Human health risks associated to trace elements and metals in commercial fish from the Brazilian Amazon.

Fish constitutes the main protein source for the Amazonian population. However, the impact of different anthropogenic activities on trace element and metal accumulation in fish and their risks for human health at a regional scale remain largely unexplored. Here we assessed exposure levels of 10 trace elements and metals (Cr, Mn, Fe, Ni, Cu, Zn, As, Cd, Pb, and Hg) in 56 samples belonging to 11 different species of fish from the Brazilian Amazon. We studied the relationship between exposure levels, fish origin, and fish feeding habits, and assessed toxicological and carcinogenic risks for the Amazonian population. No significant correlation was found between sampling site and exposure levels to the studied elements, but a significant difference was found between the accumulation of some metals and the position of the fish species in the food chain. The concentrations of Cr and Hg in fish flesh were found to exceed the Brazilian limits for human consumption. This study shows that current fish consumption patterns can lead to estimated daily intakes of Hg, As and Cr that exceed the oral reference dose, thus posing a toxicological concern. Furthermore, carcinogenic risks may be expected due to the continued exposure to Cr and As. The results of this study show that the consumption of wild caught fish in the Amazon region should be controlled. Moreover, continued monitoring of trace element and metal contamination in fish and on the health of the Amazonian population is recommended, particularly for riverine and indigenous communities.

Genome-wide characterization, phylogenetic and expression analysis of Galectin gene family in Golden pompano Trachinotus ovatus.

Galectins (Gals) are a type of S-type lectin that are widespread and evolutionarily conserved among metazoans, and can act as pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs). In this study, 10 Gals (ToGals) were identified in the Golden pompano (Trachinotus ovatus), and their conserved domains, motifs, and collinearity relationships were analyzed. The expression of ToGals was regulated following infection to Cryptocaryon irritans and Streptococcus agalactiae, indicating that ToGals participate in immune responses against microbial pathogens. Further analysis was conducted on one important member, Galectin-3, subcellular localization showing that ToGal-3like protein is expressed both in the nucleus and cytoplasm. Recombinant protein obtained through prokaryotic expression showed that rToGal-3like can agglutinate red blood cells of rabbit, carp and golden pompano and also agglutinate and kill Staphylococcus aureus, Bacillus subtilis, Vibrio vulnificus, S. agalactiae, Pseudomonas aeruginosa, and Aeromonas hydrophila. This study lays the foundation for further research on the immune roles of Gals in teleosts.

Fish ectoparasite detection, collection and curation.

Fish parasitology is a dynamic and internationally important discipline with numerous biological, ecological and practical applications. We reviewed optimal fish and parasite sampling methods for key ectoparasite phyla (i.e. Ciliophora, Platyhelminthes, Annelida and Arthropoda) as well as recent advances in molecular detection of ectoparasites in aquatic environments. Ideally, fish capture and anaesthesia as well as parasite recovery methods should be validated to eliminate potential sampling bias and inaccuracy in determining ectoparasite population parameters. There are considerable advantages to working with fresh samples and live parasites, when combined with appropriate fixation methods, as sampling using dead or decaying materials can lead to rapid decomposition of soft-bodied parasites and subsequent challenges for identification. Sampling methods differ between target phyla, and sometimes genera, with optimum techniques largely associated with identification of parasite microhabitat and the method of attachment. International advances in fish parasitology can be achieved through the accession of whole specimens and/or molecular voucher specimens (i.e. hologenophores) in curated collections for further study. This approach is now critical for data quality because of the increased application of environmental DNA (eDNA) for the detection and surveillance of parasites in aquatic environments where the whole organism may be unavailable. Optimal fish parasite sampling methods are emphasised to aid repeatability and reliability of parasitological studies that require accurate biodiversity and impact assessments, as well as precise surveillance and diagnostics.

The interaction between warming and enrichment accelerates food-web simplification in freshwater systems.

Nutrient enrichment and climate warming threaten freshwater systems. Metabolic theory and the paradox of enrichment predict that both stressors independently can lead to simpler food-webs having fewer nodes, shorter food-chains and lower connectance, but cancel each other's effects when simultaneously present. Yet, these theoretical predictions remain untested in complex natural systems. We inferred the food-web structure of 256 lakes and 373 streams from standardized fish community samplings in France. Contrary to theoretical predictions, we found that warming shortens fish food-chain length and that this effect was magnified in enriched streams and lakes. Additionally, lakes experiencing enrichment exhibit lower connectance in their fish food-webs. Our study suggests that warming and enrichment interact to magnify food-web simplification in nature, raising further concerns about the fate of freshwater systems as climate change effects will dramatically increase in the coming decades.

