Search

Cyanide, organophosphate and rodenticides are highly toxic substances widely used in agriculture and industry. These toxicants are neuro- and organotoxic to mammals at low concentrations, thus early detection of these chemicals in the aqueous environment is of utmost importance. Here, we employed the behavioral toxicity test with wildtype zebrafish larvae to determine sublethal concentrations of the above mentioned common environmental pollutants. After optimizing the test with cyanide, nine rodenticides and an organophosphate were successfully tested. The compounds dose-dependently initially (0–60-min exposure) stimulated locomotor activity of larvae but induced toxicity and reduced swimming during 60–120-min exposure. IC50 values calculated based on swimming distance after 2-h exposure, were between 0.1 and 10 mg/L for both first-generation and second-generation anticoagulant rodenticides. Three behavioral characteristics, including total distance travelled, sinuosity and burst count, were quantitatively analyzed and compared by hierarchical clustering of the effects measured by each three parameters. The toxicity results for all three behavioral endpoints were consistent, suggesting that the directly measured parameter of cumulative swimming distance could be used as a promising biomarker for the aquatic contamination. The optimized method herein showed the potential for utilization as part of a monitoring system and an ideal tool for the risk assessment of drinking water in the military and public safety.

The food composition and feeding ecology of fishes living in the intertidal zone play an essential role in understanding the energetic connectivity between terrestrial and aquatic systems. Periophthalmus chrysospilos is an amphibious fish species occurring in the intertidal zone, but data on its diet and foraging ecology is still poorly known. This study on Ps. chrysospilos was carried out from April 2020 to March 2021 at four sites within the Mekong Delta estuary to define the influence of spatio-temporal factors on the diet of this species. The diet composition and relative gut lengths (RGLs) of Ps. chrysospilos were analysed in relation to four parameters—sex, size, site, and season. A total of 1,031 individuals were collected, and their digestive tract lengths were used to calculate the RGL. The digestive tracts of only 546 individuals were with food items (approximately 1:1 of empty vs full digestive tract) and were subsequently used for further analyses. The ranges in total length and weight in both adult and juvenile individuals were 3.4–10.6 cm and 0.38–14.13 g, respectively. The RGL values varied with season, fish size and site, but was always lower than 1, indicating a predominantly carnivorous diet. The variability of food items found within the digestive tracts demonstrated its adaptability in pursuing prey items within the limits of the littoral zone, and its importance as a conduit of terrestrial-marine connectivity. This species is characterised as an opportunistic mesopredator feeding primarily on Acetes spp., Uca spp., Dolichoderus sp., and rarely on Polychaeta and Actinopterygii. Other items found within the digestive tract are Mollusca, and detritus. The diet composition of Ps. chrysospilos did not vary with season and size, but changed with sex and site parameters. Uca spp. contributed to the sexual variation in dietary component, whereas Mollusca, Uca spp., Dolichoderus sp. and detritus, were drivers for spatial variation in the dietary component. The research provides fundamental information on diet composition and feeding strategy, as well as contributes towards knowledge on foraging ecology and resource use by intertidal animal communities.

Background The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species’ vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE. Methods Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt. Results Overall, otolith size varied linearly with fish size (from 10–60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0–30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such experimental assessments across multiple developmental stages are key steps toward assessing confidence in otolith-derived metrics that are often used to assess the dynamics of wild fish populations.

Background Although the biomass of the nocturnal fishes is almost same as that of diurnal fishes, most of the ecological studies that examine feeding or reproductive behaviors are on diurnal fishes. Therefore, there is limited ecological information regarding the nocturnal fishes. This fact may be attributed to the difficulty in observing them during darkness. Members of the genus Pempheris (Pempheridae) are one of the most abundant nocturnal fishes on coral reefs. Methods The nighttime migrations of Pempheris schwenkii were observed by attaching a chemical luminescent tag. Tagged fishes were followed by an observer without torch and SCUBA, and their positions and estimated depths were plotted on an underwater topographic map. Aquarium tank observation was carried out to further describe their habits during the night. Results The new tagging method provided good data for observing the migration behavior. In all five observations, the target fishes started nighttime migration from the entrance of their cave within 1 h after sunset. All of them immediately left the inner reef and spent most of the observation time near the surface (0–5 m depth) or shallow (5–15 m depth) water-columns of the outer reef. Their migration pattern varied between days, but they migrated long distance (379–786 m/h) during each observation. The behavior observed in the aquarium tank was categorized into five patterns: schooling, shaking, migrating, spawning, and feeding. Shaking and spawning were observed during one of three observation days. Discussion The present study firstly clarified the small-scale but dynamic nocturnal migration pattern of P. schwenkii in nature by a new method using chemical luminescent tags. In addition, combined observations from nature and an aquarium could be used to estimate the behavior of this species. Pempheris schwenkii may reduce their predation risk of eggs and adults by spawning at outer reef in nighttime. It was estimated that they can potentially migrate 4–7 km/night. The rapid growth known for this species may have been supported by their feeding behavior where they can fill up their stomach every night with rich zooplankton in outer reefs. Furthermore, the behavior of this species indicates the possibility that they make an important contribution to the flow of energy and materials in their coral reef ecosystem.

Motile Aeromonas septicaemia (MAS), caused by Aeromonas hydrophila, is one of the most significant bacterial disease responsible for mortality in Indian catfish, Clarias magur, a potential aquaculture species in the Indian subcontinent. In fish, innate immunity elicited by pathogen recognition receptors (PRRs) plays an important role in providing protection against bacterial infection. Information on PRRs including Toll-like receptors (tlrs) and their response to bacterial pathogens remains unexplored in magur. Toll-like receptor 2 (tlr2), a phylogenetically conserved germ-line encoded PRR recognizes specific microbial structure and trigger MyD88-dependent signaling pathway to induce release of various cytokines responsible for innate immune response. In the present study, tlr2 gene of magur was characterized and downstream signaling was studied following challenge with A. hydrophila. The full-length cDNA of magur tlr2 (mtlr2) comprised of 3,066 bp with a single open reading frame of 2,373 bp encoding 790 amino acids having a theoretical pI value of 6.11 and molecular weight of 90 kDa. Structurally, it comprised of signal peptide (1–42aa), one leucine-rich repeat region (LRR) at N-terminal (LRR1-NT: 50–73 aa) and C-terminal (LRR-CT: 588–608 aa), twenty LRRs in between, one trans-membrane (Tm) domain (609–631aa) followed by cytoplasmic TIR domain (670–783aa). Phylogenetically, mtlr2 is closely related to pangasius and channel catfish. Highest basal expression of mtlr2, myd88 and il-1β in spleen, nf-kb in anterior kidney was observed. Lowest basal expression of mtlr2 in skin and myd88, nf-kb and il-1β in muscle was detected. Significant up-regulation of mtlr2 and downstream expression occurred at 3, 8, 24 h post infection to A. hydrophila in important immune organs such as liver, spleen, intestine and kidney. These findings highlight the vital role of tlr2 in eliciting innate immune defence against A. hydrophila infection.

Yang B, Herrmann B, Yan L, Li J, Wang T. 2021. Comparing size selectivity and exploitation pattern of diamond-mesh codends for Southern velvet shrimp (Metapenaeopsis palmensis) in shrimp trawl fishery of the South China Sea. PeerJ 9:e12436 DOI 10.7717/peerj.12436 In this study, size selectivity and exploitation pattern of six diamond-mesh codends with different mesh sizes, ranging from 25 to 54 mm, for Southern velvet shrimp (Metapenaeopsis palmensis) were tested and compared in a shrimp trawl fishery of the South China Sea (SCS). We used a codend with a mesh size of 25 mm (D25) as a starting point, which is the minimum mesh size (MMS) currently regulated in the studied area. Four different fishing population scenarios were applied to quantify and compare how mesh sizes of codends used would impact the size selectivity and exploitation pattern for the target shrimp species. The results demonstrated that the D25 codend was not proper for protecting juvenile shrimp at the studied area. By applying this legal codend, L50 (50% retention length) of the target shrimp species was below its minimum conservation reference size (MCRS, 7.0 cm total length), the retention probability of shrimp with a length of MCRS was above 95% CI [91–99] and more than 43% of undersized shrimp was retained. To mitigate the bycatch issue of undersized shrimp, increasing the mesh size in the diamond mesh codend is a simple and effective option. However, the loss of catch efficiency for marketable shrimp is a major concern while increasing the mesh size. A good compromise between releasing undersized shrimp and maintaining the legal individuals is manifested by using the codend with 35 mm mesh size (D35). Our study will be beneficial for the management of shrimp trawl fisheries in the SCS.

