Spawning habitats are critical for population persistence, yet they remain poorly resolved for many endangered and data-poor marine species. Developing effective and non-invasive approaches to identify these habitats is therefore essential for conservation and management. Here, we integrated bottom trawl surveys with environmental DNA (eDNA) metabarcoding and droplet digital PCR (ddPCR) to investigate the spawning-season distribution of an endangered marine fish, the large yellow croaker (Larimichthys crocea), in the South China Sea. Reproductive activity was suggested during autumn, with a potential aggregation hotspot identified in a narrow depth range (20–41 m), whereas no clear spawning signals were observed during the sampled spring period. This pattern suggests a seasonally aggregated potential spawning habitat, potentially associated with local hydrodynamic conditions. Across methods, eDNA approaches showed higher detection sensitivity than conventional trawl surveys, while ddPCR provided clearer spatial differentiation than metabarcoding. The consistency between molecular and fishery data suggests that eDNA captures major spatial patterns and indicates additional potential distribution areas beyond those detected by trawl surveys. Our results demonstrate that integrating eDNA with traditional surveys improves the reliability of habitat identification, while providing a practical, non-invasive approach for delineating potential critical habitats. This approach supports habitat-based management of endangered marine species, particularly where direct observation or destructive sampling is limited.

Japanese flounder (Paralichthys olivaceus) is an economically important species in China's marine fishery industry. However, due to long-term intensive fishing, its wild population has declined sharply. Artificial stock enhancement has become a core measure for restoring its resources. This study aimed to investigate the effects of different immersion durations and concentrations of SrCl2 solution (10, 20, 40, 80 mg/L) on strontium (Sr) deposition in the otoliths of P. olivaceus, and to systematically evaluate the impacts of Sr marking on the fish's antioxidant capacity and digestive enzyme activity. The results showed that the otolith Sr/Ca ratio was positively correlated with marking concentration and duration; the optimal parameters were 40 mg/L for 4 days, with the Sr/Ca ratio returning to baseline after 30 days post-marking, and a 100% marking success rate. There were no significant differences in body length, body weight, or condition factor between the experimental groups and the control group (p > 0.05), but mortality was significantly increased in the 80 mg/L group. Digestive enzymes exhibited a dose-dependent response to Sr exposure, characterized by activation at low concentrations and inhibition at high concentrations; lipase was the most sensitive, with an inhibition threshold of 10 mg/L. Sr marking within the range of 20-40 mg/L for 4-8 days significantly activated the activity of T-AOC, CAT, GPx, and SOD (p < 0.05) and reduced MDA content, indicating that the antioxidant system was activated without causing persistent oxidative damage. In conclusion, Sr marking is a safe and efficient method for otolith marking in Paralichthys olivaceus. The recommended protocol is immersion in a 40 mg/L SrCl2 solution for 4 days, followed by a 30-day recovery period in clean seawater before being used for stock enhancement evaluation. This study provides a scientific basis and technical support for assessing the effectiveness of stock enhancement in P. olivaceus.

The marine biological carbon pump is a key process in the global carbon cycle, with mesopelagic fish playing a crucial role by facilitating the transport of organic carbon from surface waters to the deep ocean through diel vertical migration (DVM). This process enhances carbon sequestration in mid-depth waters and influences carbon flux at the air-sea interface. Despite their significant biomass, the contribution of mesopelagic fish to carbon export fluxes remains poorly quantified at both global and regional scales. This review synthesizes current research on carbon export mediated by mesopelagic fish DVM, focusing on relevant carbon fluxes in the open ocean and deep regions of marginal seas (e.g., basins, continental slopes, and canyon systems) where mesopelagic fish are known to occur. The review discusses the methods used to quantify these fluxes, the associated challenges, and the implications for global carbon cycling. Finally, the review proposes future research directions to improve our understanding of the role of mesopelagic fish in marine ecosystems and their impact on ocean carbon dynamics in the context of climate change.

