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Rice–aquaculture farming has been widely recognized as a sustainable symbiosis system for its potential to increase crop yield and income for farmers and to cultivate aquaculture products simultaneously through co-culture. Nevertheless, the performance of co-culture production systems depends on various factors, but few studies have examined the factors that affect their performance, leading to a reliance on trial and error in the operation and design of these systems. In this study, a systematic review was conducted to investigate factors that impact the performance of the rice–aquaculture system, both economically and environmentally. Four main categories of factors, including field conditions and management, feeding supplement, aquaculture farming, and rice cultivation were identified to be related to the success of the rice–aquaculture system. By analyzing data from diverse geographic regions, this study also elucidated general trends, region-specific challenges, and opportunities within rice–aquaculture practices. Future directions were also proposed with the need to develop complementary guidelines for the design and management of co-culture systems to maximize economic benefit while minimizing negative environmental effects, thus improving the overall sustainability of the co-culture production system. Created with BioRender.com and farmer inset is copyright (c) 2022 pngimg.com and made available under an Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) [ABSTRACT FROM AUTHOR]

Taurine (2-aminoethanesulfonic acid) is a sulfur-containing non-protein amino acid that is widely present in the body in a free state. Taurine is a nutritional additive that maintains the normal physiological functions of fish and plays an important role in the growth and development, metabolism, osmoregulation, digestive physiology, immune enhancement, and antioxidant properties of aquatic animals. The addition of taurine can improve the negative effects of low-fishmeal feed on the production performance, health, and quality of aquatic products. The article introduces the characteristics of taurine and its synthesis and metabolic pathways, reviews the recommended dosage of taurine in lowfishmeal feed, and summarizes the impact of taurine addition in low-fishmeal feed on the growth and health of aquatic animals, providing a reference for the rational use of taurine in low-fishmeal feed for aquatic animals. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Dalian Ocean University is the property of Journal of Dalian Ocean University Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Simple Summary: To improve the quality of feedstuff for use as animal feed, four alternative pretreatment methods (extrusion, microwave irradiation, gamma irradiation, or NaOH hydrolysis) were applied for cassava chips. The proximate chemical compositions and nutritive profiles were significantly altered due to the pretreatment methods (p < 0.05), as well as the physicochemical properties in aspects to enhance enzymatic hydrolysis. Based on in vitro carbohydrate digestibility, microwave irradiation was suitable for improving nutrient bioavailability in the aquatic animal model, Nile tilapia, while microwaving, followed by extrusion or gamma irradiation, was suitable for the poultry model, broiler chicken. However, no differences were observed for the ruminant model. Our in vitro screening investigations support the use of pretreated cassava chips for animal feeding, especially for fish and broiler. Physical pretreatment procedures can significantly influence the quality of food and feed raw materials. To increase the ability to be digested in animals, cassava chips were pretreated by four alternative methods (extrusion, microwave irradiation, gamma irradiation, or NaOH hydrolysis), and then the chemical composition, physicochemical properties, and in vitro digestibility of the pretreated samples were assessed and compared with unprocessed cassava chips (control). The chemical compositions (crude protein, ether extract, neutral detergent fiber, acid detergent fiber, ash, non-fiber carbohydrate, and gross energy) were significantly altered due to the pretreatment methods (p < 0.05). The nutritive profile was qualitatively changed when assessed through Fourier-transform infrared spectroscopy. Some physicochemical properties in association with enzymatic hydrolysis, which include pH, water solubility, water absorption capacity, thermal properties (differential scanning calorimetry), diffraction pattern (X-ray diffractometry), and microstructure (scanning electron microscopy), were significantly changed. In vitro carbohydrate digestibility based on digestive enzyme extracts from Nile tilapia (Oreochromis niloticus) suggests the microwaving method for cassava chips preparation, while microwaving, followed by extrusion or gamma irradiation, was suggested for broiler (Gallus gallus domesticus). There were no differences in the pepsin-cellulase digestibility values tested for the ruminant model. These findings suggest the use of pretreated cassava chips in animal feeding. [ABSTRACT FROM AUTHOR]

Single‐visit surveys of plots are often used for estimating the abundance of species of conservation concern. Less‐than‐perfect availability and detection of individuals can bias estimates if not properly accounted for. We developed field methods and a Bayesian model that accounts for availability and detection bias during single‐visit visual plot surveys. We used simulated data to test the accuracy of the method under a realistic range of generating parameters and applied the method to Florida's east coast diamondback terrapin in the Indian River Lagoon system, where they were formerly common but have declined in recent decades. Simulations demonstrated that the method produces unbiased abundance estimates under a wide range of conditions that can be expected to occur in such surveys. Using terrapins as an example we show how to include covariates and random effects to improve estimates and learn about species‐habitat relationships. Our method requires only counting individuals during short replicate surveys rather than keeping track of individual identity and is simple to implement in a variety of point count settings when individuals may be temporarily unavailable for observation. We provide examples in R and JAGS for implementing the model and to simulate and evaluate data to validate the application of the method under other study conditions. [ABSTRACT FROM AUTHOR]

