible responses of cells and tissues to the virus.

Exploring Multifunctional Markers of Biological Age in Farmed Gilthead Sea Bream (Sparus aurata): A Transcriptomic and Epigenetic Interplay for an Improved Fish Welfare Assessment Approach

DNA methylation clocks provide information not only about chronological but also biological age, offering a high-resolution and precise understanding of age-related pathology and physiology. Attempts based on transcriptomic and epigenetic approaches arise as integrative biomarkers linking the quantification of stress responses with specific fitness traits and may help identify biological age markers, which are also considered welfare indicators. In gilthead sea bream, targeted gene expression and DNA methylation analyses in white skeletal muscle proved sirt1 as a reliable marker of age-mediated changes in energy metabolism. To complete the list of welfare auditing biomarkers, wide analyses of gene expression and DNA methylation in one- and three-year-old fish were combined. After discriminant analysis, 668 differentially expressed transcripts were matched with those containing differentially methylated (DM) regions (14,366), and 172 were overlapping. Through enrichment analyses and selection, two sets of genes were retained: 33 showing an opposite trend for DNA methylation and expression, and 57 down-regulated and hypo-methylated. The first set displayed an apparently more reproducible and reliable pattern and 10 multifunctional genes with DM CpG in regulatory regions (sirt1, smad1, ramp1, psmd2-up-regulated; col5a1, calcrl, bmp1, thrb, spred2, atp1a2-down-regulated) were deemed candidate biological age markers for improved welfare auditing in gilthead sea bream.

Effects of tire particles and associated-chemicals on the Pacific oyster (Magallana gigas) physiology, reproduction and next-generation

By 2040, tire particles (TP) are expected to dominate marine plastic contamination, raising concerns about their effects on marine animals. This study employed a multidisciplinary and multigenerational approach on the Pacific oyster Magallana gigas to investigate the effects of TP and their leachates (LEA). Effects were analyzed at the individual scale, from cellular, molecular, and microbiota changes to reproductive outputs and offspring performance. Microbiota characterization revealed potential dysbiosis in oysters treated with high concentration of both TP and LEA. RNA-seq analyses highlighted the activation of energy metabolism and stress responses in the LEA treatment. Additionally, transcriptional changes in oocytes and the reduction of motile spermatozoa suggested potential effects on gamete quality. Notably, possible oyster resilience was pointed out by the lack of significant ecophysiological modifications in adults and impacts on the growth and reproductive outputs of the offspring. Overall, the implications of the observed oyster resilience under our experimental setting are discussed in relation to available toxicity data and within a comprehensive view of coastal ecosystems, where a higher diversity of plastic/rubber materials and harsher environmental conditions occur.

Biochemical and molecular responses to long-term salinity challenges in northern quahogs Mercenaria mercenaria

Salinity is a key environmental factor for aquatic organisms for survival, development, distribution, and physiological performance. Salinity fluctuation occurs often in estuary and coastal zones due to weather, tide, and freshwater inflow and thus heavily affects coastal marine aquaculture. The northern quahog Mercenaria mercenaria is an important aquaculture species along the Atlantic coast in the US, but information on the effects of salinity stress on physiological, immunological, and molecular responses is still scarce. The goal of this study was to investigate cellular and molecular responses through challenges of long-term hypo- and hyper-salinities in northern quahogs. The objectives were to: 1) measure the survival of market-sized quahogs under a three-month salinity challenge at 15 (hyposalinity), 25 (control), and 35 ppt (hypersalinity); 2) determine cellular changes of hemocytes through analysis of immune functions; 3) determine changes of the total free amino acid concentration in gills, and 4) evaluate the molecular responses in gills using RNAseq technology with qPCR verification. After a three-month salinity challenge, no mortality was observed, and increases in body weight were identified with a significantly higher increase in the hypersalinity group. Northern quahogs equilibrated their hemolymph osmolality with the ambient seawater and were verified to be osmoconformers. Significant differences were observed in total hemocyte concentration, lysosomal presence, ROS production, and phagocytic rate, but no differences were found in cell viability. The total free amino acid concentration within gills was positively correlated to water salinity, indicating amino acids were critical organic osmolytes. The transcriptome of gills using RNAseq revealed differential expression genes (DEG) encoding amino acid transporters (SLC6A3, SLC6A6, SLC6A13, SLC25A38), ion channel proteins (T38B1, GluCl, ATP2C1), and water channel protein (AQP8) in hyposalinity or/and hypersalinity groups, indicating these genes play critical roles in intracellular isosmotic regulation. Overall, the findings in this study provided new insights into osmoregulation in northern quahogs.