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

Objective According to reported spawning characteristics of Japanese eel, Anguilla japonica, which exhibit spawning and migration patterns that are synchronized with lunar cycles and photoperiod, we hypothesized that a close association exists between specific photic signals (daylight, daylength, and moonlight) and endocrinological regulation. Given the photic control in melatonin secretion, this hypothesis was tested by investigating whether melatonin signals act as mediators relaying photic signals during testis development in the eel. Methods We examined changes in melatonin-secretion patterns using time-resolved fluorescence immunoassays in sexually immature and mature male Japanese eels under the condition of a new moon (NM) and a full moon (FM). Results The eye and plasma melatonin levels exhibited a nocturnal pattern under a 12-h light: dark cycle (12L12D) or under constant darkness (DD), but not with constant light (LL). Eye melatonin levels were similar under the 12L12D and short-day (9L15D) conditions. In the long-day condition (15L9D), secreted plasma melatonin levels were stable, whereas short-day melatonin secretion began when darkness commenced. Sexual maturation began at 8 weeks following intraperitoneal injection of human chorionic gonadotropin (hCG), and NM exposure led to significantly higher eye and plasma melatonin levels compared with those detected under FM exposure.

Fish populations that reside in completely isolated freshwater ecosystems are rare worldwide. The Vila Velha State Park (VVSP), located in southern Brazil, is recognized for its arenitic formations called sinkholes (furnas), which are completely isolated. Fish populations within, such as those of Psalidodon aff. fasciatus, often develop vertebral malformations due to this isolation from other conspecifics and other species. In this study, we analyzed geometric morphology in digital radiographs to identify congenital deformations of Psalidodon aff. fasciatus in Furna 2 of VVSP. We found many fish with spinal deformities, including wide variation in the number of caudal vertebrae and corporal deformations related to a flattened body and spinal curvature. Females were more affected than males. We also demonstrated that these deformations reflect inbreeding and an absence of gene flow in the population. In conclusion, isolated populations such as fish species in furnas are potential models for evo-devo research.

Length-weight relationship (LWR), growth pattern and condition factor (CF) play a vital role in fish resource evaluation and management but data on this is limited for Periophthalmus variabilis. This is an amphibious fish that lives in the mudflats of the mangrove forests in the Western Pacific regions, including the Vietnamese Mekong Delta (VMD). This paper contributes to the understanding of the LWR, growth pattern and CF of P. variabilis. Fish specimens were collected by hand at four sites in the VMD from April 2020 to March 2021. The analysis of 495 individual fish (259 females and 236 males) showed that fish weight could be estimated from a given fish length due to high determination values (r2 = 0.70 − 0.97). Dusky-gilled mudskippers of the VMD exhibited positive allometry, as indicated by their larger than 3 b value (b = 3.094 ± 0.045, p = 0.04). However, the growth pattern of the mudskipper between the sex and maturation stage (immature versus mature) showed isometry. These fish displayed positive allometry in the dry season (b = 3.138 ± 0.065) (>3, p = 0.04) but isometry in the wet season (b = 3.058 ± 0.061) (≈3, p = 0.34). Fish growth ranged from isometry to positive allometry and varied by site (b = 2.850 ± 0.103–3.370 ± 0.114) and month (b = 2.668 ± 0.184–3.588 ± 0.299) based on the b value. The CF of P. variabilis was not affected by sex (p = 0.29), body size (p = 0.64) or season (p = 0.43), but was affected by site (p = 0.01) and month (p = 0.01). The CF of this species (1.05 ± 0.02) was higher than 1 (p

After a long hiatus, interest in the morphology of the respiratory organs in apple snails (Ampullariidae, Caenogastropoda) and its functional and evolutionary bearings is making a comeback. The variability in the morphology of the gill and lung and its link to different lifestyles and patterns of air dependency within the Ampullariidae make research on the morphology of the respiratory organs particularly suitable for approaching the evolution of terrestriality in animals. Additionally, morphology is a valuable source of hypotheses regarding the several functions the ampullariid respiratory organs have besides respiration. However, this is an underexplored field that only recently has incorporated ultrastructural and three-dimension visualization tools and in which more research is much needed, particularly, comparisons between species representing the diversity within the Ampullariidae. In this paper, I examine Mueck, Deaton & Lee’s (2020a) assessment of the morphology of the gill and lung of Pomacea maculata and compare it with earlier and contemporary studies on other ampullariid species. I show that Mueck, Deaton & Lee’s paper combines significant morphological misinterpretations, conceptual and terminological mistakes, and crucial literature omissions. I also reinterpret their results and point to the similarities and differences between them and available data on other ampullariids.

Background Expanding fisheries in developing nations like Sri Lanka have a significant impact on threatened marine species such as elasmobranchs. Manta and devil (mobulid) rays have some of the most conservative life history strategies of any elasmobranch, and even low to moderate levels of bycatch from gillnet fisheries may lead to significant population declines. A lack of information on life history, demographics, population trends, and fisheries impacts hinders effective management measures for these species. Method We report on mobulid fishery landings over nine years between 2011 and 2020 across 38 landing sites in Sri Lanka. We collected data on catch numbers, body sizes, sex, and maturity status for five mobulid species. We used a Bayesian state-space model to estimate monthly country-wide catch rates and total annual landings of mobulid rays. We used catch curve analyses to estimate total mortality for Mobula mobular, and evaluated trends in recorded body sizes across the study period for M. mobular, M. birostris, M. tarapacana and M. thurstoni. Results We find that catch rates have declined an order of magnitude for all species across the study period, and that total annual captures of mobulid rays by the Sri Lankan artisanal fishing fleet exceed the estimated annual captures of mobulids in all global, industrial purse seine fisheries combined. Catch curve analyses suggest that M. mobular is being fished at rates far above the species’ intrinsic population growth rate, and the average sizes of all mobulids in the fishery except for M. birostris are declining. Collectively, these findings suggest overfishing of mobulid ray populations in the northern Indian Ocean by Sri Lankan artisanal fisheries. We recommend strengthening the management of these species through improved implementation of CITES, CMS, and regional fisheries management actions. In addition, we report on the demographic characteristics of mobulids landed in Sri Lanka and provide the first record of M. eregoodoo in the country.

Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.

Neuropeptides and their G protein-coupled receptors (GPCRs) regulate multiple physiological processes. Currently, little is known about the identity of native neuropeptides and their receptors in Portunus trituberculatus. This study employed RNA-sequencing and reverse transcription-polymerase chain reaction (RT-PCR) techniques to identify neuropeptides and their receptors that might be involved in regulation of reproductive processes of P. trituberculatus. In the central nervous system transcriptome data, 47 neuropeptide transcripts were identified. In further analyses, the tissue expression profile of 32 putative neuropeptide-encoding transcripts was estimated. Results showed that the 32 transcripts were expressed in the central nervous system and 23 of them were expressed in the ovary. A total of 47 GPCR-encoding transcripts belonging to two classes were identified, including 39 encoding GPCR-A family and eight encoding GPCR-B family. In addition, we assessed the tissue expression profile of 33 GPCRs (27 GPCR-As and six GPCR-Bs) transcripts. These GPCRs were found to be widely expressed in different tissues. Similar to the expression profiles of neuropeptides, 20 of these putative GPCR-encoding transcripts were also detected in the ovary. This is the first study to establish the identify of neuropeptides and their GPCRs in P. trituberculatus, and provide information for further investigations into the effect of neuropeptides on the physiology and behavior of decapod crustaceans.