Aquatic animals are an important source of food for humans, yet little is known about their potential to transfer zoonotic viruses. Multiple recent cases of SARS-CoV-2 from cold-chain aquatic food and environmental samples has evoked worldwide concerns, and even though these cases pale in comparison to poultry and livestock. To investigate the potential threat of food from aquatic animals, we map their transcriptomes to the genomes of human respiratory- and intestine-related viruses. Analyses only find an influenza virus sequence in a salmon (Salmo salar) skin transcriptome. BLAST and phylogenetic analyses identify this sequence as influenza A, and this likely owes to contamination from a worker. Thus, when prepared properly, aquatic animals can provide great nutritional benefits to humans while posing minimal health risks.

The utilization of algae in aquaculture is environmentally friendly, safe, and cost-effective and can effectively substitute for fish meal and fish oil in aquatic feeds. Incorporating algae as dietary supplements leads to significant enhancements in aquatic animals' health and also improves the aquatic ecosystem. Algae are rich sources of nutrients and serve as the foundational food source in the aquatic food chain. Currently, 40 different algae species are employed in aquaculture. Furthermore, algae contributes to elevating the overall quality of aquatic feed products. Aquaculture stands as the most vital food production sector globally; however, challenges such as infection outbreaks and aquatic environmental pollution pose significant threats to the sustainable growth of this industry. An alternative strategy for mitigating environmental issues and improving aquatic production involves the utilization of algae. The novelty in the applications of algae in aquaculture stems from their multifaceted roles and benefits, such as their capacity to improve water quality, serve as nutrient-rich feed supplements, and enhance the overall health and productivity of aquatic species. These versatile applications of algae represent a fresh and innovative approach to sustainable aquaculture practices. This review furnishes insights into the use of algae, algae extracts, or components derived from algae to enhance water quality. Additionally, it covers the utilization of algae-based feed supplements, boosting of the immune system, enhanced growth performance, and disease resistance in aquatic animals. [ABSTRACT FROM AUTHOR]

We summarized the biological characteristics, nutritional composition of earthworm and its application in aquatic feed. The research of earthworm meal, fresh earthworm and other earthworm products in different aquatic animals was briefly described. This review also summarized adding appropriate level of earthworm products in aquatic animal feed could promote aquatic animals′ growth and health. The problems existing in the process of earthworm used as aquatic feed were put forward in order to provide reference for the aquatic feed development and production. [ABSTRACT FROM AUTHOR]

Flavonoids widely exist in various organs of higher plants, and have biological functions such as high efficiency, low toxicity, promoting absorption, promoting growth and regulating immunity. Flavonoidsin can improve growth performance of animals, enhance body immunity, improve body antioxidation, which have a wide range of application prospects in animal husbandry. The paper reviews the biological functions of plant flavonoids, and summarizes the application research progress of plant flavonoids in aquatic animal growth, to provide reference for further development and utilization of plant flavonoids in aquaculture industry. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Dalian Ocean University is the property of Journal of Dalian Ocean University Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Single‐visit surveys of plots are often used for estimating the abundance of species of conservation concern. Less‐than‐perfect availability and detection of individuals can bias estimates if not properly accounted for. We developed field methods and a Bayesian model that accounts for availability and detection bias during single‐visit visual plot surveys. We used simulated data to test the accuracy of the method under a realistic range of generating parameters and applied the method to Florida's east coast diamondback terrapin in the Indian River Lagoon system, where they were formerly common but have declined in recent decades. Simulations demonstrated that the method produces unbiased abundance estimates under a wide range of conditions that can be expected to occur in such surveys. Using terrapins as an example we show how to include covariates and random effects to improve estimates and learn about species‐habitat relationships. Our method requires only counting individuals during short replicate surveys rather than keeping track of individual identity and is simple to implement in a variety of point count settings when individuals may be temporarily unavailable for observation. We provide examples in R and JAGS for implementing the model and to simulate and evaluate data to validate the application of the method under other study conditions.

Water quality determines the success of inland aquaculture. The factor determining water quality is the concentration of dissolved oxygen (DO). To find effective paddlewheel aerators to enhance DO concentration, nine model aerators were examined: aerator 4 blades, 6 blades and 8 blades with variations of 12 holes per blade, 16 holes per blade and 20 holes per blade. They were rotated at 80 RPM, 100 RPM, 120 RPM and 140 RPM. The results show the higher the rotation speed is, the bigger the increment of DO concentration is, but their relationship is not linier. There is a condition when increasing rotation does not affect the DO concentration meaningly. The results also indicate the greater number of blades increase more DO concentration. The results also suggest the greater number of holes per blade initially increase DO concentration increment, but after 16 holes the increment tends to reduce. It is predicted owing to that widening surface interaction due to the holes in the blade is taken over by reducing the volume of splashed water. In this research, likely the aerator with 8 blades, 16 holes per blade and rotated at 120 RPM is the optimum one to increase DO concentration. However, if the energy consumption is also the concern, the aerator with 6 blades and 16 holes per blade likely is the better choice.