Removal of nutrients from aquaculture wastewater using cattail (Typha spp.) constructed wetlands

The aquaculture industry is among the fastest growing food production sectors in the world. Land-based aquaculture systems continue to increase in popularity as they offer the benefits of controlling diseases, managing water quality, and minimizing threats to wild populations of fish. However, these systems discharge wastewater high in N and P. The ability of cattail (Typha spp.) constructed wetlands (CWs) to remove N and P from aquaculture wastewater (AWW) was examined here. Cattail CWs were established in mesocosms and had a gradient of AWW applied weekly for a total of 5 weeks. Total N and P loadings ranged from 13.7 to 209.2 mg m-2 and 3.01 to 45.97 mg m-2 over 28 days, respectively. Additions of AWW did not cause elevations in total dissolved N, total ammonia N, or nitrite N in CW water; however, concentrations of nitrate N and P in CW water were related to nutrient loading conditions. Elevations in P persisted for 3-4 weeks among high nutrient loading treatments, providing an opportunity for eutrophic conditions to develop in CW systems. However, after 33 days of treatment, >95% total P concentration reduction was achieved in all mesocosms with final concentrations <0.05 mg L-1, equivalent to reference conditions. High-loading treatments achieved greater P load reduction (856.8-955.0 mg m-2 year-1) than low-loading and reference treatments (591.7-792.7 mg m-2 year-1). This study demonstrates the effectiveness of cattail CWs to remove nutrients during AWW treatment and highlights the potential for end-of-season use in northern climates, providing insights regarding the operational timeline of such systems.

Bioactive compound from marine seagrass Streptomyces argenteolus TMA13: combatting fish pathogens with time-kill kinetics and live-dead cell imaging

Actinobacteria, pervasive in aquatic and terrestrial environments, exhibit a filamentous morphology, possess DNA with a specific G + C content and production of numerous secondary metabolites. This study, focused on actinobacteria isolated from marine seagrass, investigating their antibacterial activity against fish pathogens. Among 28 isolates, Streptomyces argenteolus TMA13 displayed the maximum zone of inhibition against fish pathogens-Aeromonas hydrophila (10 mm), Aeromonas caviae (22 mm), Edwardsiella tarda (17 mm), Vibrio harveyi (22 mm) and Vibrio anguillarum (12 mm) using the agar plug method. Optimization of this potent strain involved with various factors, including pH, temperature, carbon source and salt condition to enhance both yield production and antibacterial efficacy. In anti-biofilm assay shows the maximum percentage of inhibition while increasing concentration of TMA13 extract. Minimal Inhibitory Concentration (MIC) and Minimal Bactericidal Concentration (MBC) assays with TMA13 crude extract demonstrated potent activity against fish pathogens at remarkably low concentrations. Time-kill kinetics assay showcased growth curve variations over different time intervals for all fish pathogens treated with a 100 µg/ml concentration of crude extract, indicating a decline in cells viability and progression into the death phase. Additionally, fluorescence microscopic visualization of bacterial cells exposed to the extracts emitting green and red fluorescence, enabling live-dead cell differentiation was also studied. Further characterization of the crude extract through GC-MS and FT-IR analyses performed and identified secondary metabolites with functional groups exhibiting significant antibacterial activity. This study elucidates the capacity of Streptomyces argenteolus TMA13 to enhance the production of antibiotic compounds effective against fish pathogens.

Supplementation of diethyl aminoethyl hexanoate for enhancing antibiotics removal by different microalgae-based system

With the growth of the aquaculture industry, antibiotic residues in treated wastewater have become a serious ecological threat. The effects of supplementation with diethyl aminoethyl hexanoate (DA-6) on the removal of tetracycline (TC), ciprofloxacin (CPFX), and sulfamonomethoxine (SMM) from aquaculture wastewater by different microalgae-based systems were examined and systematically analyzed. The results demonstrated that C. vulgaris -S395-2-C. rosea symbiont performed best under 0.2 mg L-1 antibiotic treatment for antibiotic removal. At 10-7 M, DA-6 significantly enhanced C. vulgaris-S395-2-C. rosea symbiont removal of CPFX and SMM at 0.20 mg L-1. The removal of TC, CPFX and SMM by this strain under optimal conditions was 99.2 ± 0.4 %, 86.3 ± 6.3 %, and 91.3 ± 5.7 %, respectively. These results suggest that DA-6 may act on microalgae-bacteria-fungi three-phase symbionts for the removal of multiple antibiotics from aquaculture wastewater.

Optimizing reproductive performance in pangasius catfish broodstock: A review of dietary and molecular strategies

Pangasius catfish, a significant player in the global whitefish market, encounters challenges in aquaculture production sustainability. Quality broodstock maintenance and seed production are impeded by growth, maturation, and fecundity issues. This review investigates the efficacy of strategic nutrient composition and molecular strategies in enhancing broodstock conditions and reproductive performance across various fish species. A notable knowledge gap for Pangasius catfish hampers aquaculture progress. The review assesses nutrient manipulation's impact on reproductive physiology, emphasizing pangasius broodstock. A systematic review analysis following PRISMA guidelines was conducted to identify research trends and hotspots quantitatively, revealing a focus on P. bocourti and fertilization techniques. Addressing this gap, the review offers insights into dietary nutrients manipulation and genetic tool utilization for improved seed production, contributing to pangasius catfish aquaculture sustainability.