Background Common names are frequently used inconsistently for marine annelid species used as bait in the peer-reviewed literature, field guides and legislative material. The taxonomy of many such species based on morphology only also ignores cryptic divergences not yet detected. Such inconsistencies hamper effective management of marine annelids, especially as fishing for recreation and subsistence is increasing. This study investigates the scale of the problem by studying the use and names of bait marine annelids in the Western Cape Province of South Africa. Methods Fifteen recreational and six subsistence fishers at 12 popular fishing sites in the Western Cape Province donated 194 worms which they identified by common name. Worms were assigned scientific names according to a standard identification key for polychaetes from South Africa, and mitochondrial cytochrome oxidase I (COI) amplified and sequenced. Results This study identified 11 nominal species known by 10 common names, in the families Siphonosomatidae, Arenicolidae, Sabellaridae, Lumbrineridae, Eunicidae, Onuphidae and Nereididae. Cryptic diversity was investigated through employing mitochondrial COI sequences and these data will facilitate future identifications among widely distributed species. Several species (Siphonosoma dayi, Abarenicola gilchristi, Scoletoma species, Marphysa corallina, Lysidice natalensis, Heptaceras quinquedens, Perinereis latipalpa) are reported as bait for the first time, and while the names blood- and moonshineworms were consistently applied to members of Arenicolidae and Onuphidae, respectively, coralworm was applied to members of Sabellaridae and Nereididae. Analysis of COI sequences supported morphological investigations that revealed the presence of two taxonomic units each for specimens initially identified as Gunnarea gaimardi and Scoletoma tetraura according to identification keys. Similarly, sequences for Scoletoma species and Lysidice natalensis generated in this study do not match those from specimens in China and India, respectively. Further research is required to resolve the species complexes detected and also to refine the use of names by fishermen over a wider geographic range.

The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction’s bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp’s gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.

The aim of the study was to investigate the influence of dietary level and ratio of n-6/n-3 fatty acids (FA) on growth, disease progression and expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) following challenge with Paramoeba perurans. Fish (80 g) were fed four different diets with different ratios of n-6/n-3 FA; at 1.3, 2.4 and 6.0 and one diet with ratio of 1.3 combined with a higher level of n-3 FA and n-6 FA. The diet with the n-6/n-3 FA ratio of 6.0 was included to ensure potential n-6 FA effects were revealed, while the three other diets were more commercially relevant n-6/n-3 FA ratios and levels. After a pre-feeding period of 3 months, fish from each diet regime were challenged with a standardized laboratory challenge using a clonal culture of P. perurans at the concentration of 1,000 cells L−1. The subsequent development of the disease was monitored (by gross gill score), and sampling conducted before challenge and at weekly sampling points for 5 weeks post-challenge. Challenge with P. perurans did not have a significant impact on the growth of the fish during the challenge period, but fish given the feed with the highest n-6/n-3 FA ratio had reduced growth compared to the other groups. Total gill score for all surfaces showed a significant increase with time, reaching a maximum at 21 days post-challenge and declined thereafter, irrespective of diet groups. Challenge with P. perurans influenced the mRNA expression of examined genes involved in immune and inflammatory response (TNF-α, iNOS, IL4-13b, GATA-3, IL-1β, p53, COX2 and PGE2-EP4), but diet did not influence the gene expression. In conclusion, an increase in dietary n-6/n-3 FA ratio influenced the growth of Atlantic salmon challenged with P. perurans; however, it did not alter the mRNA expression of immune genes or progression of the disease.

Background Microbial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management. Method In light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp (Litopenaeus stylirostris) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method. Results We found a core microbiota made of taxa related to Aestuariibacter, Alteromonas, Vibrio, SAR11, HIMB11, AEGEAN 169 marine group and Candidatus Endobugula associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas and Marinobacterium genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process.

Sustainable development of the important economic species, Asian paddle crab (Charybdis japonica), has attracted attention in the coastal waters of the Yellow Sea, China. The commonly used round pots are almost nonselective, resulting in severe bycatch of juveniles. In this study, we explored a method to improve the size selectivity for C. japonica by mounting escape vents on the side panels of each pot. The selectivity of pots with escape vent sizes of 70 mm × 20 mm, 70 mm × 25 mm, 70 mm × 30 mm, and 70 mm × 35 mm was tested using a catch comparison method. The estimated minimum landing size (MLS) of carapace height (27 mm), according to the regulated MLS of carapace length (50 mm), was used as a reference point to explain the results. Significant increases in the size of crabs caught by pots were found with the enlargement of escape vent size (Kruskal–Wallis test, P < 0.01). The pots with 70 mm × 20 mm, 70 mm × 25 mm and 70 mm × 30 mm escape vents released nearly 50%, 75% and 95% of undersized individuals, respectively, and these three types of pots retained approximately 90% of legal-sized individuals compared with the control pots without escape vents. The pots with 70 mm × 35 mm escape vents released nearly all undersized individuals, but they also released most legal-sized individuals. Pots with an escape vent size of 70 mm × 30 mm were recommended for the sustainable development of C. japonica in the Yellow Sea of China. The results of this study reiterate the importance of carapace height for determining the size selectivity, which can serve as a reference to formulate management regulations in the coastal waters of the Yellow Sea, China.

To date, 19 species of spiny lobsters from the genus Panulirus have been discovered, of which only P. japonicus, P. penicilatus, P. stimpsoni, and P. versicolor have been documented in South Korean waters. In this study, we aimed to identify and update the current list of spiny lobster species that inhabit South Korean waters based on the morphological features and the phylogenetic profile of cytochrome oxidase I (COI) of mitochondrial DNA (mtDNA). Spiny lobsters were collected from the southern and eastern coasts of Jeju Island, South Korea. Phylogenetic analyses were performed using neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The ML tree was used to determine the spiny lobster lineages, thereby clustering the 17 specimens collected in this study into clades A, B, C, and D, which were reciprocally monophyletic with P. japonicus, P. homarus homarus, P. longipes, and P. stimpsoni, respectively. These clades were also supported by morphological examinations. Interestingly, morphological variations, including the connected pleural and transverse groove at the third abdominal somite, were observed in four specimens that were genetically confirmed as P. japonicus. This finding is novel within the P. japonicus taxonomical reports. Additionally, this study updates the documentation of spiny lobsters inhabiting South Korean waters as P. longipes and P. homarus homarus were recorded for the first time in this region.

Seafood is very perishable and can quickly spoil due to three mechanisms: autolysis, microbial degradation, and oxidation. Primary commercial sectors within the North Atlantic fisheries include demersal, pelagic, and shellfish fisheries. The preservation techniques employed across each sector can be relatively consistent; however, some key differences exist across species and regions to maintain product freshness. Freezing has long been employed as a preservation technique to maintain product quality for extended periods. Freezing allows seafood to be held until demand improves and shipped long distances using lower-cost ground transportation while maintaining organoleptic properties and product quality. Thawing is the opposite of freezing and can be applied before additional processing or the final sale point. However, all preservation techniques have limitations, and a properly frozen and thawed fish will still suffer from drip loss. This review summarizes the general introduction of spoilage and seafood spoilage mechanisms and the latest preservation techniques in the seafood industry, focusing on freezing and thawing processes and technologies. This review also considers the concept of global value chains (GVC) and the points to freeze and thaw seafood along the GVC to improve its quality with the intention of helping Newfoundland and Labrador’s emerging Northern cod (Gadus morhua) fisheries enhance product quality, meet market demands and increase stakeholder value.