Autophagy is a conserved intracellular degradation process that is required to maintain host homeostasis and cope with invading pathogens. Over the past few decades, studies on mammals have greatly increased our understanding of the relationship between autophagy and virus infection. Autophagy may convey the invader to lysosomes to degrade or activate the host immune response against virus replication. However, many viruses have developed some strategies that evade the degradative nature of autophagy or hijack this pathway for their gain. It follows that autophagy during viral infection is a double‐edged sword. In contrast to mammals, the review on autophagy modulated by the aquatic animal virus is limited. Here, after a brief description of the main information about autophagy, we highlight current progress on the interplays between autophagy and virus infection in aquatic animals, including the phenomenon of autophagy upon virus infection, the effect of modulating autophagy on virus replication, and the crosstalk between autophagy and immune response during virus infection. This review will help us better understand the pathogenic mechanism of aquatic animal viruses and develop proper antiviral countermeasures aimed at modulating autophagy. [ABSTRACT FROM AUTHOR]

Physical pretreatment procedures can significantly influence the quality of food and feed raw materials. To increase the ability to be digested in animals, cassava chips were pretreated by four alternative methods (extrusion, microwave irradiation, gamma irradiation, or NaOH hydrolysis), and then the chemical composition, physicochemical properties, and in vitro digestibility of the pretreated samples were assessed and compared with unprocessed cassava chips (control). The chemical compositions (crude protein, ether extract, neutral detergent fiber, acid detergent fiber, ash, non-fiber carbohydrate, and gross energy) were significantly altered due to the pretreatment methods (p < 0.05). The nutritive profile was qualitatively changed when assessed through Fourier-transform infrared spectroscopy. Some physicochemical properties in association with enzymatic hydrolysis, which include pH, water solubility, water absorption capacity, thermal properties (differential scanning calorimetry), diffraction pattern (X-ray diffractometry), and microstructure (scanning electron microscopy), were significantly changed. In vitro carbohydrate digestibility based on digestive enzyme extracts from Nile tilapia (Oreochromis niloticus) suggests the microwaving method for cassava chips preparation, while microwaving, followed by extrusion or gamma irradiation, was suggested for broiler (Gallus gallus domesticus). There were no differences in the pepsin-cellulase digestibility values tested for the ruminant model. These findings suggest the use of pretreated cassava chips in animal feeding.

The demand for high-quality aquatic products is gradually increasing with the gradual improvement of people's living standards. And the increase in aquaculture density will induce a series of aquatic animal diseases and aquatic environmental problems. Therefore, it is urgent to find a green, safe and effective means to solve the problems caused by high-density aquaculture. Probiotic assisted aquaculture technology has shown good results in resolving this difficult problem and has a broad application prospect. This paper mainly introduces probiotics and their preparations commonly used in aquaculture, and summarizes the mechanism of probiotics promoting the efficiency of high-density aquaculture, aiming to provide theoretical basis for the further application of probiotics in high-density aquaculture. [ABSTRACT FROM AUTHOR]

Biofloc meal, a by-product from biofloc technology, is gaining more and more attention from researchers as a non grain new protein source due to its high content of probiotics and rich bioactive compounds, sustainability and no competition with human food. Relevant studies at home and abroad have confirmed that biofloc meal has a positive effect on the growth and organism health of aquatic animals. In this paper, based on the reference of relevant studies at home and abroad, the nutritional characteristic of biofloc meal and its effects on growth performance, digestive function, immune function, antioxidant capacity and disease resistance were summarized, aiming to provide a basis for rational development and utilization of no grain protein sources, saving fish meal protein and optimizing the feed formulated of aquatic animal. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Dalian Ocean University is the property of Journal of Dalian Ocean University Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

People expect pollution-free and residue-free green aquatic products earnestly. However, in recent years, with the rapid expansion of aquaculture farming density and scale, aquatic animal diseases are frequent, and problems such as strain resistance caused by the abuse of antibiotics have gradually emerged, which bring challenges to the sustainable and green development of aquaculture. Chitosan oligosaccharides and chitin oligosaccharides due to non-toxic, nonharmful, and residue-free characteristics, with a variety of bioactive functions and a wide range of sources, is gradually valued and studied by many scholars. Chitosan oligosaccharides are oligosaccharides obtained from chitin or chitosan by enzymatic, chemical or physical methods. Chitin oligosaccharides are degradation products of chitin or acetylation products of oligochitosan. At present, experimental studies on chitosan oligosaccharides and chitin oligosaccharides as green feed additives, vaccine adjuvants and aquatic products water retention and freshness have been carried out, and they have broad development space and application prospects in aquaculture. Based on this, this review summarizes the preparation methods of chitosan oligosaccharides and chitin oligosaccharides, and discusses the application of Chitosan oligosaccharides and chitin oligosaccharides in aquatic animal feed additives, vaccine adjuvants and aquatic products water preservation and freshness, highlighting their biological activities in regulating aquatic animal immunity, promoting growth, anti-oxidation and affecting fish body composition, with a view to providing references for further research and industrial application of Chitosan oligosaccharides and chitin oligosaccharides in aquaculture.