Resolution of a chronic occipital wound with exposed skull bone with a fish skin graft: a successful treatment approach.

Chronic skin defects in the head, face and neck pose challenges for closure, especially after multiple surgeries or radiation therapy. We report the case of a woman in her 70s with a chronic occipital wound following squamous cell carcinoma resections, resulting in exposed skull bone. Despite various options, we successfully treated the 4 cm x 5 cm wound with a Kerecis fish skin graft (FSG), observing significant improvement within a week. The FSG promoted granulation tissue formation, enabling subsequent full-thickness skin grafting from the patient's groin. Complete wound closure was achieved within 2 weeks, indicating FSG's efficacy in complex wound management. Our experience highlights FSG's potential as a valuable tool in wound healing and reconstruction, particularly in challenging cases involving the head and neck.

Awareness and perceptions of contaminants in the Dehcho and sahtú regions of the Northwest Territories.

The development and dissemination of health messaging is a critical component of reducing health disparities. Participants (n = 87) from a human biomonitoring study in six Dene communities responded to a survey about health communication regarding contaminants. The survey included questions on awareness of health messages and risk perceptions related to country foods and contaminants. The vast majority of participants reported eating country foods (99%) and heard that country foods had beneficial nutrients (90%). Seventy per cent of respondents had heard or seen messages about fish with high levels of mercury, and 60% had concerns about the safety or quality of country foods they consumed. Respondents who reported decreasing the number of fish they ate since hearing the messages about fish and mercury had lower (p = 0.04) mercury concentration in hair, compared to those who had not heard the messages. However, no differences in hair mercury were observed for respondents who reported to have changed their fishing location, chosen smaller fish or eaten less predatory fish since hearing the messages. Results indicate the need to examine reasons for self-reported behaviour changes, in addition to awareness. The conclusions of this study can inform the development of messaging and risk management decisions about contaminants within Indigenous populations.

Effect of local and regional factors on the structure of the fish communities associated with aquatic macrophyte stands in oxbow lakes on the Amazon floodplain.

The Amazon floodplain is home to an extremely high diversity of fish, with lakes playing an important role in the establishment of this biological richness. These lacustrine environments are subject to constant fluctuations caused by the annual flood pulse, with local factors and other regional patterns also contributing to the variation in fish community structure. The present study verified how local (depth and transparency of the water, the size and species composition of the macrophyte stands) and regional factors (spatial distribution of the stands and the hydrological phase) influence the structure of the fish community of the floodplain lakes of the Môa River, in northern Brazil. Fish species richness was influenced by the depth of the water and the spatial distribution of the macrophyte stands. Fish species composition was influenced by local environmental variables, spatial structure, and the hydrological phase. However, variation partitioning indicated that only the hydrological phase explained the variation in fish composition. These findings indicate that the local environment, the spatial structure, and the hydrological phase drive changes in the structure of the fish communities associated with aquatic macrophytes in the floodplain lakes of the Amazon basin.

MIPs: multi-locus intron polymorphisms in species identification and population genomics.

The study of species groups in which the presence of interspecific hybridization or introgression phenomena is known or suspected involves analysing shared bi-parentally inherited molecular markers. Current methods are based on different categories of markers among which the classical microsatellites or the more recent genome wide approaches for the analyses of thousands of SNPs or hundreds of microhaplotypes through high throughput sequencing. Our approach utilizes intron-targeted amplicon sequencing to characterise multi-locus intron polymorphisms (MIPs) and assess genetic diversity. These highly variable intron regions, combined with inter-specific transferable loci, serve as powerful multiple-SNP markers potentially suitable for various applications, from species and hybrid identification to population comparisons, without prior species knowledge. We developed the first panel of MIPs highly transferable across fish genomes, effectively distinguishing between species, even those closely related, and populations with different structures. MIPs offer versatile, hypervariable nuclear markers and promise to be especially useful when multiple nuclear loci must be genotyped across different species, such as for the monitoring of interspecific hybridization. Moreover, the relatively long sequences obtained ease the development of single-locus PCR-based diagnostic markers. This method, here demonstrated in teleost fishes, can be readily applied to other taxa, unlocking a new source of genetic variation.

Extraction of high-molecular-weight DNA from Streptococcus spp. for nanopore sequencing in resource-limited settings.

