Aquaculture is critical to reduce protein deficiencies and supplement the world’s demand for seafood. However, the culture environment predisposes farmed animals to infectious diseases. In particular, the high density of fish, crustacean, mollusk, sea cucumber or algal species allows for the rapid spread of infectious diseases resulting in devastating losses. Massive amounts of antibiotics have been used to sustain aquaculture production. This has led to the critical need to evaluate the impact of current control measures and optimize disease management schemes with an emphasis on global impact and sustainability. Furthermore, local and global changes have enhanced the pathogens’ effects over aquaculture settings because increased temperature and pollution may trigger virulence genes and toxin production. Technological developments including biofloc technology, integrated multitrophic systems, recirculating aquaculture systems and probiotics have contributed to enhancing aquaculture sustainability and reducing the need for high loads of antibiotics and other chemicals. Furthermore, biotechnological tools (e.g., omics and cell biology) have shed light on cellular processes in the health and disease of reared organisms. Metagenomics is a reliable and relatively quick tool to identify microbial communities in aquaculture settings.

Climate change will impact coastal ecosystems, threatening subsistence fisheries including those in mangrove forests. Despite their global contributions and roles in nutrition and cultural identity, mangrove subsistence fisheries are poorly studied. Here, we offer a foundation for improving the management of mangrove subsistence fisheries to deal with the impending effects of climate change. This multidisciplinary review—drawing on organismal biology, ecology, fisheries, and social science—focuses on the climate impacts relevant to mangrove ecosystems: heat waves, low-category, and high-category typhoons. First, we provide an overview of the mangroves, their harvestable stocks (fish, crustaceans, molluscs), and the fishers, offering an understanding of how they may be affected by relevant environmental variables; i.e., shifts in temperature, salinity, oxygen, flooding, and sediments. Then, we examine the potential effects of climate change on mangrove stocks and fishers, indicating the scope of impending changes. By combining the above information, we develop a simple model that forecasts the number of “fishing-days” lost by fishers due to climate change over the next decade (between 11 and 21 days will be lost per year per fisher). This indicates which aspects of climate change will have the greatest impacts on stocks and fishers. We found that high-category typhoons had more impacts than heat waves, which in turn had a greater impact than low-category typhoons). Finally, recognising gaps in our knowledge and understanding, we offer recommendations for approaches for future work to improve our predictions.

Genomic selection (GS) applied to the breeding of aquatic animals has been of great interest in recent years due to its higher accuracy and faster genetic progress than pedigree-based methods. The genetic analysis of complex traits in GS does not escape the current excitement around artificial intelligence, including a renewed interest in deep learning (DL), such as deep neural networks (DNNs), convolutional neural networks (CNNs), and autoencoders. This article reviews the current status and potential of DL applications in phenotyping, genotyping and genomic estimated breeding value (GEBV) prediction of GS. It can be seen from this article that CNNs obtain phenotype data of aquatic animals efficiently, and without injury; DNNs as single nucleotide polymorphism (SNP) variant callers are critical to have shown higher accuracy in assessments of genotyping for the next-generation sequencing (NGS); autoencoder-based genotype imputation approaches are capable of highly accurate genotype imputation by encoding complex genotype relationships in easily portable inference models; sparse DNNs capture nonlinear relationships among genes to improve the accuracy of GEBV prediction for aquatic animals. Furthermore, future directions of DL in aquaculture are also discussed, which should expand the application to more aquaculture species. We believe that DL will be applied increasingly to molecular breeding of aquatic animals in the future.

Understanding the potential areas suitable for offshore mariculture is crucial to global seafood security. Here, we map the potential global offshore mariculture areas for 23 principal commercial finfish using an ensemble model. The model involves the temporal–spatial heterogeneity of environments and constraints of temperature-dependent hypoxia and cold edges of cultured finfish by metabolic index and lower thermal safety margin, respectively. Our results show that currently, there is 9.16 ± 1.22 million km² of potentially suitable area for offshore finfish mariculture. Under climate change, the potential suitable area will be reduced to between 86.7% and 91.7% of the current size by 2050. Compared to the decline in tropical regions, the expanded potential areas in temperate and polar regions will become more important for global seafood security. The potential offshore finfish mariculture area responds differently to global change among species, and cold-water finfish may benefit from global warming. Overall, despite changes in the distribution of global offshore mariculture areas and replacements of local potential mariculture species, offshore finfish mariculture still holds immense potential in the future.