Mesopelagic fish are important components of pelagic food webs and contributors to the redistribution of organic matter through diel vertical migration. However, mesopelagic fish communities are often treated as functionally similar groups in ecosystem and biogeochemical studies, despite potential differences in feeding ecology among species. We examined the feeding ecology of two sympatric myctophids, Bolinichthys longipes and Ceratoscopelus warmingii, in the deep scattering layer of the Xisha area, South China Sea, using stomach content analysis combined with trophic niche metrics, diel feeding patterns, and daily ration estimates. Despite co-occurrence at similar depths and trophic levels, both species differed consistently in prey utilization and feeding schedules. Ceratoscopelus warmingii consumed a broad range of prey, including amphipods and euphausiids, whereas B. longipes fed predominantly on copepods. Biomass-based niche metrics indicated separation in dietary contribution of prey, and size-related dietary variation was evident in C. warmingii but limited in B. longipes. Feeding periodicity also contrasted between species: C. warmingii showed a stronger nocturnal increase in stomach fullness, while B. longipes showed no clear diel peak. Daily ration estimates indicated substantial ingestion in both species, but the timing of feeding relative to vertical migration differed. These results suggest that co-occurring mesopelagic fish may interact with different components of the pelagic food web and differ in the coupling between feeding and vertical migration. Recognizing trophic heterogeneity within mesopelagic communities may improve representation of these assemblages in ecosystem and biogeochemical frameworks.

Mesopelagic fishes are important components of pelagic food webs and contributors to the redistribution of organic matter through diel vertical migration, yet their ecological roles are often represented using functionally homogeneous assumptions. We examined the feeding ecology of two sympatric myctophids, Bolinichthys longipes and Ceratoscopelus warmingii, in the deep scattering layer of the Xisha area, South China Sea, using stomach content analysis combined with trophic niche metrics, diel feeding patterns, and daily ration estimates. Despite co-occurrence at similar depths and trophic levels, the species differed consistently in prey utilization and feeding schedules. C. warmingii incorporated a broader range of prey categories, whereas B. longipes fed predominantly on copepods. Biomass-based niche metrics indicated separation in dietary contribution of prey, and ontogenetic dietary shifts were evident in C. warmingii but limited in B. longipes. Feeding periodicity also contrasted between species: C. warmingii showed a distinct nocturnal feeding peak, while B. longipes fed more continuously. Daily ration estimates indicated substantial ingestion in both species, but the timing of feeding relative to vertical migration differed. These results suggest that co-occurring mesopelagic fishes may interact with different components of the pelagic food web and differ in the coupling between feeding and vertical migration. Consequently, species-level trophic behavior may influence pathways by which surface-derived organic matter is processed and redistributed in the ocean interior. Recognizing trophic heterogeneity within mesopelagic communities may improve representation of these assemblages in ecosystem and biogeochemical frameworks.

Golden pompano (Trachinotus ovatus) ranks among the most commercially important and high-yield marine finfish species in Chinese mariculture. In response to the requirement for monitoring fish in aquaculture, this study employed Adaptive Resolution Imaging Sonar (ARIS) to observe the body length, swimming speed, and spatial distribution of untreated (GI group), anesthetized (GII group), and injured (GIII group) T. ovatus in a small offshore cage (1.5 × 1.5 × 2.5 m3). The results demonstrated that the relative error range of the length measurement of the T. ovatus spanned from −3.24 to 4.35, and there was no significant difference between the observed and actual body lengths (ANOVA, p > 0.05). We failed to detect a significant difference in the average speed between the untreated group and the anesthetized group (ANOVA, p > 0.05; Tukey’s HSD, p > 0.05). The injured fish exhibited a significantly lower swimming speed compared to untreated and anesthetized individuals (ANOVA, p < 0.01; Tukey’s HSD, p < 0.01). Untreated individuals and fish with physical injuries exhibited mean vertical distribution depths of 1.06 ± 0.47 m and 1.70 ± 0.51 m, respectively, with the injured fish occupying a significantly greater water depth than the untreated conspecifics (one-way ANOVA, p < 0.01). There was a highly significant association between the treatment status of the fish (untreated/injured) and the frequency of water layer distribution (χ2(2) = 196.78, p < 0.01). The findings of the present study can furnish specific methodological references for the imaging sonar-based monitoring of T. ovatus within aquaculture cage systems. Nevertheless, the study is subject to several inherent limitations, including a small sample size for the injured group (n = 3), the employment of an artificial injury model, and the confinement of experimental subjects to a closed cage environment; these factors may introduce statistical uncertainty and thus exert a considerable impact on the external validity of the study’s results.