Klebsiella pneumoniae can cause life-threatening pneumonia in humans. The bacterium is also the causative agent of nosocomial infection diseases. In our recent research, we reported, for the first time, the presence of K. pneumoniae in fourteen species of aquatic animals sampled in Shanghai, China. Here, we further investigated the bacterial survival and genome evolution traits. The results revealed that K. pneumoniae isolates (n = 7), recovered from 7 species of commonly consumed aquatic animals, had multiple antibiotic and heavy metal resistance profiles. The isolates were capable of growing vigorously at pH 4.5−7.5 and 0.5−1.0% NaCl in TSB medium at 37 °C. Draft genome sequences of the K. pneumoniae isolates were determined (5,256,522−5,857,823 bp, 56.35–57.81% GC contents), which carried many mobile genetic elements, including genomic islands (n = 87), prophages (n = 14), integrons (n = 4), and insertion sequences (n = 22), indicating possible active horizontal gene transfer during the genome evolution. Meanwhile, numerous strain-specific (n = 199−605) genes, antibiotic resistance (n = 20−35, e.g., β-lactamase) genes, and virulence (n = 43−59, e.g., enterobactin)-related genes, were also identified, demonstrating considerable genome variation in the K. pneumoniae isolates. Overall, the results of this study fill prior gaps in understanding the K. pneumoniae genomes derived from aquatic animals. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Chinese Ritual, Theatre & Folklore / Mínsú Qǔyì is the property of Shih Ho-Cheng Folk Culture Foundation and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In aquatic animals, the gut microbiota has a significant function in host health and is impacted by the environmental microbiota. To conveniently monitor, assess and predict aquatic animals’ health, a general and effective microbiota health index (microHI) would be helpful, and the correlation between the aquatic environmental microHI and wildlife gut microHI could be expected. Here, we proposed a general microHI based on the microbial phenotypes of mobile element content, potential pathogenicity and oxidative stress tolerance, and then tested the reliability of the fish gut microHI and its correlation with the environmental microHI in the middle Yangtze River. The results showed that there were positive correlations among the abundance ratios of microbes with the microbial phenotypes of mobile element content, potential pathogenicity and oxidative stress tolerance, suggesting that defining the microHI using the average abundance ratios of microbes without these microbial phenotypes is suitable. Fish gut samples with a lower microHI were more likely to have been obtained from specimens with a disordered microbiota (always means unhealthy host), indicating that the gut microHI has the potential to be used to evaluate the health status of aquatic animals. In the middle Yangtze River, the aquatic environmental microHI had hundred-kilometers-scale high spatial heterogeneity but month-scale low temporal heterogeneity from June to September 2020, and in the section with a low aquatic environmental microHI, the fish gut samples were more likely to have relatively low gut microHIs, indicating that the environmental microHI has the potential to be used to predict the health status of aquatic animals at the community level. The current work initially showed the possibility of using environmental microHI to predict aquatic animals’ health although it was not very exact and precise. We encourage more researches to assess the quantitative relationship between the aquatic environmental microHI and aquatic animal gut microHI.

The utilization of algae in aquaculture is environmentally friendly, safe, and cost-effective and can effectively substitute for fish meal and fish oil in aquatic feeds. Incorporating algae as dietary supplements leads to significant enhancements in aquatic animals’ health and also improves the aquatic ecosystem. Algae are rich sources of nutrients and serve as the foundational food source in the aquatic food chain. Currently, 40 different algae species are employed in aquaculture. Furthermore, algae contributes to elevating the overall quality of aquatic feed products. Aquaculture stands as the most vital food production sector globally; however, challenges such as infection outbreaks and aquatic environmental pollution pose significant threats to the sustainable growth of this industry. An alternative strategy for mitigating environmental issues and improving aquatic production involves the utilization of algae. The novelty in the applications of algae in aquaculture stems from their multifaceted roles and benefits, such as their capacity to improve water quality, serve as nutrient-rich feed supplements, and enhance the overall health and productivity of aquatic species. These versatile applications of algae represent a fresh and innovative approach to sustainable aquaculture practices. This review furnishes insights into the use of algae, algae extracts, or components derived from algae to enhance water quality. Additionally, it covers the utilization of algae-based feed supplements, boosting of the immune system, enhanced growth performance, and disease resistance in aquatic animals.