South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing 10 nominal and six morphologically distinct but undescribed species. We sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delimited lineages using four different single-locus species discovery methods (mPTP-15 lineages; LocMin-14 lineages; bGMYC-18 lineages; and GMYC-30 lineages). The six morphologically distinct but undescribed species were also delimited by the majority of the species discovery methods. Five of these lineages are restricted to a single collection site or a watershed and their habitats are threatened by human activities such as deforestation, agricultural activities and construction of hydroelectric plants. Our results also highlight the importance of combining DNA and morphological data in biodiversity assessment studies especially in taxonomically diverse tropical biotas.

Background Freshwater fish populations are facing multiple stressors, including climate change, species invasion, and anthropogenic interference. Temporal studies of fish functional diversity and community assembly rules based on trait-environment relationships provide insights into fish community structure in riverine ecosystems. Methods Fish samples were collected in 2015 in the Min River, the largest freshwater riverine system in Southeastern China. Fish functional diversity was compared with the background investigation in 1979. Changes in functional richness, functional evenness, functional divergence, and functional beta diversity were analyzed. Relationships between functional diversity and environmental factors were modeled by random forest regression. Correlations between fish functional traits and environmental factors were detected by fourth-corner combined with RLQ analysis. Results Functional richness was significantly reduced in 2015 compared with 1979. Functional beta diversity in 2015 was significantly higher than that in 1979, with functional nestedness being the driving component. Reduction of functional richness and domination of functional nestedness is associated with species loss. Trait convergence was the dominant mechanism driving the temporal changes of functional diversity. Precipitation, temperature, species invasion, and human population were the most significant factors driving fish functional diversity. Higher precipitation, higher temperature, and presence of invasive species were significantly associated with higher swimming factor and higher relative eye diameter, while the opposite environmental conditions were significantly associated with higher pectoral fin length and eurytopic water flow preference. Conclusions Environmental filtering is the dominant temporal assembly mechanism shaping fish community structure. This work contributes to the understanding of temporal freshwater fish community assembly and the associations between fish functional structure and local environmental conditions, which will be informative for future freshwater fish conservation.

Accurately tracking a group of small biological organisms using algorithms to obtain their movement trajectories is essential to biomedical and pharmaceutical research. However, object mis-detection, segmentation errors and overlapped individual trajectories are particularly common issues that restrict the development of automatic multiple small organism tracking research. Extending on previous work, this paper presents an accurate and generalised Multiple Small Biological Organism Tracking System (MSBOTS), whose general feasibility is tested on three types of organisms. Evaluated on zebrafish, Artemia and Daphnia video datasets with a wide variety of imaging conditions, the proposed system exhibited decreased overall Multiple Object Tracking Precision (MOTP) errors of up to 77.59%. Moreover, MSBOTS obtained more reliable tracking trajectories with a decreased standard deviation of up to 47.68 pixels compared with the state-of-the-art idTracker system. This paper also presents a behaviour analysis module to study the locomotive characteristics of individual organisms from the obtained tracking trajectories. The developed MSBOTS with the locomotive analysis module and the tested video datasets are made freely available online for public research use.

The microstructure and nanostructure of nacre in Pteria colymbus were studied with high-resolution field emission scanning electron microscopy (FESEM). The tablets were found to be flat and polyhedral with four to eight sides, and lengths ranging from 0.6 to 3.0 µm. They consisted of nanocrystals 41 nm wide, growing in the same direction. X-ray diffraction showed the crystals to be mineral phase aragonite, which was confirmed by Raman spectroscopy. Fourier transform infrared spectroscopy identified a band at 1,786.95 cm−1 attributed to carboxylate (carbonyl) groups of the proteins present in the organic matrix as well as bands characteristic of calcium carbonate. X-ray fluorescence showed the nacre to contain 98% calcium carbonate, as well as minor elements (Si, Na, S and Sr) and trace elements (Mg, P, Cu, Al, Fe, Cl, K and Zn).

The jack mackerel (Trachurus japonicus) is both a dominant pelagic fish species and an important fishing target in the Beibu Gulf, South China Sea. However, the resource status of this species fluctuates dramatically, and it has recently been added to a “red list” of threatened species of the International Union for Conservation of Nature (IUCN). Despite its economic importance and decreasing population status, limited research on its spatiotemporal distribution has been undertaken over the last decades. In order to evaluate the most crucial factors that influence the spatiotemporal variability of T. japonicus and to determine GAM performance and predictability, we analyze catch per unit effort (CPUE) of T. japonicus from Beibu Gulf over four seasons (months) from 2013 to 2014. A generalized additive model (GAMs) is populated with water depth and remotely sensed sea surface temperature (SST), sea surface salinity (SSS), sea surface chlorophyll-a concentration (Chl-a) and sea level anomaly (SLA). The CPUE of T. japonicus varies seasonally, with higher CPUE in summer and autumn than in spring and winter, and the highest CPUE in summer. GAM results explain 57% of the deviation explained in CPUE, with the most important variables being SLA, Month, Depth, SSS, and SST , each explaining 21.2%, 18.7%, 10.7%, 5.1%, and 1.3% of the variation in CPUE, respectively. This species occurs mainly between 50 and 75 m depth, SSS values 32.3–33.5 PSU and SST 25–30.5 °C. High CPUE sites occur near SLA ≤ 0 m, on the edge of cold eddies, and there is a certain catch near the sea surface with SLA ≥ 0 m. The spatial and temporal distribution of T. japonicus is affected by the season and the marine hydrological environment. This study might contribute to a better understanding of the distributional patterns of T. japonicus as well as provide a basis for sustainable management in the Beibu Gulf.

Background Many coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific. Methods Methods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health. Results There were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.

Understanding the anthropogenic impact of oyster farms is essential for the management and conservation of marine fishes. In Japan, Hiroshima Bay is the region with the most intense oyster farming and thus suitable to study the impact of these farms. Here, we surveyed spherical planktonic eggs of the black sea bream Acanthopagrus schlegelii, one of the most abundant fish in the Bay. Our survey was performed at fourteen stations which included places with oyster farms and historical spawning grounds. We found the highest egg densities in four stations, one with historical spawning aggregations and three with major oyster farms. Besides, surveys at the innermost part of Hiroshima Bay, where two major rivers discharge, showed a low density of eggs indicating that black sea bream avoids spawning in low salinity areas. Our study suggests that oyster farms benefit spawners of black sea bream by providing more food sources than historical spawning grounds for efficient spawning. Yet, whether oyster farms represent a full advantage for the species remains unclear, particularly because they are known to host jellyfishes that prey on eggs and limit water flow that can influence the survival of fish eggs.

The highly migratory Atlantic bluefin tuna (ABFT) is currently managed as two distinct stocks, in accordance with natal homing behavior and population structuring despite the absence of barriers to gene flow. Larval fish are valuable biological material for tuna molecular ecology. However, they have hardly been used to decipher the ABFT population structure, although providing the genetic signal from successful breeders. For the first time, cooperative field collection of tuna larvae during 2014 in the main spawning area for each stock, the Gulf of Mexico (GOM) and the Mediterranean Sea (MED), enabled us to assess the ABFT genetic structure in a precise temporal and spatial frame exclusively through larvae. Partitioning of genetic diversity at nuclear microsatellite loci and in the mitochondrial control region in larvae spawned contemporarily resulted in low significant fixation indices supporting connectivity between spawners in the main reproduction area for each population. No structuring was detected within the GOM after segregating nuclear diversity in larvae spawned in two hydrographically distinct regions, the eastern GOM (eGOM) and the western GOM (wGOM), with the larvae from eGOM being more similar to those collected in the MED than the larvae from wGOM. We performed clustering of genetically characterized ABFT larvae through Bayesian analysis and by Discriminant Analysis of Principal Components (DAPC) supporting the existence of favorable areas for mixing of ABFT spawners from Western and Eastern stocks, leading to gene flow and apparent connectivity between weakly structured populations. Our findings suggest that the eastern GOM is more prone for the mixing of breeders from the two ABFT populations. Conservation of this valuable resource exploited for centuries calls for intensification of tuna ichthyoplankton research and standardization of genetic tools for monitoring population dynamics. This collaborative study was supported by “ECOLATUN” PROJECT CTM2015-68473-R (MINECO/FEDER) funded by Spanish Ministry of Economy and Competitiveness; “TUNAGEN” project funded by Instituto Español de Oceanografía (IEO); and “BLUEFIN” project financed by IEO and Balearic Island Observing and Forecasting System (SOCIB). This research was funded by NASA (NNX11AP76G S07), the NOAA National Marine Fisheries Science Service through the Southeast Fisheries Science Center, as well as by the Cooperative Institute for Marine and Atmospheric Studies under Cooperative Agreement NA15OAR43200064 at the University of Miami, Miami, FL, USA. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. En prensa