Gill lesions are the main cause of death in yellowfin seabream (Acanthopagrus latus) following infection with Amyloodinium ocellatum

Amyloodiniosis, caused by the ectoparasite Amyloodinium ocellatum, affects the healthy development of mariculture. This study used a local infection method to identify the pathogenic target organ responsible for the death of infected fish. Comparing the relationship between the abundance of trophonts in gills and skin with the mortality of infected fish using local infection showed that severe gill infections cause the mortality of infected fish. At the 40 % survival rate of infected fish, the parasite abundance in the gill was 14,167 ± 4371. The gill filaments of the infected fish were structurally disordered, with pronounced lesions associated with the presence of trophonts, such as epithelial cell degeneration and massive lymphocytic infiltration. However, the skin showed no obvious pathological changes. The TUNEL assay showed a significant presence of apoptotic cells concentrated in the area of A. ocellatum infection. The trophonts on the gills developed faster than those parasitising the skin and fins. Microbiome analysis revealed that at the phylum level, Proteobacteria, Bacteroidota, and Firmicutes are abundant in the skin, while Verrucomicrobiota, Bacteroidota, and Proteobacteria are abundant in the gills of A. latus. Furthermore, A. ocellatum infection significantly reduced (p < 0.05) the richness and diversity of the gill microbial community of A. latus. Infection by A. ocellatum increased the relative abundance of several putative pathogenic bacteria (Flavobacterium and Nocardia) in the gill and skin of A. latus, possibly increasing the likelihood of disease in the host. In conclusion, these results evidenced that severe gill infections by A. ocellatum cause mortality in infected fish, which clarifies the direction for exploring the pathogenesis of amyloodiniosis.

Effects of solid-state fermentation product of yeast supplementation on liver and intestinal health, and resistance of common carp (Cyprinus carpio) against spring viraemia carp virus

This study aimed to investigate the effects of solid-state fermentation products of yeast (SFPY) on liver and intestinal health and disease resistance of common carp (Cyprinus carpio). A total of 200 common carp with an initial average weight of 2.55 ± 0.004 g were divided into 5 groups (4 replications per group and 10 fish per replication), and were fed with one of five diets, including a control diet and 4 diets supplemented with 2‰ (Y2), 3‰ (Y3), 4‰ (Y4), or 5‰ (Y5) SFPY, respectively, for 8 weeks. Results indicated that, the addition of SFPY to the diet of common carp did not affect the growth performance or survival rate of fish (P = 0.253). Interestingly, with the addition of SFPY, the triacylglycerol (TAG) content of the liver presented a linear decreasing tendency (P = 0.004), with significantly decreased in Y4 and Y5 groups (P = 0.035) compared with control. Serum lipopolysaccharide (LPS) content and diamine oxidase (DAO) activity presented a negative linear relationship with the addition of SFPY (P = 0.015, P = 0.030), while serum lipopolysaccharide binding protein (LBP) content first decreased and then increased (P < 0.001). The total antioxidant capacity (T-AOC) in the intestine of fish increased continuously with increasing SFPY supplementation (P = 0.026), reaching the highest level in Y5 group. The villus height in all experimental groups were significantly higher than that in the control group (P < 0.001). Furthermore, compared to the control, adding 3‰ SFPY to the control diet of common carp significantly increased the relative abundance of Fusobacteria (P = 0.018) and decreased that of Proteobacteria (P = 0.039) at phylum level, and increased the relative abundance of Cetobacterium (P= 0.018) and decreased that of Shewanella (P = 0.013) at genus level. Compared with the control, the relative mRNA expression level of spring viraemia of carp virus N protein (SVCV -n) in the kidney was lower than that of the control group without significance and bottomed out in Y4 group (P = 0.138). In conclusion, dietary SFPY enhanced the SVCV resistance capacity of common carp by improving liver and intestinal health and modulating the gut microbiota. Thus, SFPY is a potential feed additive to be used in aquaculture to reduce the huge economic loss of common carp due to SVCV disease. Based on liver TAG content and intestinal villus height, the optimal addition level of SFPY was 3.02‰ and 2.72‰, respectively.