Simplified cylindrical twine models were widely adopted to reduce computational cost in CFD simulation of fishing nets, but they ignored woven microstructures and induced systematic hydrodynamic prediction errors. This study established three identical-solidity net models (cylindrical, twisted, warp-knitted) and conducted k-ω SST simulations at Reynolds number (Re) =1800 and angles of attack (AOAs) from 0° to 90°. Results revealed drag coefficients followed the order warp-knitted > twisted > cylindrical; at 90° AOA, cylindrical net underpredicted drag by 5.20% and 11.71% compared with twisted and warp-knitted nets, respectively. All nets produced single-peak lift curves with maximum values at 45°. The high-fidelity woven models achieved 89.2%–99.1% prediction accuracy to real net, while cylindrical models only reached 80%–87.4%. Helical grooves and interlaced interstices aggravated boundary layer separation and small-scale vortices, which smooth cylindrical twines failed to reproduce. Pressure drag dominated total drag force, and mesh knot cross-sections generated the largest flow-field discrepancies. Root mean square error (RMSE), mean bias error (MBE), and relative error (RE) were applied to quantitatively separated pressure and frictional drag deviations. Hierarchical simulation schemes and linear correction formulas were proposed to balance computational accuracy and cost for the design of aquaculture cages and fishing gear.

In the summer of 2019, an investigation was conducted using data obtained from a fishery hauls survey to analyze the influence of a dipole eddy on the fish community within the West-central South China Sea (WC_SCS). This dipole eddy consisted of a cyclonic eddy (CE) and an anticyclonic eddy (AE) that coexisted in the study area during the survey. A total of 8381 individual fish were captured, with 1241 found in the AE, 329 in the CE, and 6811 in the dipole frontal zone. The predominant fish families observed were Scombridae, Nomeidae, and Carangidae, which collectively represented over 97% in the AE, 21% in the CE, and 98% in the frontal zone. While ten species were present in the two dipole eddies and the associated front, one species was exclusive to the AE, two species were exclusive to the CE, and seven species were exclusive to the frontal zone. Notably, there were significant disparities in fish abundance among the AE, CE, and frontal zone, with average abundances of 177, 54, and 1,703 ind/2h, respectively. Abundance levels ranged from 7 to 3119 ind/2h, with the highest concentrations observed in the frontal zone, and relatively high abundance was also noted in the core of the AE and in the transition zone between the AE core and the dipole front. Through cluster analysis, three distinct fish groups (A, B, and C) were identified. Groups A and C correspond to the CE and AE edges, while group B aligns with the AE core, the front zone, and the transition zone between the AE core and the front. Within the study area, fish abundance exhibited a negative correlation with sea surface currents in the longitudinal direction. However, in the region characterized by weak currents, referred to as group B, which displayed the highest fish abundance, the fish population demonstrated a positive correlation with sea surface chlorophyll-a concentration. Despite the three moonless stations among the four located in the frontal zone having a higher abundance compared to the remaining moonlit station, these four stations are grouped together in the results of the cluster analysis. These findings highlight the significant impact of the dipole eddy on the structure and distribution of fish communities in the WC_SCS.

We estimated, for the first time, the age of Diaphus watasei (Jordan & Starks, 1904) in the South China Sea (SCS) based on otolith microstructure. According to one-way ANOVA, differences were not observed between the sexes with regard to standard length, body mass, or age. Based on 137 specimens, the sex ratio and relationship between standard length and body mass was 1.32:1 (male/female) and W = 0.0000433L2.78 (r2 = 0.923), respectively. The von Bertalanffy model was fitted as Lt = 171.38 [1 − exp(−0.00206(t − 3.82))], r2 = 0.645 (n = 92), which indicated a maximum growth rate of 0.356 mm/day. The speculated birth date of the 92 specimens of D. watasei occurred across almost all months of the year.

A live female megamouth shark (Megachasma pelagios Taylor, Compagno & Struhsaker) was accidentally captured during a scientific survey conducted in the southwestern waters near Zhubi Dao in the South China Sea, using a midwater trawl. Based on its distinctive morphological characteristics, the shark was promptly identified as M. pelagios. The estimated total length of the shark was about 5.0 m. Clear photographs and video recordings were taken of the individual, which was ultimately released back into the ocean. This observation represents a rare live sighting and valuable visual documentation in the South China Sea region. Recorded on 18 September 2018, it is the earliest-known field record of a megamouth shark in the South China Sea with clear scientific survey documentation, as well as a successful release case.