Background Acute hepatopancreatic necrosis syndrome (AHPND) caused by Vibrio parahaemolyticus strain (VPAHPND) impacts the shrimp industry worldwide. With the increasing problem of antibiotic abuse, studies on quorum sensing (QS) system and anti-QS compounds bring potential breakthroughs for disease prevention and treatment. Methods In this study, the cell-free culture supernatant (CFCS) and its extract of V. alginolyticus BC25 were investigated for anti-QS activity against a reporter bacteria, Chromobacterium violaceum DMST46846. The effects of CFCS and/ or extract on motility, biofilm formation and extracellular polymeric substances (EPSs) of VPAHPND PSU5591 were evaluated. Moreover, the effects of V. alginolyticus BC25 on virulence of VPAHPND PSU5591 were investigated by shrimp challenge test. The potentially active anti-QS compounds presented in the extract and effect on gene expression of VPAHPND PSU5591 were identified. Results The CFCS of V. alginolyticus BC25 and its extract showed a significant anti-QS activity against the reporter bacteria as well as swimming and swarming motilities, biofilms, and EPSs production by VPAHPND PSU5591. Transcriptome analysis revealed that V. alginolyticus BC25 extract significantly reduced the flagella genes involved in biofilm formation and iron-controlled virulence regulatory gene of VPAHPND PSU5591. Whereas, the LuxR family transcriptional regulator gene, c-factor, a cell-cell signaling gene, and capsular polysaccharide were up-regulated. The potentially active anti-QS compounds identified in extract were Cyclo-(L-Leu-L-Pro), and Cyclo-(L-Phe-L-Pro). Furthermore, V. alginolyticus BC25 enhanced disease resistance against VPAHPND PSU5591 in tested shrimp larvae. Conclusion These findings suggest that V. alginolyticus BC25 could provide natural anti-QS and anti-biofilms compounds and has great ability to be used as biocontrol agent against VPAHPND infection in shrimp aquaculture.

Background Invasive gibel carp, Carassius gibelio (Bloch, 1782) has become well-established in the Hungarian waters and now are spreading in the European waters. On major concern now is the potential hybridization between gibel carp and the other invasive species in the Carassius auratus complex (CAC), which may further accelerate the spread of the whole invasive species complex. The identification of gibel carp and their hybrids is difficult because of its morphological similarity to the other species in CAC. Here we carry out a genomic assessment to understand the history of gibel carp invasion and its phylogenetic relationship with the other species in CAC. Three loci of the mitochondrial genome (D-loop, CoI, Cytb) were used to determine the phylogenetic origin of individuals and relarionship among six gibel carp populations and the other species in the CAC. Methodolgy A total of 132 gibel carp samples from six locations in Southern Transdanubia (Hungary) were collected after phenotypic identification to measure the genetic diversity within and among gibel carp populations of Southern Transdanubia (Hungary). The genetic background was examined by the sequences of the mitochondrial genome: D-loop, Cytochrome c oxidase I (CoI) and Cytochrome b (Cytb). Mitochondrial genetic markers are excellent tools for phylogenetic studies because they are maternally inherited. Successfully identified haplotypes were aligned and with reference sequences in nucleotide databases (i.e., NCBI-BLAST: National Centre for Biotechnology Information and BOLD: Barcode of Life Data System). The phylogenetic relationships among gibel carp populations were then analyzed together with the reference sequences to understand the relationship and the level of hybridization with the species in CAC. Results Among the 132 aligned D-loop sequences 22 haplotypes were identified. Further examination of representative individuals of the 22 haplotypes, six Cytb and four CoI sequences were detected. The largest number of haplotypes of all three loci were found in Lake Balaton, the largest shallow lake in Central Europe. Based on the NCBI-BLAST alignment of the D-loop, haplotypes of Carassius auratus auratus and Carassius a. buergeri in CAC were identified in the C. gibelio samples. Further analysis of haplotypes with the other two mitochondrial markers confirmed the occurrence of intragenus hybridization of C. gibelio in the Hungarian waters. Conclusion By using three mitochondrial markers (D-loop, Cytb, CoI), we genomically characterized a gibel carp-complex in Hungarian waters and assessed the C. gibelio phylogenetic status between them. Hybrid origin of locally invasive Carassius taxon was detected in Hungary. It points out that invasive species are not only present in Hungary but reproduce with each other in the waters, further accelerating their spread.

In order to develop a sustainable salmonid aquaculture, it is essential to continue to reduce the use of the protein-rich fishmeal. One promising solution to do so is the use of plant-derived carbohydrates in diet destined to broodstock. However, in mammals, the reduction of protein content (replaced by carbohydrates) in parental diet is known to have strong adverse effects on offspring phenotypes and metabolism. For the first time, the effect of a paternal and a maternal high carbohydrate-low protein diet was assessed on progeny at long term in the rainbow trout. A 30% protein diminution in both males and females broodstock diet during 10 month and 5 months, respectively, did not trigger adverse consequences on their offspring. At the molecular level, offspring transcriptomes were not significantly altered, emphasizing no effect on metabolism. Tenuous differences in the biochemical composition of the liver and the viscera were observed. The recorded effects remained in the normal range of value and accordingly offspring growth were not negatively affected over the long term. Overall, we demonstrated here that a 30% protein diminution during gametogenesis is feasible, confirming the possibility to increase the proportion of plant-derived carbohydrates in female broodstock diets to replace fishmeal proteins.

Background Quorum Sensing (QS) is a cell-to-cell communication system that bacteria utilize to adapt to the external environment by synthesizing and responding to signalling molecules called autoinducers. The psychrotrophic bacterium Aliivibrio wodanis 06/09/139, originally isolated from a winter ulcer of a reared Atlantic salmon, produces the autoinducer N-3-hydroxy-decanoyl-homoserine-lactone (3OHC10-HSL) and encodes the QS systems AinS/R and LuxS/PQ, and the master regulator LitR. However, the role of QS in this bacterium has not been investigated yet. Results In the present work we show that 3OHC10-HSL production is cell density and temperature-dependent in A. wodanis 06/09/139 with the highest production occurring at a low temperature (6 °C). Gene inactivation demonstrates that AinS is responsible for 3OHC10-HSL production and positively regulated by LitR. Inactivation of ainS and litR further show that QS is involved in the regulation of growth, motility, hemolysis, protease activity and siderophore production. Of these QS regulated activities, only the protease activity was found to be independent of LitR. Lastly, supernatants harvested from the wild type and the ΔainS and ΔlitR mutants at high cell densities show that inactivation of QS leads to a decreased cytopathogenic effect (CPE) in a cell culture assay, and strongest attenuation of the CPE was observed with supernatants harvested from the ΔlitR mutant. Conclusion A. wodanis 06/09/139 use QS to regulate a number of activities that may prove important for host colonization or interactions. The temperature of 6 °C that is in the temperature range at which winter ulcer occurs, plays a role in AHL production and development of CPE on a Chinook Salmon Embryo (CHSE) cell line.