Dietary fishmeal replacement by Clostridium autoethanogenum protein meal influences the nutritional and sensory quality of turbot (Scophthalmus maximus) via the TOR/AAR/AMPK pathways

Clostridium autoethanogenum protein (CAP) is a promising protein source for aquaculture; however, how CAP influences fish quality is worth extensive research. We randomly allocated 630 turbot with initial body weights of about 180 g into 6 groups, with fishmeal-based control diet or diet with CAP replacing 15% (CAP15), 30% (CAP30), 45% (CAP45), 60% (CAP60), or 75% (CAP75) of fishmeal protein. After a 70-d feeding trial, the fillet yield (P = 0.015) and content of protein (P = 0.017), collagen (P < 0.001), hydroxyproline (P < 0.001), C20:5n-3 (P = 0.007), and ∑n-3/∑n-6 polyunsaturated fatty acids ratio (P < 0.001) in turbot muscle was found to decrease linearly with increasing CAP. However, turbot fed CAP15 diet maintained these parameters (P > 0.05). By contrast, the muscle hardness increased linearly with increasing CAP (P = 0.004), accompanied by linear reduction of muscle fiber area (P = 0.003) and expression of myogenesis-related genes, including cathepsin D (ctsd P < 0.001) and muscle ring finger protein 1 (murf 1, P < 0.001). Phosphorylation of protein kinase B (Akt, P < 0.001), target of rapamycin (TOR, P = 0.001), eukaryotic initiation factor 4E-binding protein 1 (4E-BP1, P < 0.001), and ribosomal protein S6 (S6, P < 0.001) decreased linearly; however, phosphorylation of AMP-activated protein kinase (AMPK, P < 0.001), eukaryotic initiation factor 2α (eIF2α, P < 0.001), and the abundance of activating transcription factor 4 (ATF4, P < 0.001) increased with increasing CAP, suggesting that the TOR signaling pathway was inhibited, and the amino acid response (AAR) and AMPK pathways were activated. Additionally, expression of genes related to protein degradation, including myogenic factor 5 (myf 5, P < 0.001), myogenic differentiation (myod, P < 0.001), paired box 7 (pax 7, P < 0.001), and ctsd (P < 0.001), decreased linearly with increasing CAP. In conclusion, CAP could be used to replace up to 15% of fishmeal without negatively impacting turbot quality. However, higher levels of CAP decreased fillet yield, muscle protein content, and muscle fiber diameter while increasing muscle hardness, which could be attributed to the inhibition of the TOR pathway and activation of the AAR and AMPK pathways.

Sustainable agriculture: leveraging microorganisms for a circular economy

Microorganisms serve as linchpins in agricultural systems. Classic examples include microbial composting for nutrient recovery, using microorganisms in biogas technology for agricultural waste utilization, and employing biofilters to reduce emissions from stables or improve water quality in aquaculture. This mini-review highlights the importance of microbiome analysis in understanding microbial diversity, dynamics, and functions, fostering innovations for a more sustainable agriculture. In this regard, customized microorganisms for soil improvement, replacements for harmful agrochemicals or antibiotics in animal husbandry, and (probiotic) additives in animal nutrition are already in or even beyond the testing phase for a large-scale conventional agriculture. Additionally, as climate change reduces arable land, new strategies based on closed-loop systems and controlled environment agriculture, emphasizing microbial techniques, are being developed for regional food production. These strategies aim to secure the future food supply and pave the way for a sustainable, resilient, and circular agricultural economy. KEY POINTS: • Microbial strategies facilitate the integration of multiple trophic levels, essential for cycling carbon, nitrogen, phosphorus, and micronutrients. • Exploring microorganisms in integrated biological systems is essential for developing practical agricultural solutions. • Technological progress makes sustainable closed-entity re-circulation systems possible, securing resilient future food production.

Exploring the variations in molecular characteristics of dissolved organic matter driven by aquaculture types

In recent decades, global aquaculture has expanded rapidly, raising concerns about coastal environmental degradation due to unregulated or poorly regulated discharge of aquaculture tailwater. Despite the crucial role of dissolved organic matter (DOM) in biogeochemical processes and aquatic biodiversity, the influence of aquaculture type on the molecular characteristics of DOM remains largely unexplored. Herein, this study investigated the variations in chemical and spectroscopic properties as well as molecular characteristics and composition of DOM across different aquaculture types including crustacean, fish and shellfish. Our findings revealed notable differences in DOM quantities among different aquaculture types, with crustacean and fish aquaculture water containing higher DOM amount compared to shellfish aquaculture water. This disparity can be attributed to the more frequent formulated feeds of crustacean and fish in contrast to shellfish aquaculture. Furthermore, distinct differences were also observed in the characteristics and composition of DOM among the different aquaculture waters. Specifically, DOM in shellfish aquaculture water exhibited a higher abundance of unsaturated and reduced molecules as well as increased aromaticity compared to the other two aquaculture waters. Conversely, DOM from fish aquaculture water showed a greater contribution from terrestrial origin characterized by elevated levels of plant-based components such as lignin-like and tannin-like compounds. Interestingly, DOM from shellfish aquaculture water contained lower levels of microbial-derived components such as lipid-like and protein-like compounds, likely due to reduced microorganism populations resulting from lower nutrients availability and higher salinity. Overall, these significant variations in characteristics and composition of DOM underscore the potential impacts of aquaculture type on the DOM biogeochemical cycle and the environmental quality in aquatic ecosystems.

Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming

(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism-environment-ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources.

Retention of prions in the polychaete Hediste diversicolor and black soldier fly, Hermetia illucens, larvae after short-term experimental immersion and feeding with brain homogenate from scrapie infected sheep

Finding alternative protein and lipid sources for aquafeeds is crucial for the sustainable growth of fed aquaculture. Upcycling industrial side streams and byproducts using extractive species can reduce waste and help reduce the sector's dependence on fish meal and fish oils. Polychaete worms (Hediste diversicolor) and black soldier fly (Hermetia illucens) larvae (BSFL) are promising candidates for converting waste materials into valuable protein and lipid sources. However, further research and evaluations are needed to ensure the safety and regulatory compliance of these alternative feed sources, especially regarding prions spreading potential in the unlikely case that prions would be introduced in the value chain via feedstocks. In the present investigation, BSFL and juvenile polychaetes that had received a massive dose of scrapie prions through immersion and oral inoculation were found to harbour detectable prions using an ultrasensitive amplification method known as PMCA. This observation suggests that both H. diversicolor and BSFL have the potential to serve as mechanical vectors for prions diseases. However, it is important to note that insects, lacking the prion protein gene, are incapable of propagating prions. Therefore, the quantity of prions present in the larvae will inevitably be lower than the amount of prions they encountered. This is the first study to report on the fate of prions through ingestion by these marine and terrestrial invertebrate species.

Comparing feces collection methods for evaluating the apparent digestibility coefficient of brewers' spent yeast in juvenile Atlantic salmon (Salmo salar)

Brewer's spent yeast (BSY), derived from Saccharomyces cerevisiae used in beer production, is a valuable protein source for aquafeeds. Estimations of apparent digestibility coefficients (ADC) for nutrients in BSY are crucial for its inclusion in aquafeeds. ADC estimations for Saccharomyces cerevisiae protein in rainbow are hardly comparable from a methodological point of view, whereas the ADC estimations for BSY protein in Atlantic salmon are only based on stripped feces, which are known to produce underestimations. Therefore, new determinations of ADC of BSY nutrients are necessary for the inclusion of this ingredient in practical diets for salmonids. This study is focused on determining unbiased ADC values for protein and energy from BSY in juvenile Salmo salar. To reduce systematic biases, fecal samples were collected using stripping and decantation methods, which are known to produce under-and overestimations, respectively. 780 fish (25.16 ± 4.88 g) were stocked in six tanks. A reference diet (50% protein, 20% lipid, 1% Cr2O3) was provided to three tanks, and a test diet (70,30 reference diet to BSY) to the other three. ADC for BSY protein was 84.70 ± 1.04% (decantation) and 70.50 ± 4.03% (stripping). For gross energy, stripped feces yielded an ADC of 52.04 ± 5.30%, while decantation resulted in 63.80 ± 1.17%. Thus, ADC estimates were taken as the average of the stripping-value and the decantation-value, resulting in 77.6% for BSY crude protein, which is appreciably higher than previously measured values in S. salar fed undisrupted S. cerevisiae, and in 57.9% for gross energy.

Coping with environmental degradation: Physiological and morphological adjustments of wild mangrove fish to decades of aquaculture-induced nutrient enrichment

The impact of eutrophication on wild fish individuals is rarely reported. We compared physiological and morphological traits of Siganus lineatus chronically exposed to aquaculture-induced eutrophication in the wild with individuals living at a control site. Eutrophication at the impacted site was confirmed by elevated organic matter (up to 150 % higher), phytoplankton (up to 7 times higher), and reduced oxygen (up to 60 % lower). Physiological and morphological traits of S. lineatus differed significantly between the two sites. Fish from the impacted site exhibited elevated hypoxia tolerance, increased gill surface area, shorter oxygen diffusion distances, and altered blood oxygen-carrying capacity. Elevated blood lactate and scope for anaerobic ATP production were observed, suggesting enhanced survival below critical oxygen levels. A significant 8.5 % increase in metabolic costs and altered allometric scaling, related to environmental degradation, were recorded. Our study underscores eutrophication's profound impact at the organism-level and the importance to mitigate it.