People expect pollution-free and residue-free green aquatic products earnestly. However, in recent years, with the rapid expansion of aquaculture farming density and scale, aquatic animal diseases are frequent, and problems such as strain resistance caused by the abuse of antibiotics have gradually emerged, which bring challenges to the sustainable and green development of aquaculture. Chitosan oligosaccharides and chitin oligosaccharides due to non-toxic, nonharmful, and residue-free characteristics, with a variety of bioactive functions and a wide range of sources, is gradually valued and studied by many scholars. Chitosan oligosaccharides are oligosaccharides obtained from chitin or chitosan by enzymatic, chemical or physical methods. Chitin oligosaccharides are degradation products of chitin or acetylation products of oligochitosan. At present, experimental studies on chitosan oligosaccharides and chitin oligosaccharides as green feed additives, vaccine adjuvants and aquatic products water retention and freshness have been carried out, and they have broad development space and application prospects in aquaculture. Based on this, this review summarizes the preparation methods of chitosan oligosaccharides and chitin oligosaccharides, and discusses the application of Chitosan oligosaccharides and chitin oligosaccharides in aquatic animal feed additives, vaccine adjuvants and aquatic products water preservation and freshness, highlighting their biological activities in regulating aquatic animal immunity, promoting growth, anti-oxidation and affecting fish body composition, with a view to providing references for further research and industrial application of Chitosan oligosaccharides and chitin oligosaccharides in aquaculture. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Applied Ecology / Yingyong Shengtai Xuebao is the property of Chinese Journal of Applied Ecology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Klebsiella pneumoniae can cause serious pneumonitis in humans. The bacterium is also the common causative agent of hospital-acquired multidrug-resistant (MDR) infections. Here we for the first time reported the genetic diversity of K. pneumoniae strains in 14 species of edible aquatic animals sampled in the summer of 2018 and 2019 in Shanghai, China. Virulence-related genes were present in the K. pneumoniae strains (n = 94), including the entB (98.9%), mrkD (85.1%), fimH (50.0%), and ybtA (14.9%) strains. Resistance to sulfamethoxazole-trimethoprim was the most prevalent (52.1%), followed by chloramphenicol (31.9%), and tetracycline (27.7%), among the strains, wherein 34.0% had MDR phenotypes. Meanwhile, most strains were tolerant to heavy metals Cu2+ (96.8%), Cr3+ (96.8%), Zn2+ (91.5%), Pb2+ (89.4%), and Hg2+ (81.9%). Remarkably, a higher abundance of the bacterium was found in bottom-dwelling aquatic animals, among which mollusk Tegillarca granosa contained K. pneumoniae 8-2-5-4 isolate from serotype K2 (ST-2026). Genome features of the potentially pathogenic isolate were characterized. The enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR)–based genome fingerprinting classified the 94 K. pneumoniae strains into 76 ERIC genotypes with 63 singletons, demonstrating considerable genetic diversity in the strains. The findings of this study fill the gap in the risk assessment of K. pneumoniae in edible aquatic animals. [ABSTRACT FROM AUTHOR]

Marine organisms' lipid metabolism contributes to marine ecosystems by producing a variety of lipid molecules. Historically, research focused on the lipid metabolism of the organisms themselves. Recent microbiome studies, however, have revealed that gut microbial communities influence the amount and type of lipids absorbed by organisms, thereby altering the organism's lipid metabolism. This has highlighted the growing importance of research on gut microbiota. This review highlights mechanisms by which gut microbiota facilitate lipid digestion and diversify the lipid pool in aquatic animals through the accelerated degradation of exogenous lipids and the transformation of lipid molecules. We also assess how environmental factors and pollutants, along with the innovative use of probiotics, interact with the gut microbiome to influence lipid metabolism within the host. We aim to elucidate the complex interactions between lipid metabolism and gut microbiota in aquatic animals by synthesizing current research and identifying knowledge gaps, providing a foundation for future explorations. [Display omitted] • The gut microbiota of aquatic animals release lipases to breakdown and absorb lipids. • Microbiota metabolize primary bile acids. • Desaturase and elongase activity alter fatty acid profiles. • Gut microbiota make SCFAs from indigestible carbohydrates. • Environmental variables alter gut microbiome. [ABSTRACT FROM AUTHOR]

The river hyporheic zone is the main area of surface-subsurface connection and exchange. Surface-subsurface water exchange promotes the transport and transformation of biogenic substances and can conserve water resources, stabilize regional ecological environment, which provide a great habitat for aquatic life. Therefore, understanding the relationship between the activities of aquatic animals and surface-subsurface water exchange is the key to deep cognition and scientific protection of aquatic ecosystems. This paper reviews previous studies on the feedback of aquatic activities to the surface-subsurface water exchange process, for example, the biofilm formed by benthic microorganisms can absorb or retain biogenic substances, prolonging and changing the migration time and path of substances; the activities of aquatic animals can affect the physical characteristics of riverbed, such as permeability and porosity of streambed, which in turn affect the hyporheic exchange flux and substances transformation efficiency; the block and disturbance of water flow by aquatic plants can also affect the surface-subsurface water exchange process. According to the current researches in this field, three important research directions of the relationship between river hyporheic exchange and aquatic organisms are proposed in this study: the theory of mutual feeding between hyporheic exchange and aquatic organisms; relationship between surface-subsurface water exchange and aquatic ecological function; biogeochemical coupling processes in hyporheic zone. [ABSTRACT FROM AUTHOR]