The objective of many fish and wildlife restoration programs is to utilize management actions to change the state of a system. Because restoration programs are often expensive, iteratively assessing whether the restoration is having the desired outcome is a critical aspect of learning how to inform ongoing and sampling designs to evaluate proposed restoration programs. We provide an example of how we are using data resampling as part of an adaptive restoration process to test the effectiveness of a restoration action and associated monitoring program to restore the degraded Lone Cabbage oyster reef in Suwannee Sound, Florida in the northeast Gulf of Mexico. We use a resampling framework through simulations to inform the progress of the restoration efforts by examining the direction and magnitude of the differences in live oyster counts between restored and unrestored (wild) reefs over time. In addition, we evaluated the effort (number of sites sampled) needed to determine the effect of restoration to understand how many surveys should be conducted in subsequent sampling seasons. These efforts allow us to provide timely insight into the effectiveness of both our monitoring efforts and restoration strategy which is of critical importance not only to the restoration of Lone Cabbage Reef but to larger restoration efforts within the Gulf of Mexico as part of the consolidated Deepwater Horizon settlements and funded restoration efforts.

A partial skeleton of a hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of Dorset, England, is described and designated as a new genus and species, Durnonovariaodus maiseyi gen. et sp. nov. The holotype and only known specimen, which is represented by disarticulated splanchnocranial elements with associated teeth, a single dorsal fin spine, the pelvic girdle, as well as unidentifiable cartilage fragments, plus countless dermal denticles, exhibits a puzzling combination of dental and skeletal features, providing important new insights into the morphological and ecological diversity of hybodontiforms. Durnonovariaodus gen. nov. displays a unique set of dental characters, showing close morphological resemblance to Secarodus from the Middle Jurassic of England, which was erected for distinctive, strongly labio-lingually compressed multicuspid cutting teeth originally described as Hybodus polyprion. Skeletally, Durnonovariaodus gen. nov. resembles Hybodus and Egertonodus in having a palatoquadrate with a palatobasal process and an ethmoidal articular surface, combined with the possession of dorsal fin spines ornamented with costae. Therefore, and given the absence of any conclusive phylogenetic framework, Durnonovariaodus maiseyi gen. et sp. nov. is here tentatively referred to Hybodontidae until more complete material becomes available in order to enable a more reliable suprageneric identification. The holotype of Durnonovariaodus maiseyi gen. et sp. nov. contains two separate pelvic half-girdles, a feature previously considered as evolutionarily primitive among hybodontiforms. However, unfused pelvic half-girdles also occur in the supposedly closely related species Hybodus hauffianus and may in fact have been more widely distributed among hybodontiforms than previously thought, thus rendering the phylogenetic utility of separated pelvic half-girdles for inferring hybodontiform interrelationships difficult and unresolved.

The black sea bream Acanthopagrus schlegelii (Bleeker, 1854) is a commercially important species in Japanese waters. Assessing its population structure is essential to ensure its sustainability. In the Northwestern Pacific, historical glacial and interglacial periods during the Pleistocene have shaped the population structure of many coastal marine fishes. However, whether these events affected the population of black sea bream remains unknown. To test this hypothesis and to assess the population structure of black sea bream, we used 1,046 sequences of the mitochondrial control region from individuals collected throughout almost the entire Japanese coastal waters and combined them with 118 sequences from populations distributed in other marginal seas of the Northwestern Pacific Ocean. As in other coastal marine fish with similar distribution, we also found evidence that the glacial refugia on the marginal seas prompted the formation of three lineages in black sea bream. These lineages present signatures of population growth that coincided with the interglacial periods of the Pleistocene. While the origin of Lineages B and C remains unclear, the higher relative frequency of Lineage A in the southernmost location suggests its origin in the South China Sea. The non-significant pairwise ΦST and AMOVA of Japanese populations and the presence of these three lineages mixed in Japanese waters; strongly suggest that these lineages are homogenized in both the Sea of Japan and the Pacific Ocean. Our results indicate that the black sea bream should be managed as a single stock in Japan until the strength of connectivity in contemporary populations is further addressed using non-coding nuclear markers.

Background The argus snakehead (Ophiocephalus argus Cantor) is a highly nutritious, freshwater, cultured bony fish with a high economic value. The health of the fish is closely related to its blood cells, which are critical for oxygen transport, natural defense, and immunity. We investigated the morphometry, microstructure, and cytochemical characteristics of the peripheral blood cells of O. argus. Our results may provide the basic reference values needed to monitor the health of this fish for large-scale cultivation. Methods The number of blood cells in O. argus were counted on a hemocytometer and their size was measured using a micrometer under light microscope. The morphology and classification of the blood cells were studied using Wright’s staining and the cytochemical characteristics were studied using seven chemical stains including peroxidase (POX), Sudan black B (SBB), periodic acid-Schiff (PAS), acid phosphatase (ACP), alkaline phosphatase (ALP), chloroacetic acid AS-D naphthol esterase (AS-D), and α-naphthol acetate esterase (α-NAE). Results The peripheral blood cells in O. argus can be classified as erythrocytes, leukocytes, and thrombocytes; of which, females had 2.9597 million/mm3, 88,400/mm3, and 43,600/mm3, respectively, and males had 3.0105 million/mm3, 105,500/mm3, and 34,000/mm3, respectively. Leukocytes consisted of neutrophils, monocytes, large lymphocytes, and small lymphocytes. Eosinophils and basophils were not found. Monocytes were the most numerous leukocytes identified, followed by neutrophils and small lymphocytes, while large lymphocytes were the least frequently identified. Cytochemical staining showed that erythrocytes were only positive for PAS staining. Neutrophils were strongly positive for POX, SBB, and ACP, and positive for all the other cytochemical stains. Monocytes were positive for PAS and α-NAE and were weakly positive for ACP and AS-D staining. Large lymphocytes were positive for PAS and were weakly positive for ALP, AS-D, and α-NAE staining. Small lymphocytes were positive for PAS and weakly positive for AS-D and α-NAE staining. Thrombocytes were positive for PAS and were weakly positive for ACP and AS-D, but negative for the remaining cytochemical stains. The morphology of peripheral blood cells in O. argus was generally similar to that of other fish species, while the cytochemical staining patterns showed clear species specificity.

Swimming crabs have a characteristic fifth pair of legs that are flattened into paddles for swimming purposes. The dactyl of these legs bears a thick seta along its edge. The chemoreceptive and feeding properties of the seta are supported with scientific evidence; however, there is no available data on the sensitivity of the setae in portunid crabs. The underlying mechanisms of the chemo- and mechano-sensitivity of appendages and their involvement in feeding activities of the mud crab (Scylla paramamosain) were investigated using electrocardiography and behavioural assay, which focused on the responses of the mud crab to chemical and touch stimulus. Electrocardiography revealed the sensory properties of the appendages. The dactyls of swimming legs and the antennules were chemosensitive, but not mechanosensitive and vice versa for the antennae. However, the mouthparts, claws, and walking legs were chemo- and mechanosensitive. Only the chemosensitive appendages, including the swimming legs, were directly involved in feeding. The flattened dactyls of the swimming legs were more efficient than the pointed dactyls of the walking legs in detecting the food organism crawling on the substrate. The structural features enhanced the capacity of the crab in coming into contact with scattered food items. This study revealed that the swimming legs are important appendages for feeding in the mud crab.