Monitoring fish diversity in open ocean environments presents substantial challenges, particularly due to the limitations of traditional sampling methods such as trawling, which are costly, labor-intensive, and ineffective for deeper water layers. Environmental DNA (eDNA) technology offers an economical and efficient alternative, complementing conventional survey techniques. In this study, eDNA analysis was employed to characterize fish species composition and diversity in the central South China Sea (SCS). Additionally, generalized additive models (GAMs) were applied for the 5 m and 200 m depth layers to assess the influence of environmental variables on fish communities. A total of 190 fish species, spanning 32 orders, 68 families, and 135 genera, were detected across eight sampling sites. The 5 m and 200 m depth layers harbored 184 and 178 species, respectively, with 172 species common to both layers. α-and β-diversity analyses revealed no significant differences in fish species composition or diversity between the two depths (p > 0.05). GAM results highlighted temperature as a key environmental driver of fish distribution, with significant effects on species abundance at both depths (p < 0.05). These findings underscore the utility of eDNA for monitoring fish diversity and elucidating the ecological mechanisms shaping vertical species distribution in deep-sea ecosystems. Given the logistical constraints of traditional survey methods in deep-sea environments, eDNA-based approaches offer valuable insights for the sustainable management and conservation of fishery resources in the central SCS.

We conducted an experiment of planting a dead cow and a metal-framed cage with cameras on the 1629 m deep sea floor off the southeast coast of Hainan Island in the northwestern South China Sea, using ROV diving and setting up a video camera on the cage to observe animals who came to eat the bait. The deep-sea cameras captured footage of eight Pacific sleeper sharks (Somniosus pacificus) swimming and feeding around the dead cow. To our knowledge, this is the first time the occurrence of such a shark species has been reported in the South China Sea. Eight individuals were differentiated based on the characteristic differences displayed in the images, with lengths of 1.9 to 5.1 m estimated. The video camera also recorded the predators’ behavior of tearing at the dead cow on the seabed. It was discovered that Pacific sleeper sharks are not strictly solitary and exhibit queue-feeding behavior. This study is significant as it documents a record of a data-scarce shark species, for which little information is available in the literature. It also documents an expansion of the species’ known habitat from the north Pacific Ocean into the South China Sea. Such sharks diving into the deep sea to predate on dead animals also suggests that occurrences of large chunks of dead organic bodies falling onto the deep sea might have been more frequent than we previously thought in the South China Sea. The findings have implications for understanding the geographic connectivity of large swimming animals between the South China Sea and the Pacific Ocean and provide scientific evidence for formulating conservation and management strategies for sharks and other large animals in the oceans.

Coral reef fish are important groups of coral reefs, which have great economic and ecological value. Meiji Reef is a representative tropical semi-enclosed atoll in the South China Sea, with rich fish resources. Based on the data from hand-fishing, line-fishing, and gillnet surveys of fish in Meiji Reef from 1998 to 2018, this study summarized the fish species list of Meiji Reef and analyzed the species composition, inclusion index at the taxonomic level (TINCL), genus–family diversity index (G–F index), average taxonomic distinctness index (Δ+), and variation in taxonomic distinctness (Λ+) and their changes. The results revealed that from 1998 to 2018, there were 166 reef-dwelling fish species on Meiji Reef, belonging to 69 genera, 33 families, and 11 orders, of which 128 species were from 20 families of Perciformes, accounting for 77.10% of the total cataloged species. Regarding the dependence of fish on coral reefs, there were 155 reef-dependent species or resident species (accounting for 93.37%) and 11 reef-independent species or wandering species (accounting for 6.63%). The TINCL of the order, families, and genus of fish in Meiji Reef were very high. The genus diversity index (G index), family diversity index (F index), and G–F index of fish in Meiji Reef were very high, and the G index of fish in Meiji Reef in 1998–1999 was higher than that in 2016–2018. The Δ+ and Λ+ values of fish in Meiji Reef from 1998 to 2018 were 56.1 and 148.5, respectively. Compared with 1998–1999, Δ+ and Λ+ of fish increased during 2016–2018, reflecting that the relatives of fish in Meiji Reef became further distant, and the uniformity of taxonomic relationships among species decreased. The research findings indicated that fish exhibited a high taxonomic diversity in Meiji Reef; however, it also revealed significant fluctuations in the fish diversity of Meiji Reef over an extended period, emphasizing the urgent need for timely protection measures. This investigation significantly contributes to our comprehension of the intricate dynamics governing fish species within Meiji Reef and holds broader implications for biodiversity conservation in tropical marine ecosystems.