In vivo multiscale analyses of spring viremia of carp virus (SVCV) infection: From model organism to target species

Spring viremia of carp virus (SVCV) has a broad fish host spectrum and is responsible for a disease that generally affects juvenile fishes with a mortality rate of up to 90%. In the absence of treatments or vaccines against SVCV, the search for prophylactic or therapeutic solutions is thus relevant, particularly to identify solutions compatible with mass vaccination. In addition to being a threat to aquaculture and ecosystems, SVCV is a unique pathogen to study virus-host interactions in the zebrafish model. Establishing the first reverse genetics system for SVCV and the design of recombinant SVCV (rSVCV) expressing fluorescent or bioluminescent proteins adds a new dimension for the study of these interactions using innovative imaging techniques. The infection by bath immersion of zebrafish larvae with rSVCV expressing mCherry allows us to define the first SVCV replication sites and the host innate immune responses using different transgenic lines of zebrafish. The fins were found as the main initial sites of infection in both zebrafish and carp, its natural host. Hence, new insights into the physiopathology of SVCV infection have been described. We report that neutrophils are recruited at the sites of infection and persist up to the death of the animal leading to an uncontrolled inflammation correlated with the expression of the pro-inflammatory cytokine IL1β. Tissue damage was observed at the site of initial replication, a likely consequence of virus-induced injury or the pro-inflammatory response. Interestingly, SVCV infection by bath immersion triggers a persistent pro-inflammatory response rather than activation of the antiviral IFN signaling pathway as observed following intravenous injection, highlighting the importance of the route of infection on the progression of pathogenicity. Thus, this model of zebrafish larvae infection by rSVCV offers new perspectives to study in detail virus-host interactions and to discover new prophylactic or therapeutic solutions.

Microscopic photoplethysmography-based evaluation of cardiotoxicity in whitefish larvae induced by acute exposure to cadmium and phenol

Toxic environmental pollutants pose a health risk for both humans and animals. Accumulation of industrial contaminants in freshwater fish may become a significant threat to biodiversity. Comprehensive monitoring of the impact of environmental stressors on fish functional systems is important and use of non-invasive tools that can detect the presence of these toxicants in vivo is desirable. The blood circulatory system, by virtue of its sensitivity to the external stimuli, could be an informative indicator of chemical exposure. In this study, microscopic photoplethysmography-based approach was used to investigate the cardiac activity in broad whitefish larvae (Coregonus nasus) under acute exposure to cadmium and phenol. We identified contamination-induced abnormalities in the rhythms of the ventricle and atrium. Our results allow introducing additional endpoints to evaluate the cardiac dysfunction in fish larvae and contribute to the non-invasive evaluation of the toxic effects of industrial pollutants on bioaccumulation and aquatic life.

Feed Components and Timing to Improve the Feed Conversion Ratio for Sustainable Aquaculture Using Starch

Aquaculture contributes to the sustainable development of food security, marine resource conservation, and economy. Shifting aquaculture feed from fish meal and oil to terrestrial plant derivatives may result in cost savings. However, many carnivorous fish cannot be sustained on plant-derived materials, necessitating the need for the identification of important factors for farmed fish growth and the identification of whether components derived from terrestrial plants can be used in feed. Herein, we focused on the carnivorous fish leopard coral grouper (P. leopardus) to identify the essential growth factors and clarify their intake timing from feeds. Furthermore, we evaluated the functionality of starch, which are easily produced by terrestrial plants. Results reveal that carbohydrates, which are not considered essential for carnivorous fish, can be introduced as a major part of an artificial diet. The development of artificial feed using starch offers the possibility of increasing the growth of carnivorous fish in aquaculture.

Evolution of parasites in the Anthropocene: new pressures, new adaptive directions

The Anthropocene is seeing the human footprint rapidly spreading to all of Earth's ecosystems. The fast-changing biotic and abiotic conditions experienced by all organisms are exerting new and strong selective pressures, and there is a growing list of examples of human-induced evolution in response to anthropogenic impacts. No organism is exempt from these novel selective pressures. Here, we synthesise current knowledge on human-induced evolution in eukaryotic parasites of animals, and present a multidisciplinary framework for its study and monitoring. Parasites generally have short generation times and huge fecundity, features that predispose them for rapid evolution. We begin by reviewing evidence that parasites often have substantial standing genetic variation, and examples of their rapid evolution both under conditions of livestock production and in serial passage experiments. We then present a two-step conceptual overview of the causal chain linking anthropogenic impacts to parasite evolution. First, we review the major anthropogenic factors impacting parasites, and identify the selective pressures they exert on parasites through increased mortality of either infective stages or adult parasites, or through changes in host density, quality or immunity. Second, we discuss what new phenotypic traits are likely to be favoured by the new selective pressures resulting from altered parasite mortality or host changes; we focus mostly on parasite virulence and basic life-history traits, as these most directly influence the transmission success of parasites and the pathology they induce. To illustrate the kinds of evolutionary changes in parasites anticipated in the Anthropocene, we present a few scenarios, either already documented or hypothetical but plausible, involving parasite taxa in livestock, aquaculture and natural systems. Finally, we offer several approaches for investigations and real-time monitoring of rapid, human-induced evolution in parasites, ranging from controlled experiments to the use of state-of-the-art genomic tools. The implications of fast-evolving parasites in the Anthropocene for disease emergence and the dynamics of infections in domestic animals and wildlife are concerning. Broader recognition that it is not only the conditions for parasite transmission that are changing, but the parasites themselves, is needed to meet better the challenges ahead.