Indole signaling has been regarded as a promising target to control aquatic diseases. However, the relationship between exogenous indole and the virulence of Edwardsiella piscicida is obscure. E. piscicida is a facultative intracellular pathogen, and has been a model strain in aquaculture. In this study, we investigated the effect of exogenous indole on stress resistance and virulence of E. piscicida in the presence of and absence of endogenous indole (WT and ΔtnaA, respectively). Our results showed that exogenous indole reduced the resistance of WT against strong acidic stress, but enhanced that of ΔtnaA. Also, we found that exogenous indole abated viability of E. piscicida at high temperature, repressed bacterial biofilm formation, impaired bacterial envelope integrity, and weakened bacterial proliferation in macrophages, irrespective of the presence or absence of endogenous indole. These virulence-related phenotypes caused by exogenous indole are reasonably explained by the observation that exogenous indole downregulated the expressions of CpxRA and its target YccA via being responded by CpxA. The effects of exogenous indole on strong acid resistance are partially achieved by changing the expression of GadD, the key functional enzyme of acid resistance system (AR2). We believe that this is the first report about the impact of exogenous indole on strong acid stress and membrane integrity of pathogenic bacteria. Also, we reveal the likely mechanism by which exogenous indole regulates the expressions of virulence-related genes. These findings provide a new understanding on pathogenesis of E. piscicida and contribute to the prevention and control strategies of edwardsiellosis.

Viral nervous necrosis (VNN) caused by a betanodavirus (NNV) is one of the major diseases in Asian seabass (Lates calcarifer) hatcheries. Our previous studies showed that the tbx21 gene was in a QTL for NNV resistance in linkage group 23 in Asian seabass. The expression of this gene was changed in tissues of Asian seabass challenged with NNV. However, the role of tbx21 in NNV resistance remains largely unknown. In this study, tbx21 of Asian seabass was characterized. This gene consists of an ORF of 1866 bp, a 5′ UTR of 357 bp, and a 3′ UTR of 4674 bp. The TBX21 protein showed substantial amino acid similarity (70–96%) with other fish but exhibited lower identity (47–52%) with mammals. One SNP identified in the first intron was significantly associated with NNV resistance. In healthy fish, tbx21 was expressed in all tissues examined, and was highly expressed in the kidney and liver. The expression of tbx21 increased in the eye, gills, heart, kidney and gut, but decreased in the brain and spleen at five days after NNV challenge. Overexpression of tbx21 reduced the replication of NNV, whereas knockdown increased viral expression and virus titers. These results suggest that tbx21 plays a key role in NNV resistance. The SNP in this gene could be used as a marker to facilitate marker-assisted selection for NNV resistance. Further investigation of polymorphisms in the 5’ and 3’ UTRs of tbx21 may provide additional insights into the gene's role in NNV resistance.

Given the importance of the intestinal microbiota in life-long health, increasing attention has been paid to ecological mechanisms that govern microbial succession. Both environmental dispersal and host priority effect play important roles in intestinal microbiota succession of aquatic animals, but their relative importance is unknown. Here, we explore the intestinal microbiota succession and assembly of Litopenaeus vannamei across larvae, postlarvae, juvenile, and preadult stages. We aimed to clarify the relative contributions between environmental dispersal and host priority effect on intestinal microbiota succession. We found that both α- and β-diversity of the intestinal microbiota changed dynamically along with host development. In particular, the intestinal microbiota assemblies were dominated by stochastic processes, except with the larvae stage. The succession of shrimp intestinal microbiota was clearly influenced by internal communities in the intestines of larvae, as well as the external communities in water and sediment. Importantly, the impact of environmental dispersal on the intestinal microbiota succession outweighed the host priority effect during the larvae and postlarvae stages. However, this situation was largely reversed during the juvenile and preadult stages. The possible reason is that, during the larvae and postlarvae stages, shrimp mainly feed on plankton from the environment, and their digestive system remains underdeveloped, the host recruits numerous microbes from the environment and selects specific microbes to aid digestion and nutrient absorption. These findings enhance our understanding of alternate effects of environmental and host factors on the intestinal microbiota succession of aquatic animals and provide a foundation for developing microecological management strategies in shrimp culture.