Neopterygii is a taxonomically diverse clade of ray-finned fishes, including Teleostei, Holostei and closely related fossil taxa. The Colobodontidae is a stem group of large-sized neopterygians with a durophagous feeding adaption from the Middle to Late Triassic marine ecosystems in Europe and South China. Here, we report the discovery of a new colobodontid, Feroxichthys panzhouensis sp. nov., based on a well-preserved specimen from the early Middle Triassic (Anisian) of Panzhou (formerly known as Panxian), Guizhou, China. The discovery extends the geographical distribution of Feroxichthys from eastern Yunnan into western Guizhou, and demonstrates a more rapid diversification of early colobodontids than previously thought. The new species possesses diagnostic features of Feroxichthys (e.g., a fused lacrimal-maxilla), but it is easily distinguished from the type species Feroxichthys yunnanensis and other colobodontids by some derived features on the skull and, especially, the relatively short and deep body with a prominent postcranial hump. This body form, previously unknown in colobodontids, implicates a morphological adaptation to structurally complex habitats in light of ecological studies of modern ray-finned fishes with a similar body form. In addition, the feeding apparatus suggests a more obligate durophagous diet for F. panzhouensis sp. nov. than other colobodontids. Results of a cladistic analysis recover the new species as a sister taxon of F. yunnanensis within the Colobodontidae, and suggest that a hump-backed body form has independently evolved multiple times in Triassic neopterygians. As such, the new finding provides an important addition for our understanding of the morphological and ecological diversity of neopterygian fishes from the Triassic marine ecosystems in South China.

BackgroundThe fishTotoaba macdonaldiis endemic to the Upper Gulf of California. Its migratory movements involve sites with high levels of trace elements in the environment that can accumulate in tissues. In this study, lead (Pb), copper (Cu), cadmium (Cd), zinc (Zn) and iron (Fe) concentrations in male and female totoaba liver and muscle were quantified at various sexual maturity stages along the species’ geographic distribution.MethodsGeneralized linear models were used to explore associations between trace element concentrations and season of the year, sex/maturity stage, and total fish length.ResultsNo detectable Pb concentrations were recorded in liver or muscle; Cu, Cd, Zn and Fe contents in totoaba liver and muscle were typical of fish inhabiting areas with no contamination issues and are within international maximum permissible levels for human consumption. Variations in the content of Cd, Cu, Zn and Fe in liver of totoaba seem to be more related to the feeding and reproductive physiology of this species than as result of environmental exposure. Results suggest that consumption of totoaba muscle does not pose a public health risk. Furthermore, depending on the sex/maturity stage of totoaba, this fish’s muscle may provide approximately 70% Cu, 60% Zn and 100% Fe of the recommended dietary reference intake.

Finding new alternatives to traditional live preys such as Artemia and rotifers, which do not always promote optimal fish growth and survival, is required for the successful aquaculture of highly specialized predatory species, including seahorses. The present study assessed the nutritional value of an interesting marine amphipod (Parhyale hawaiensis), and evaluates through a feeding trial its potential use as a natural prey for 10-months lined seahorse, Hippocampus erectus. P. hawaiensis showed high levels of valuable lipids (20.4–26.7% on dry matter basis) and polyunsaturated fatty acids (PUFAs) ( 26.4–41% of total FAs), including the long-chain PUFAs (LC-PUFAs) arachidonic acid (ARA) (2.9–7.7%), eicosapentaenoic acid (EPA) (4.3–6.5%) and docosahexaenoic acid (DHA) (2.1–6.2%). A comparison between wild-captured and cultured amphipods revealed a significant improvement of the amphipod FA profile in terms of DHA%, total omega-3 (n3) FAs and n3/n6 ratio when employing both a conventional amphipod culture based on a commercial shrimp diet, and, to a lesser extent, a large (3,500 L) biofloc system. Seahorses fed with frozen/wild amphipods, either singly or in combination with Artemia enriched with Super Selco® (INVE Aquaculture, Belgium) for 57 days, substantially improved seahorse growth and FA profiles in terms of ARA, EPA and DHA%, including indices associated to marine sources, such as Σn3 and n3/n6, compared to a diet based solely on enriched Artemia. These results support the use of marine amphipods as an alternative food organism for juvenile H. erectus and suggest a potential use for general marine aquaculture.

Behavioural types (i.e., personalities or temperament) are defined as among individual differences in behavioural traits that are consistent over time and ecological contexts. Behavioural types are widespread in nature and play a relevant role in many ecological and evolutionary processes. In this work, we studied for the first time the consistency of individual aggressiveness in the pearly razorfish, Xyrichtys novacula, using a mirror test: a classic method to define aggressive behavioural types. The experiments were carried out in semi-natural behavioural arenas and monitored through a novel Raspberry Pi-based recording system. The experimental set up allowed us to obtain repeated measures of individual aggressivity scores during four consecutive days. The decomposition of the phenotypic variance revealed a significant repeatability score (R) of 0.57 [0.44–0.60], suggesting high predictability of individual behavioural variation and the existence of different behavioural types. Aggressive behavioural types emerged irrespective of body size, sex and the internal condition of the individual. Razorfishes are a ubiquitous group of fish species that occupy sedimentary habitats in most shallow waters of temperate and tropical seas. These species are known for forming strong social structures and playing a relevant role in ecosystem functioning. Therefore, our work provides novel insight into an individual behavioural component that may play a role in poorly known ecological and evolutionary processes occurring in this species., This work was carried out as part of the research project Cronofish (AAEE 101/2017) funded by Balearic Islands Government. In addition, this project also received financing from the CLOCKS project from the Spanish Government (PID2019-104940GA-I00). Martina Martorell-Barceló was supported by an FPI predoctoral fellowship (ref. FPI/2167/2018) from the Balearic Islands Government General Direction of Innovation and Research. Josep Alós was supported by a Ramon y Cajal Grant (grant no. RYC2018-024488-I) and the intramural research project JSATS (grant no. PIE 202030E002) funded by the Spanish Ministry of Science and Innovation, and the Spanish National Research Council.

The objective of this study was to evaluate long term trends of fish taxa in southern Lake Michigan while incorporating their functional roles to improve our understanding of ecosystem level changes that have occurred in the system over time. The approach used here highlighted the ease of incorporating ecological mechanisms into population models so researchers can take full advantage of available long-term ecosystem information. Long term studies of fish assemblages can be used to inform changes in community structure resulting from perturbations to aquatic systems and understanding these changes in fish assemblages can be better contextualized by grouping species according to functional groups that are grounded in niche theory. We hypothesized that describing the biological process based on partial pooling of information across functional groups would identify shifts in fish assemblages that coincide with major changes in the ecosystem (e.g., for this study, shifts in zooplankton abundance over time). Herein, we analyzed a long-term Lake Michigan fisheries dataset using a multi-species state space modeling approach within a Bayesian framework. Our results suggested the population growth rates of planktivores and benthic invertivores have been more variable than general invertivores over time and that trends in planktivores can be partially explained by ecosystem changes in zooplankton abundance. Additional work incorporating more ecosystem parameters (e.g., primary production, etc.) should be incorporated into future iterations of this novel modeling concept.

The aim of this study is to investigate the effect of three daily fish feeding frequencies, two, four and eight times per day (FF2, FF4, and FF8, respectively) on growth performance of sea bass (Dicentrarchus labrax)and lettuce plants (Lactuca sativa) reared in aquaponics. 171 juvenile sea bass with an average body weight of 6.80 ± 0.095 g were used, together with 24 lettuce plants with an average initial height of 11.78 ± 0.074 cm over a 45-day trial period. FF2 fish group showed a significantly lower final weight, weight gain and specific growth rate than the FF4 and FF8 groups. Voluntary feed intake was similar for all the three feeding frequencies treatmens (p > 0.05). No plant mortality was observed during the 45-day study period. All three aquaponic systems resulted in a similar leaf fresh weight and fresh and dry aerial biomass. The results of the present study showed that the FF4 or FF8 feeding frequency contributes to the more efficient utilization of nutrients for better growth of sea bass adapted to fresh water while successfully supporting plant growth to a marketable biomass.