Enhancing Human Health and Wellbeing through Sustainably and Equitably Unlocking a Healthy Ocean's Potential

A healthy ocean is essential for human health, and yet the links between the ocean and human health are often overlooked. By providing new medicines, technologies, energy, foods, recreation, and inspiration, the ocean has the potential to enhance human health and wellbeing. However, climate change, pollution, biodiversity loss, and inequity threaten both ocean and human health. Sustainable realisation of the ocean's health benefits will require overcoming these challenges through equitable partnerships, enforcement of laws and treaties, robust monitoring, and use of metrics that assess both the ocean's natural capital and human wellbeing. Achieving this will require an explicit focus on human rights, equity, sustainability, and social justice. In addition to highlighting the potential unique role of the healthcare sector, we offer science-based recommendations to protect both ocean health and human health, and we highlight the unique potential of the healthcare sector tolead this effort.

Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes

Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.

Marine aquaculture can deliver 40% lower carbon footprints than freshwater aquaculture based on feed, energy and biogeochemical cycles

Freshwater aquaculture is an increasingly important source of blue foods but produces substantial methane and nitrous oxide emissions. Marine aquaculture, also known as mariculture, is a smaller sector with a large growth potential, but its climate impacts are challenging to accurately quantify. Here we assess the greenhouse gas emissions from mariculture's aquatic environment in global potentially suitable areas at 10 km resolution on the basis of marine biogeochemical cycles, greenhouse gas measurements from research cruises and satellite-observed net primary productivity. Mariculture's aquatic emissions intensities are estimated to be 1-6 g CH4 kg-1 carcass weight and 0.05-0.2 g N2O kg-1 carcass weight, >98% and >80% lower than freshwater systems. Using a life-cycle assessment approach, we show that mariculture's carbon footprints are ~40% lower than those of freshwater aquaculture based on feed, energy use and the aquatic environment emissions. Adoption of mariculture alongside freshwater aquaculture production could offer considerable climate benefits to meet future dietary protein and nutritional needs.

Evaluation of quercetin in alleviating the negative effects of high soybean meal diet on spotted sea bass Lateolabrax maculatus

The aim of this study was to investigate the effects of quercetin (QUE) on alleviating the negative effects of high soybean meal diet for spotted sea bass Lateolabrax maculatus. A healthy control group fed a 44% fishmeal diet was used, while the induction control group replaced 50% fishmeal with soybean meal. Subsequently, QUE was added at concentrations of 0.25, 0.50, 0.75, and 1.00 g/kg in the experimental groups. A total of 540 tailed spotted sea bass were randomly divided into 6 groups and fed the corresponding diet for 56 days. The results showed that 40% soybean meal significantly decreased the growth performance and immunity, increased the intestinal mucosal permeability, and caused damage to the intestinal tissue morphology; moreover, there were alterations observed in the composition of the intestinal microbiota, accompanied by detectable levels of saponins in the metabolites. However, the addition of QUE did not yield significant changes in growth performance; instead, it notably reduced the permeability of the intestinal mucosa, improved the body's immunity and the structural integrity of the intestinal tissue, increased the proportion of Proteobacteria, and enhanced the richness and diversity of intestinal microorganisms to a certain extent. In addition, QUE up-regulate the metabolism of amino acids and their derivatives and energy-related metabolites such as uridine and guanosine; furthermore, it appears to regulate transporters through the ABC transporters pathway to promote the absorption and utilization of QUE by enterocytes.

The potential climate benefits of seaweed farming in temperate waters

Seaweed farming is widely promoted as an approach to mitigating climate change despite limited data on carbon removal pathways and uncertainty around benefits and risks at operational scales. We explored the feasibility of climate change mitigation from seaweed farming by constructing five scenarios spanning a range of industry development in coastal British Columbia, Canada, a temperate region identified as highly suitable for seaweed farming. Depending on growth rates and the fate of farmed seaweed, our scenarios sequestered or avoided between 0.20 and 8.2 Tg CO2e year-1, equivalent to 0.3% and 13% of annual greenhouse gas emissions in BC, respectively. Realisation of climate benefits required seaweed-based products to replace existing, more emissions-intensive products, as marine sequestration was relatively inefficient. Such products were also key to reducing the monetary cost of climate benefits, with product values exceeding production costs in only one of the scenarios we examined. However, model estimates have large uncertainties dominated by seaweed production and emissions avoided, making these key priorities for future research. Our results show that seaweed farming could make an economically feasible contribute to Canada's climate goals if markets for value-added seaweed based products are developed. Moreover, our model demonstrates the possibility for farmers, regulators, and researchers to accurately quantify the climate benefits of seaweed farming in their regional contexts.