The diel vertical migration of mesopelagic fishes in the southern (S-May station and S-Nov station) and central (C-Jun station and C-Dec station) South China Sea was investigated through a series of continuous field surveys conducted in May, June, November, and December 2017. These surveys employed a combination of mid-water trawl and acoustics techniques. The diel migration process, vertical distribution, acoustic migration proportion, and migration pattern of mesopelagic fishes were analyzed. The results revealed that mesopelagic fishes initiated an upward migration before sunset, with the process concluding within 30–120 min after dark. Subsequently, they commenced a downward migration before dawn, which terminated within 10–50 min after sunrise. The mesopelagic deep-sea layers of mesopelagic fishes at the S-May, S-Nov, C-Jun, and C-Dec stations ranged from 360 to 700 m, 350 to 680 m, 350 to 520 m, and 300 to 700 m, respectively. The acoustic migration proportions of mesopelagic fishes at the corresponding stations were found to be approximately 44.5%, 25.7%, 29.8%, and 58.0%, respectively. There were seasonal and regional differences in the vertical migration and distribution patterns of mesopelagic fishes in the South China Sea. A total of 228 species were identified, including 203 fish species, 23 cephalopod species, and 2 shark species. Among these, a subset of 43 fish and cephalopod species exhibited extensive diel vertical migrating behavior. Specifically, this subset comprised 23 lanternfish species, 8 cephalopod species, and 12 other fish species. Lanternfishes were the predominant diel vertical migratory species, while cephalopods also played a significant role in diel vertical migration. The diel migration behavior was found to be slight for Diaphus lucidus, Melamphaes microps, Argyropelecus affinis, and six other fish species. Non-migratory behavior was observed in Sternoptyx obscura, Argyropelecus sladeni, Sternoptyx diaphana, and 13 other fish species. The diel migration habits of 178 additional species of fish, cephalopods, and sharks could not be definitively determined.

Mesopelagic fishes are one of the most abundant marine organisms and have a wide distribution in the world's oceans, thereby playing a central role in global marine ecology. We determined the length-weight relationships (LWRs) of 24 mesopelagic fish species, representing 11 families and 6 orders, inhabiting the South China Sea (SCS), and also assessed their growth types and various condition factors, using samples acquired from midwater trawls at depths of 70-750 m during eight cruises by a single fishing vessel in 2015-2018. Based on 894 specimens, the LWRs of the species were calculated for the first time. The values of the b coefficients in the LWRs ranged from 2.2669 (for Sigmops gracilis) to 3.5471 (for Ichthyococcus ovatus), except 2 species exhibited b values less than 2.5. The 95% confidence intervals of the a and b values were tested to identify the growth patterns: 10 species exhibited isometric growth, 7 species negative allometric growth, and 7 species positive allometric growth. The means of Fulton's condition factor (K-c) ranged from 0.234 +/- 0.046 (for S. gracilis) to 3.318 +/- 0.781 (for Caristius macropus); the allometric condition factor (K-a) from 0.149 +/- 0.014 (for Scopelosaurus hoedti) to 6.758 +/- 1.162 (C. macropus); and the relative weight condition factor (K-n) from 1.000 +/- 0.090 (for Scombrolabrax heterolepis) to 1.023 +/- 0.208 (for Macropinna microstoma). The K-c values of fish in the families Opisthoproctidae and Myctophidae were mostly > 1, denoting species tending to have a relatively short, compressed, and deep body; conversely, fish with K-c values of < 1 tended to have an elongated body shape or a long, narrow tail. The K-a values were > 2 for 5 species, indicating the best condition compared with the other species; the values of 9 species ranged from 1.132 +/- 0.135 to 1.938 +/- 0.276, indicating a better condition; and the values of 10 species were < 1, indicating a poorer condition. The K-n values ranged from 0.983 +/- 0.137 to 1.031 +/- 0.249, whereby the results for 22 species reflected a good growth condition (K-n > 1), with the values of just two species being scarcely less than 1.000. In conclusion, these data will be helpful in future studies of mesopelagic fishes and provide basic biological data useful to fishery assessments and conservation of the mesopelagic fish resources in the SCS.