The freshwater pulmonate snail Planorbella trivolvis is a common species in various bodies of water but is not native to China. Planorbella trivolvis usually live on diets with high fiber content, such as water grasses, algae and fallen leaves. These snails can attach to the wall of a water tank or to water grass and can be transported overseas to China through the ornamental fish trade. There are few studies investigating the intestinal microbiota of freshwater snails. In this study, using culture-independent molecular analysis, we assessed for the first time the complexity of bacterial communities in the intestines of reared snails. The intestinal microbiota in the snails fed different diets, that is, herbivorous feed (HV) with high cellulose and non-herbivorous feed (NHV) with low cellulose, were analyzed by Illumina sequencing. The results showed that the NHV-based diet significantly increased the body mass, shell diameter and specific growth rate of the snails after 60 days of rearing (P < 0.05). Histological experiments showed that the fat droplets in the epithelium columnar cells of the intestines of the NHV snails increased, and the cilia on these cells fell off. The sequencing results identified 486 and 195 OTUs in HV and NHV, respectively. Lots of bacteria were not reported previously in snails. The intestinal microbiota diversity index (Shannon, Simpson, Ace and Chao) in the NHV snails was significantly lower than that in the HV snails. The gut microbiota in the HV snails were predominantly Proteobacteria (52.97%) and Bacteroidetes (28.75%), while the gut microbiota in NHV snails were predominantly Proteobacteria (95.23%). At the genus level, Cloacibacterium (24.60%), Pseudomonas (4.47%), OM6ON (6.12%), and Rhodobacter (5.79%) were observed to be abundant in HV snails. However, Aeromonas (85.4%) was determined to be predominant in NHV snails. Functional prediction of the gut microbiome in snails by PICRUSt demonstrated a significant difference between the two groups, and the HV snails exhibited higher lignocellulose enzyme activity than did the NHV snails. This study represents a first step in characterizing the gut microbiota of the freshwater snail. Most of these microbes can process plant biomass and digest cellulose and lignocellulose, and the enzymes of these bacteria may have potential biotechnological applications in a variety of industrial processes.

Background Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.

The benthic impact of aquaculture waste depends on the area and extent of waste accumulation on the sediment surface below and around the farm. In this study we investigated the effect of flow on biodeposit transport and initial deposition by calculating a rough aquaculture “footprint” around an oyster aquaculture farm in the Damariscotta River, ME. We also compared a site under the farm to a downstream “away” site calculated to be within the footprint of the farm. We found similar sediment biogeochemical fluxes, geochemical properties and macrofaunal communities at the site under the farm and the away site, as well as low organic enrichment at both sites, indicating that biodeposition in this environment likely does not have a major influence on the benthos. To predict accumulation of biodeposits, we measured sediment erodibility under a range of shear stresses and found slightly higher erosion rates at the farm than at the away site. A microalgal mat was observed at the sediment surface in many sediment cores. Partial failure of the microalgal mat was observed at high shear velocity, suggesting that the mat may fail and surface sediment erode at shear velocities comparable to or greater than those calculated fromin situ flow measurements. However, this study took place during neap tide, and it is likely that peak bottom velocities during spring tides are high enough to periodically “clear” under-farm sediment of recent deposits.

The endangered Chiapas killifish Tlaloc hildebrandi is an endemic freshwater species that lives in four subbasins of the Grijalva and Usumacinta basins, and one of the most geographically restricted species of the Produndulidae family. The species was originally described as endemic to springs in the high limestone plateau in San Cristóbal de Las Casas in the Río Amarillo subbasin (upper Grijalva basin). However, it was recently recorded in the Jataté and Tzaconejá subbasins in the upper Usumacinta basin, thereby expanding its known distribution range. The discovery of these populations is relevant not only for the conservation of the species but also for a better understanding of its evolutionary history. Currently, the scarce populations of T. hildebrandi, found in only a few localities in the Grijalva and Usumacinta basins, are fragmented and living under unfavorable conditions. Here, we analyzed three mitochondrial (mt-atp8&6 and mt-nd2) and one nuclear (nuc-s7) marker in order to assess the genetic diversity and population structure of T. hildebrandi. We found that, in comparison with other endangered freshwater fish species from Mexico, T. hildebrandi showed a lower level of genetic diversity (mt-nd2: h = 0.469, π = 0.0009; mt-atp8&6: h = 0.398, π = 0.001; and nuc-S7: h = 0.433, π = 0.001). Moreover, the analyzed populations exhibited a strong genetic structure in accordance with their geographic distribution, and can be placed into three genetic clusters: (1) Amarillo plus Chenhaló in the upper Grijalva basin, (2) Jataté, and (3) Tzaconejá, both in the upper Usumacinta basin. On the basis of our results, we propose the recognition of at least three evolutionarily significant units (ESUs) for the species and the urgent implementation of ex situ and in situ conservation and management efforts that consider the genetic background of the species.

Malaysia is one of the top ten countries in the world that produce freshwater ornamental fishes. This industry can offer better livelihood opportunities to many poor households. However, most of the produced ornamental fishes are alien to Malaysia. In this study, we explore the contribution of alien freshwater fishes to the income of ornamental fish store owners and their attitude towards alien freshwater fishes within Klang Valley, Malaysia. Using a structured questionnaire, we surveyed 70 pet stores out of which 54 (81.42%) store owners responded. Most of the pet store owners were male (72%), Chinese (83%), and the highest educational level was at the secondary level (79%). Most of the pet store owners reported a monthly income of RM 2001–RM 5000 (78%) and were married (73%). Using Chi-square (χ2) test, significant relationships (p < 0.05) existed between the attitude of store owners towards alien ornamental fish species versus educational level (χ2 = 16.424, p = 0.007) and contribution of alien ornamental fishes to the pet store owners’ income (χ2 = 27.266, p = 0.003). Fish sales as the main income source also related significantly with the impact of fish selling business on income level (χ2 = 10.448, p = 0.007). This study showed that the ornamental fish sales contributed over half of the income (51–100%) from the businesses of store owners. Almost half of the respondents (42%) reported that alien ornamental fish was the highest contributor to their income from the ornamental fish sale. While the mismanagement of alien ornamental fishes could give various negative ecological impacts, the socio-economic benefits of these fishes cannot be denied.

Background Marine soundscape is the aggregation of sound sources known as geophony, biophony, and anthrophony. The soundscape analysis, in terms of collection and analysis of acoustic signals, has been proposed as a tool to evaluate the specific features of ecological assemblages and to estimate their acoustic variability over space and time. This study aimed to characterise the Capo Caccia-Isola Piana Marine Protected Area (Italy, Western Mediterranean Sea) soundscape over short temporal (few days) and spatial scales (few km) and to quantify the main anthropogenic and biological components, with a focus on fish biophonies. Methods Within the MPA, three sites were chosen each in a different protection zone (A for the integral protection, B as the partial protection, and C as the general protection). In each site, two underwater autonomous acoustic recorders were deployed in July 2020 at a depth of about 10 m on rocky bottoms. To characterise the contribution of both biophonies and anthrophonies, sea ambient noise (SAN) levels were measured as sound pressure level (SPL dB re: 1 μ Pa-rms) at eight 1/3 octave bands, centred from 125 Hz to 16 kHz, and biological and anthropogenic sounds were noted. Fish sounds were classified and counted following a catalogue of known fish sounds from the Mediterranean Sea based on the acoustic characteristic of sound types. A contemporary fish visual census had been carried out at the test sites. Results SPL were different by site, time (day vs. night), and hour. SPLs bands centred at 125, 250, and 500 Hz were significantly higher in the daytime, due to the high number of boats per minute whose noise dominated the soundscapes. The loudest man-made noise was found in the A zone, followed by the B and the C zone, confirming that MPA current regulations do not provide protection from acoustic pollution. The dominant biological components of the MPA soundscape were the impulsive sounds generated by some invertebrates, snapping shrimps and fish. The vast majority of fish sounds were recorded at the MPA site characterized by the highest sound richness, abundance, and Shannon-Wiener index, coherently with the results of a fish visual census. Moreover, the acoustic monitoring detected a sound associated with a cryptic species (Ophidion spp.) never reported in the study area before, further demonstrating the usefulness of passive acoustic monitoring as a complementary technique to species census. This study provides baseline data to detect future changes of the marine soundscapes and some suggestions to reduce the impact of noise on marine biodiversity.