Abstract The commercial aquatic animal microbiome may markedly affect the successful host's farming in various aquaculture systems. However, very little was known about it. Here, two different aquaculture systems, the rice–fish culture (RFC) and intensive pond culture (IPC) systems, were compared to deconstruct the skin, oral, and gut microbiome, as well as the gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis). Higher alpha‐diversity and functional redundancy of P. sinensis microbial community were found in the RFC than those of the IPC. The aquaculture systems have the strongest influence on the gut microbiome, followed by the skin microbiome, and finally the oral microbiome. Source‐tracking analysis showed that the RFC's microbial community originated from more unknown sources than that of the IPC across all body regions. Strikingly, the RFC's oral and skin microbiome exhibited a significantly higher proportion of generalists and broader habitat niche breadth than those of the IPC, but not the gut. Null model analysis revealed that the RFC's oral and skin microbial community assembly was governed by a significantly greater proportion of deterministic processes than that of the IPC, but not the gut. We further identified the key gene and microbial contribution to five significantly changed gut metabolites, 2‐oxoglutarate, N‐acetyl‐d‐mannosamine, cis‐4‐hydroxy‐d‐proline, nicotinamide, and l‐alanine, which were significantly correlated with important categories of microbe‐mediated processes, including the amino acid metabolism, GABAergic synapse, ABC transporters, biosynthesis of unsaturated fatty acids, as well as citrate cycle. Moreover, different aquaculture systems have a significant impact on the hepatic lipid metabolism and body shape of P. sinensis. Our results provide new insight into the influence of aquaculture systems on the microbial community structure feature and assembly mechanism in an aquatic animal, also highlighting the key microbiome and gene contributions to the metabolite variation in the gut microbiome‐metabolome association.

• Microplastic has adverse effects on the respiratory system of aquatic animals. • Prolonged exposure to microplastics induces oxidative stress. • Fish are more prone to lipid peroxidation than shellfish. • PS has the greatest neurotoxic impact on aquatic organisms. The presence of microplastics in the aquatic environment has attracted widespread attention. A large number of studies have assessed the effects of microplastics on the respiratory system of aquatic animals, but the results are not directly comparable across studies due to inconsistent evaluation criteria. Therefore, we adopted an integrated research approach that can integrate and parse complex data to improve reliability, conducted a systematic review and meta-analysis of 35 published studies, and elucidated the mechanisms of microplastic damage to cells. The results showed that PE had the greatest impact on aquatic animals, and fish were the most sensitive to the effects caused by microplastics, with oxidative stress induced by exposure concentrations exceeding 1000 µg/L or exposure times exceeding 28 days, leading to depletion of antioxidant defenses, cellular damage, inflammatory responses, and behavioral abnormalities. As this review is based on existing studies, there may be limitations in terms of literature quality, data availability and timeliness. In conclusion, we suggest to combat microplastic pollution by limiting plastic use, promoting plastic substitution and recycling, and enhancing microplastic capture degradation technologies. [Display omitted] [ABSTRACT FROM AUTHOR]

Klebsiella pneumoniae can cause life-threatening pneumonia in humans. The bacterium is also the causative agent of nosocomial infection diseases. In our recent research, we reported, for the first time, the presence of K. pneumoniae in fourteen species of aquatic animals sampled in Shanghai, China. Here, we further investigated the bacterial survival and genome evolution traits. The results revealed that K. pneumoniae isolates (n = 7), recovered from 7 species of commonly consumed aquatic animals, had multiple antibiotic and heavy metal resistance profiles. The isolates were capable of growing vigorously at pH 4.5−7.5 and 0.5−1.0% NaCl in TSB medium at 37 °C. Draft genome sequences of the K. pneumoniae isolates were determined (5,256,522−5,857,823 bp, 56.35–57.81% GC contents), which carried many mobile genetic elements, including genomic islands (n = 87), prophages (n = 14), integrons (n = 4), and insertion sequences (n = 22), indicating possible active horizontal gene transfer during the genome evolution. Meanwhile, numerous strain-specific (n = 199−605) genes, antibiotic resistance (n = 20−35, e.g., β-lactamase) genes, and virulence (n = 43−59, e.g., enterobactin)-related genes, were also identified, demonstrating considerable genome variation in the K. pneumoniae isolates. Overall, the results of this study fill prior gaps in understanding the K. pneumoniae genomes derived from aquatic animals.