Polybrominated diphenyl ethers (PBDEs) and their alternative halogenated flame retardants (AHFRs) have gained global attention due to their ubiquitous occurrence, bioaccumulation, and toxic properties. However, the biomagnification of halogenated flame retardants (HFRs), particularly AHFRs, in various food chains is not yet well understood. In this study, yellowfin tuna (Thunnus albacares), along with its prey, flying squid (Sthenoteuthis oualaniensis) and round scad (Decapterus maruadsi), were sampled from the South China Sea (SCS) to investigate the biomagnification potential of PBDEs and AHFRs, including dechlorane plus (DP) and decabromodiphenyl ethane (DBDPE). The results showed that PBDEs were the predominant HFRs detected in all fish samples. However, the levels of PBDEs in the present study were lower than those reported in previous studies, indicating a recent reduction in PBDE contamination in the SCS. The average biomagnification factor (BMF) values for all target HFRs, except for BDE 99 and BDE 183, were in the range of 1.03 to 57.61, suggesting that these compounds were biomagnified from prey fish to predator of yellowfin tuna. In contrast, BDE 99 and BDE 183 were biodiluted in the flying squid-yellowfin tuna food chain. Additionally, the BMF values decreased with the increased log Kow of PBDEs in these two food chains. Lastly, the average estimated daily intakes of PBDEs, DP, and DBDPE suggest that consuming these marine species is unlikely to pose significant health risks.

We report on the feeding ecology of two species, the short-headed lanternfish Diaphus brachycephalus and Warming's lanternfish Ceratoscopelus warmingii, using data collected over five surveys from 2015 to 2017 in the open South China Sea. D. brachycephalus feed mainly on copepods, with few differences in food composition between different-sized individuals; the diet of C. warmingii is more diverse, including crustacean zooplankton, gelatinous animals, and Mollusca, and differs significantly between fishes >55 mm in body length and smaller fishes. Interspecific competition for food between these two species is not strong, while intraspecific competition may be more intense in D. brachycephalus than in C. warmingii. Trophic levels of D. brachycephalus (3.46) and C. warmingii (3.38) identify both species as third-trophic-level lower carnivores. The diel feeding patterns of D. brachycephalus and C. warmingii differ: the former feeds actively both day and night when food is plentiful, and feeds primarily in the upper layer at night and in the mesopelagic layer during the daytime, and the latter ascends into the upper 100 m at night to feed, but stomach fullness is lower than D. brachycephalus. Dry-body-weight daily ration estimates for D. brachycephalus range from 5.19% to 16.46%, and those for C. warmingii range from 1.38% to 4.39%.

In this study, we analyzed the effects of mesoscale eddies on the fish community in the western South China Sea (WSCS) using data from a fishery resource survey performed in the summer of 2019. During the survey, an anticyclonic eddy (AE) and a cyclonic eddy (CE) coexisted in our cruising area. In total, 3537 samples were collected, of which 3389 and 148 were obtained from the AE and CE, respectively. The average CPUE and abundance in the AE were 12.33 and 15.11 times higher than in the CE, respectively. The abundance significantly differed between these two eddy types. There were eleven common species in all eddies, seven exclusive to the AE, and five exclusive to the CE. The fish catch per unit effort (CPUE) ranged from 0.001 to 205 kg·h-1 and presented higher values at the AE than at CE. The abundance distribution of Scombrida and Carangidae was predominant in AE. Other families present slight variations in abundance distribution. Two fish groups, corresponding to the AE and CE, were obtained based on hierarchical cluster analysis, indicating a strong dependence of the fish community on the characteristics of mesoscale eddies. The abundance was negatively correlated with the sea surface current. The results showed that the AE and CE play important roles in shaping the community structure and fish assemblages in the WSCS.