Towards cleaner environment: recycling microalgal co-product to reduce emissions and impacts while eliminating fishmeal in rainbow trout feed for sustainable aquaculture

The rapid increase in aquaculture over the last several decades has led to concerns about the environmental impact of fish feeds relying on marine resources for fishmeal (FM). We aim to assess Nannochloropsis sp. QH25 co-product as a viable and sustainable replacement for FM in juvenile rainbow trout, Oncorhynchus mykiss, feeds. We formulated four experimental diets: a reference (FM based), 33N, 66N, and 100N diet (33%, 66%, and 100% co-product replacement). Rainbow trout were randomly assigned to one of 16 tanks and randomly assigned an experimental diet to consume throughout the experiment (64 days total), with four replicate tanks per diet. We compared the phosphorus (P) and nitrogen (N) digestibility, emissions, and growth between diets and, compared six environmental impacts (biotic resource use (BRU), global warming potential (GWP), water use, land use, marine eutrophication potential (MEP), and freshwater eutrophication potential (FEP)) of each diet. Our results indicate that replacing FM with co-product did not significantly alter growth. P digestibility of the experimental and reference diets was comparable. BRU conversion ratio was significantly lower in the experimental diets. However, there were significantly higher water and land use conversion ratios but insignificantly higher results in GWP, MEP, and FEP between the reference and 100N diet.

Effect of Biofloc Technology Enriches the Growth of Litopenaeus vannamei (Boone, 1931)

The use of probiotics in shrimp farms has expanded as an alternative to antibiotics, improving shrimp health, growth, disease control and water quality. However, the efficacy of probiotics in intensive systems using biofloc remains uncertain. This study investigated bioremediation and biocontrol of commercial probiotics using biofloc, analysing water quality and bacterial groups influencing shrimp performance. Thirteen microbial colonies were observed in the biofloc samples, and their evolutionary history was inferred using the neighbour-joining method. Analysis using MEGA6 software revealed 99.6% similarity between colony 1P1 and Virgibacillus sp. and 99.8% similarity between colony 2P2 and Bacillus kochii. The study analysed the biochemical and amino acid content of shrimp cultured using biofloc technology for 85 days. The study found that biofloc-cultured L. Vannamei flesh had higher levels of moisture (31%), ash (15.2%), protein (34%) and lipid (12.6%). No seasonal variations were observed between biofloc samples in winter and summer seasons. Protein levels were found to be appropriate for shrimp growth in both ex situ and in situ biofloc systems. The average growth rate (kg/m2) of biofloc-cultured shrimp was significantly greater than in normal pond shrimp in both samples. The feed conversion ratio in the biofloc tank was lower than in the usual pond-cultured shrimp, possibly due to lower growth rate, lower feeding frequency (2 times per day) and higher density. The growth of L. vannamei shrimp is influenced by stocking density, with higher stocking density affecting the average weight. The study also examined the growth biochemical and amino acid content of shrimp cultured using biofloc technology.

Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages

To promote sustainable aquaculture, the formulation of Atlantic salmon (Salmo salar) feeds has changed in recent decades, focusing on replacing standard marine-based ingredients with plant-based alternatives, increasingly demonstrating successful outcomes in terms of fish performance. However, little is known about how these plant-based diets may impact the gut microbiota at first feeding and onwards. Nutritional programming (NP) is one strategy applied for exposing fish to a plant-based (V) diet at an early stage in life to promote full utilisation of plant-based ingredients and prevent potential adverse impacts of exposure to a plant-rich diet later in life. We investigated the impact of NP on gut microbiota by introducing fish to plant ingredients (V fish) during first feeding for a brief period of two weeks (stimulus phase) and compared those to fish fed a marine-based diet (M fish). Results demonstrated that V fish not only maintained growth performance at 16 (intermediate phase) and 22 (challenge phase) weeks post first feeding (wpff) when compared to M fish but also modulated gut microbiota. PERMANOVA general effects revealed gut microbiota dissimilarity by fish group (V vs. M fish) and phases (stimulus vs. intermediate vs. challenge). However, no interaction effect of both groups and phases was demonstrated, suggesting a sustained impact of V diet (nutritional history) on fish across time points/phases. Moreover, the V diet exerted a significant cumulative modulatory effect on the Atlantic salmon gut microbiota at 16 wpff that was not demonstrated at two wpff, although both fish groups were fed the M diet at 16 wpff. The nutritional history/dietary regime is the main NP influencing factor, whereas environmental and host factors significantly impacted microbiota composition in M fish. Microbial metabolic reactions of amino acid metabolism were higher in M fish when compared to V fish at two wpff suggesting microbiota played a role in digesting the essential amino acids of M feed. The excessive mucin O-degradation revealed in V fish at two wpff was mitigated in later life stages after NP, suggesting physiological adaptability and tolerance to V diet. Future studies are required to explore more fully how the microbiota functionally contributes to the NP.