Fisheries are social-ecological systems. Evaluating the sustainability of fisheries requires methods to measure performance from ecological, economic, social, and governance aspects. Whereas a number of multi-dimensional evaluation tools such as fishery performance indicators (FPIs) have been used for assessing fishery management systems, fishery management practices and data availability are likely to differ substantially among fisheries in different countries. This makes it at least somewhat problematic to precisely adapt this methodology to fisheries within a given country. This study constructed a practical tool to evaluate and compare fishery systems in China. On the basis of an established indicator library and the FPIs tool, indicators in the newly developed tool for comprehensive fisheries evaluation were selected according to the management objectives, data availability, and the authority of relevant indicators. The sustainability assessment tool for Chinese fisheries (SAT-fish) provides a three-tier hierarchical framework covering 60 indicators, of which 48 indicators were extracted from the FPIs tool and 12 indicators were associated with policy statements. Applicability and comprehensiveness of this tool in comparison with six other well-established frameworks were investigated. This tool offers a promising new method to assess the sustainability of fishery systems in China, with great potential to guide Chinese fisheries towards a higher level of sustainability.

Improving the accuracy of fishing ground prediction for oceanic economic species has always been one of the most concerning issues in fisheries research. Recent studies have confirmed that deep learning has achieved superior results over traditional methods in the era of big data. However, the deep learning-based fishing ground prediction model with a single environment suffers from the problem that the area of the fishing ground is too large and not concentrated. In this study, we developed a deep learning-based fishing ground prediction model with multiple environmental factors using neon flying squid (Ommastrephes bartramii) in Northwest Pacific Ocean as an example. Based on the modified U-Net model, the approach involves the sea surface temperature, sea surface height, sea surface salinity, and chlorophyll a as inputs, and the center fishing ground as the output. The model is trained with data from July to November in 2002–2019, and tested with data of 2020. We considered and compared five temporal scales (3, 6, 10, 15, and 30 days) and seven multiple environmental factor combinations. By comparing different cases, we found that the optimal temporal scale is 30 days, and the optimal multiple environmental factor combination contained SST and Chl a. The inclusion of multiple factors in the model greatly improved the concentration of the center fishing ground. The selection of a suitable combination of multiple environmental factors is beneficial to the precise spatial distribution of fishing grounds. This study deepens the understanding of the mechanism of environmental field influence on fishing grounds from the perspective of artificial intelligence and fishery science.

The genus Callistoctopus comprises 13 species, and has been reported mostly in the Western Pacific Ocean. Here, we described three new species from China, Ca. paucilamellus sp. nov., Ca. sparsus sp. nov., and Ca. gracilis sp. nov., based on morphometric and meristic characteristics. The diagnoses, descriptions and detailed morphometric data are provided for each species. The cytochrome c oxidase I (COI) genes of the three new species are sequenced, and compared with related species and analyzed for their systematic positions. Both phylogenetic trees constructed using three mitochondrial genes (12S rRNA, 16S rRNA, COI) and one nuclear gene (Rhodopsin) revealed that our new species formed into two distinct clades with strong support values. One clade included Ca. gracilis sp. nov., Ca. sp. 1, Ca. xiaohongxu, Ca. tenuipes and Ca. paucilamellus sp. nov., which clustered together. The other clade showed that Ca. sparsus sp. nov. was closely related to Ca. sp. 2 and Ca. sp. 3. Ca. luteus and Ca. macropus were located at the base of the Callistoctopus group. Based on our integrative studies, both morphological and molecular evidence suggested strongly that O. minor is more likely to be classified as a species of Callistoctopus. Morphological comparisons were made between the three new species and related taxa, which could be recognized based on the 7–8 gill lamellae of each demibranch, numerous small black spots on the subdermal layer of the arms, and an elongated body.