Adding appropriate amount of microorganisms to aquatic animal bait can promote its growth and maintain the body's health. The article reviews the effects of adding microorganisms, microbial components, microbial metabolites and compound addition of microorganisms and exogenous substances to freshwater aquaculture aquatic animal feed, in order to provide references for the promotion and application of feed microorganisms in freshwater aquaculture. [ABSTRACT FROM AUTHOR]

Local understanding of migratory species is critical towards the global conservation agenda. The present study, conducted from 2016–2018, aimed to (i) examine the demographic characteristics of fishers operating within Ilaje axis in the Atlantic Ocean; (ii) determine species and status of sea turtles in the area; (iii) investigate their sighting periods; (iv) evaluate fishers' behaviour towards sea turtles; (v) assess fishers' sea turtles' conservation awareness; (vi) determine the roles of demographic factors on the fishers' level of sea turtles utilisation and conservation. A multi-stage sampling procedure was employed to select the study sites and respondents. The sample size consisted of 364 fishers from six communities. Data were collected using personal interviews, a structured questionnaire and direct observation. During each interview, photographs of six sea turtles reportedly found in Nigeria were presented for easy identification. Data collected were analysed using descriptive statistics, Pearson's correlation and multiple linear regressions. The results revealed that all fishers hunting along the Atlantic Ocean from Ilaje axis are male. The majority of them (97.2%) are within the active age of 21–60 years old with over two-third of them educated (81.0%). Two species of sea turtles (Lepidochelys olivacea, Dermochelys coriacea) are foraging in the area, although L. olivacea was mostly encountered. These sea turtles migrate into the area from April and vacate around October in each year. During this period, some L. olivacea individuals were accidentally trapped inside nets set for hunting crustaceans especially Malacostraca: Decapoda. About 92.3% of the accidental captured sea turtles had a good physical appearance with a body condition index of 1.77 ± 0.09 and 1.36 ± 0.04 in male and female, respectively. Accidentally captured sea turtles are consumed as meat indiscriminately. The predictors of sea turtles utilisation were fishers' age (β = 0.15, p < 0.05) and family size (β = -0.02, p < 0.05) while the fishers' educational level is the predictor of sea turtles' conservation (β = 0.02, p < 0.05). Also, the study showed that there were positive and significant relationships between fishers' personal factors and their rationale for capturing sea turtles (r = 0.23, p < 0.01) and sea turtle's conservation awareness (r = 0.22, p < 0.01). A low knowledge regarding sea turtles' conservation status and its non-consumptive benefits are suggested responsible for high indiscriminate consumption and little participation in its conservation. Urgent sea turtles' conservation awareness in the study area is hereby recommended.

Aquaculture is a rapidly growing industry that brings huge economic benefits. Genome-wide association study (GWAS) is critical for aquaculture species’ productivity, sustainability, and product quality. The current integrated GWAS pipeline either includes only specific limited steps or requires a complex prerequisite environment and configurations. In this study, we developed AquaGWAS, a highly user-friendly graphical user interface (GUI) GWAS pipeline, by integrating four well-known GWAS models. AquaGWAS is a complete GWAS pipeline from preprocessing, multiple choice of GWAS models, postprocessing to visualizations. AquaGWAS offers GUI easy running on Linux and automatically generates running command lines for high-performance computing (HPC) or non-GUI servers. AquaGWAS is free from installation, configurations, and complicated augment inputs. It offers whole packages of required reference files for 27 common aquatic species. Furthermore, aiming at the issue that the availability of genomic reference sequences limits single-nucleotide polymorphism (SNP) detection, we attempted to detect SNPs in Pacific abalone using classical alignment-based reference-required strategy and k-mer-based reference-free strategy combined with downstream AquaGWAS. On 222 resequencing data of Pacific abalone, two strategies detected 221,061 and 230,213 variants, respectively, with 180,161 common variants. The two strategies emphasized different variant situations: capturing variants missed by incomplete or inaccurate reference genomic sequence (k-mer-based) and capturing the indel variants having the baseline of genomic sequence (alignment-based). Combining the two strategies offers a complementary framework to obtain the accurate and complete GWAS analysis for non-model organism species. AquaGWAS is available at https://github.com/Ying-Lab/AquaGWAS.

Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) sense microbial-associated molecular patterns (MAMPs) to activate the innate immune responses. RLRs in aquatic animals include RIG-I, MDA5, LGP2, mollusc RIG-I-like and MDA5-like proteins, which exhibit structural and functional diversity. RLRs data from 30 species of aquatic animals were collected for analysis. Not all species contain all the RLR members. RIG-I is absent in the orders of Perciformes, Cichliformes and Pleuronectiformes, and LGP2-like protein is absent in the class of Bivalvia. Due to the differences in species and variants, the homologous proteins have different responses to pathogens. LGP2 works as an immune homeostasis regulator to balance the immune response. The phylogenetic analysis demonstrates RIG-I and mollusc RIG-I-like present in the same evolutionary branch and appear in the early stage. RIG-I is an ancient PRR in innate antiviral immunity. The prototype of antiviral immune system has emerged in aquatic mollusc. Aquatic animal RLRs were analyzed and summarized in terms of structures, functions, and evolutions, which provide the basic information for future researches in RLRs. Base on the diversity of species and RLRs, more and in-depth studies in aquatic animal RLRs should be done.

Klebsiella pneumoniae can cause serious pneumonitis in humans. The bacterium is also the common causative agent of hospital-acquired multidrug-resistant (MDR) infections. Here we for the first time reported the genetic diversity of K. pneumoniae strains in 14 species of edible aquatic animals sampled in the summer of 2018 and 2019 in Shanghai, China. Virulence-related genes were present in the K. pneumoniae strains (n = 94), including the entB (98.9%), mrkD (85.1%), fimH (50.0%), and ybtA (14.9%) strains. Resistance to sulfamethoxazole-trimethoprim was the most prevalent (52.1%), followed by chloramphenicol (31.9%), and tetracycline (27.7%), among the strains, wherein 34.0% had MDR phenotypes. Meanwhile, most strains were tolerant to heavy metals Cu2+ (96.8%), Cr3+ (96.8%), Zn2+ (91.5%), Pb2+ (89.4%), and Hg2+ (81.9%). Remarkably, a higher abundance of the bacterium was found in bottom-dwelling aquatic animals, among which mollusk Tegillarca granosa contained K. pneumoniae 8-2-5-4 isolate from serotype K2 (ST-2026). Genome features of the potentially pathogenic isolate were characterized. The enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR)–based genome fingerprinting classified the 94 K. pneumoniae strains into 76 ERIC genotypes with 63 singletons, demonstrating considerable genetic diversity in the strains. The findings of this study fill the gap in the risk assessment of K. pneumoniae in edible aquatic animals.

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Single-cell RNA sequencing (scRNA-seq) is widely adopted for identifying the signature molecular markers or regulators in cells, as this would benefit defining or isolating various types of cells. Likewise, the signature transcriptome profile analysis at the single cell level would well illustrate the key regulators or networks involved in gametogenesis and gonad development in animals; however, there is limited scRNA-seq analysis on gonadal cells in lower vertebrates, especially in the sexual reversal fish species. In this study, we analyzed the molecular signature of several distinct cell populations of Asian seabass adult ovaries through scRNA-seq. We identified five cell types and also successfully validated some specific genes of germ cells and granulosa cells. Likewise, we found some key pathways involved in ovarian development that may concert germline-somatic interactions. Moreover, we compared the transcriptomic profiles across fruit fly, mammals, and fish, and thus uncovered the conservation and divergence in molecular mechanisms that might drive ovarian development. Our results provide a basis for studying the crucial features of germ cells and somatic cells, which will benefit the understandings of the molecular mechanisms behind gametogenesis and gonad development in fish.

The interactions between sediment microbial assemblages and submerged macrophytes in aquatic ecosystems can be potentially regulated by benthic macrofauna, and the regulation effect may be closely related to macrophyte species with distinct properties; however, little information on this is available. An aquarium experiment was designed to evaluate the role of snail Bellamya aeruginosa (Reeve) in regulating sediment bacterial communities associated with two common types of submerged macrophytes, Ceratophyllum demersum (L.) and Hydrilla verticillata (L. f.) Royle. The results showed that the effect of B. aeruginosa on sediment bacterial diversity and richness was plant species-specific; the presence of B. aeruginosa increased the bacterial diversity and richness in C. demersum systems while slightly decreased them in H. verticillata systems. Similar variations in the predicted microbial functions related to matter cycle in these systems were observed. Bacterial community composition patterns were also modified by B. aeruginosa; in its presence, the discrepancy between systems harbouring two different plants diminished, although the effect was limited. Application of the linear discriminant analysis effect size (LEfSe) method showed that the presence of B. aeruginosa resulted in appearance of significantly different bacterial taxa mainly in the C. demersum systems. Redundancy analysis showed that available phosphorus and NH4+ were significantly related to the observed variations in bacterial community compositions across the samples. Overall, a plant species-specific role of B. aeruginosa in modifying sediment bacterial communities and functions was found. [ABSTRACT FROM AUTHOR]

The paper provides a short overview of Brazilian aquaculture production and some of the influences affecting its development. Data on total and species‐specific production are provided along with the locations, numbers of producers, their market contributions and influences. The focus is on some of the key groups, not all, especially tilapia, tambaqui, shrimp, prawn and mollusc farming. The wider influences on production including markets, management practices, technology, resources and research and also consumer and global influences are briefly mentioned to locate the developments in a wider context. [ABSTRACT FROM AUTHOR]

Aquatic vertebrates are very abundant in the world, and they are of tremendous importance in providing global food security and nutrition. However, emergent and resurgent viruses, such as ranavirus (e.g., Rana grylio virus, RGV and Andriasd avidianus ranavirus, ADRV), herpesvirus (e.g., Carassius carassius herpesvirus, CaHV), reovirus (e.g., grass carp reovirus 109, GCRV-109, Scophthal musmaximus reovirus, SMReV and Micropterus salmoides reovirus, MsReV), and rhabdovirus (e.g., Siniper cachuatsi rhabdovirus, SCRV and Scophthal musmaximus rhabdovirus, SMRV) can cause severe diseases in aquaculture animals and wild lower vertebrates, such as frogs, giant salamanders, fish, and so on. Here, we will briefly describe the symptoms produced by the aforementioned viruses and the molecular basis of the virus–host interactions. This manuscript aims to provide an overview of viral diseases in lower vertebrates with an emphasis on visible symptomatic manifestations and pathogenesis.