The long-read sequencing platform MinION, developed by Oxford Nanopore Technologies, enables the sequencing of bacterial genomes in resource-limited settings, such as field conditions or low- and middle-income countries. For this purpose, protocols for extracting high-molecular-weight DNA using nonhazardous, inexpensive reagents and equipment are needed, and some methods have been developed for gram-negative bacteria. However, we found that without modification, these protocols are unsuitable for gram-positive Streptococcus spp., a major threat to fish farming and food security in low- and middle-income countries. Multiple approaches were evaluated, and the most effective was an extraction method using lysozyme, sodium dodecyl sulfate, and proteinase K for lysis of bacterial cells and magnetic beads for DNA recovery. We optimized the method to consistently achieve sufficient yields of pure high-molecular-weight DNA with minimal reagents and time and developed a version of the protocol which can be performed without a centrifuge or electrical power. The suitability of the method was verified by MinION sequencing and assembly of 12 genomes of epidemiologically diverse fish-pathogenic Streptococcus iniae and Streptococcus agalactiae isolates. The combination of effective high-molecular-weight DNA extraction and MinION sequencing enabled the discovery of a naturally occurring 15 kb low-copy number mobilizable plasmid in S. iniae, which we name pSI1. We expect that our resource-limited settings-adapted protocol for high-molecular-weight DNA extraction could be implemented successfully for similarly recalcitrant-to-lysis gram-positive bacteria, and it represents a method of choice for MinION-based disease diagnostics in low- and middle-income countries.

Twenty-five emerging questions when detecting, understanding, and predicting future fish distributions in a changing climate.

The 2023 Annual Symposium of the Fisheries Society of the British Isles hosted opportunities for researchers, scientists, and policy makers to reflect on the state of art of predicting fish distributions and consider the implications to the marine and aquatic environments of a changing climate. The outcome of one special interest group at the Symposium was a collection of questions, organized under five themes, which begin to capture the state of the field and identify priorities for research and management over the coming years. The five themes were Physiology, Mechanisms, Detect and Measure, Manage, and Wider Ecosystems. The questions, 25 of them, addressed concepts which remain poorly understood, are data deficient, and/or are likely to be impacted in measurable or profound ways by climate change. Moving from the first to the last theme, the questions expanded in the scope of their considerations, from specific processes within the individual to ecosystem-wide impacts, but no one question is bigger than any other: each is important in detecting, understanding, and predicting fish distributions, and each will be impacted by an aspect of climate change. In this way, our questions, particularly those concerning unknown mechanisms and data deficiencies, aimed to offer a guide to other researchers, managers, and policy makers in the prioritization of future work as a changing climate is expected to have complex and disperse impacts on fish populations and distributions that will require a coordinated effort to address.

Stock assessment models overstate sustainability of the world's fisheries.

Effective fisheries management requires accurate estimates of stock biomass and trends; yet, assumptions in stock assessment models generate high levels of uncertainty and error. For 230 fisheries worldwide, we contrasted stock biomass estimates at the time of assessment with updated hindcast estimates modeled for the same year in later assessments to evaluate systematic over- or underestimation. For stocks that were overfished, low value, or located in regions with rising temperatures, historical biomass estimates were generally overstated compared with updated assessments. Moreover, rising trends reported for overfished stocks were often inaccurate. With consideration of bias identified retrospectively, 85% more stocks than currently recognized have likely collapsed below 10% of maximum historical biomass. The high uncertainty and bias in modeled stock estimates warrants much greater precaution by managers.

Taking stock of global fisheries.

Current stock assessment models overestimate productivity and recovery trajectory.

Lumpfish, Cyclopterus lumpus, distribution in the Gulf of Maine, USA: observations from fisheries independent and dependent catch data.

The Gulf of Maine (GoM) is one of the fastest-warming parts of the world's oceans. Some species' distributional shifts have already been documented, especially for commercially-important species. Less is known about species that are not currently exploited but may become so in the future. As a case study into these issues, we focus on lumpfish (Cyclopterus lumpus) because of the recognized and timely need to understand wild lumpfish population dynamics to support sustainable fisheries and aquaculture developments. Using occurrence data from five different fisheries-dependent and independent surveys, we examined lumpfish distribution over time in the GoM. We found that lumpfish presence was more likely in Fall and correlated with deeper waters and colder bottom temperatures. Since 1980, lumpfish presence has increased over time and shifted north. Given a limited set of data, these findings should be interpreted with caution as additional work is needed to assess if the actual distribution of lumpfish is changing. Nevertheless, our work provides preliminary information for resource managers to ensure that lumpfish are harvested sustainably for use in emergent lumpfish aquaculture facilities.

Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples.

Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA gene markers, in comparison to morphology-based methods for fish species identification in ichthyoplankton samples. Two transects with four coastal distance categories were sampled along the southern coast of Portugal, being each sample divided for molecular and morphological analyses. A total of 76 fish species were identified by both approaches, with DNA metabarcoding overperforming morphology-75 versus 11 species-level identifications. Linking species-level DNA identifications with higher taxonomic morphological identifications resolved several uncertainties associated with traditional methods. Multi-marker DNA metabarcoding improved fish species detection by 20-36% compared to using a single marker/amplicon, and identified 38 species in common, reinforcing the validity of our results. PERMANOVA analysis revealed significant differences in species communities based on the primer set employed, transect location, and distance from the coast. Our findings underscore the potential of DNA metabarcoding to assess ichthyoplankton diversity and suggest that its integration into routine surveys could enhance the accuracy and comprehensiveness of fish stock assessments.

Insights into aging mechanisms from comparative genomics in orange and silver roughies.

The demersal fish orange roughy (Hoplostethus atlanticus) can live for up to 250 years, twenty times more than its congener silver roughy (Hoplostethus mediterraneus). Studies of Hoplostethus have focused mainly on its ecology and conservation due to its vulnerability to commercial fishing. In this work, we present the de novo genomes of orange and silver roughies and explore the genomic mechanisms that could contribute to such differential longevities. Using comparative genomics on a list of more than 400 genes, we identified gene candidates with differential residue changes in Hoplostethus that are related to genomic instability, disabled macroautophagy and intercellular communication. We hypothesized that these mechanisms could have been selected as adaptations to the deep environment and, as an epiphenomenon of these mechanisms, may have contributed to an extension of the lifespan of H. atlanticus.

The formation of sulfur metabolites during in vitro gastrointestinal digestion of fish, white meat and red meat is affected by the addition of fructo-oligosaccharides.

The formation of sulfur metabolites during large intestinal fermentation of red meat may affect intestinal health. In this study, four muscle sources with varying heme-Fe content (beef, pork, chicken and salmon), with or without fructo-oligosaccharides (FOS), were exposed to an in vitro gastrointestinal digestion and fermentation model, after which the formation of sulfur metabolites, protein fermentation metabolites, and short (SCFA) and branched (BCFA) chain fatty acids was assessed. When FOS were present during muscle fermentation, levels of SCFA (+54%) and H2S (+36%) increased, whereas levels of CS2 (-37%), ammonia (-60%) and indole (-30%) decreased, and the formation of dimethyl sulfides and phenol was suppressed. Red meat fermentation was not accompanied by higher H2S formation, but beef ferments tended to contain 33 to 49% higher CS2 levels compared to the ferments of other muscle sources. In conclusion, there is a greater effect on sulfur fermentation by the addition of FOS to the meats, than the intrinsic heme-Fe content of meat.

Draft Genome of Akame (Lates Japonicus) Reveals Possible Genetic Mechanisms for Long-Term Persistence and Adaptive Evolution with Low Genetic Diversity.

It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes and low levels of genetic polymorphisms. To understand the genetic mechanisms of long-term persistence in threatened species, we determined the whole genome sequences of akame (Lates japonicus), which has survived for a long time with extremely low genetic variations. Genome-wide heterozygosity in akame was estimated to be 3.3 to 3.4 × 10-4/bp, one of the smallest values in teleost fishes. Analysis of demographic history revealed that the effective population size in akame was around 1,000 from 30,000 years ago to the recent past. The relatively high ratio of nonsynonymous to synonymous heterozygosity in akame indicated an increased genetic load. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions, including genes involved in immunity, synaptic development, and olfactory sensory systems, have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, suggesting adaptive evolution to temperate waters after the speciation of akame and its close relative, barramundi (Lates calcarifer). Our results indicate that the functional genetic diversity likely contributed to the long-term persistence of this species by avoiding the harmful effects of the population size reduction.

Analysis of total microcystins by Lemieux oxidation and liquid chromatography-mass spectrometry in fish and mussels tissues: Optimization and comparison of protocols.

Microcystins (MCs) can be detected in various matrices in two forms: a freely extractable fraction and a total (free and covalently protein-bound) fraction. Although the majority of MCs analyses are limited to the free fraction, they do not allow the analysis of all MCs variants or protein-bound forms. Other methods, known as total MCs analysis methods, enable simultaneous analysis of all MCs variants, as well as bound forms, which may be a major form of toxin accumulation in organisms. Among these techniques, the chemical oxidation method (e.g. Lemieux) allows the detection of total forms of MC (and nodularins) by oxidizing the common part to all MC and nodularins, and analyzing the resultant MMPB product (2-methyl-3-methoxy-4-phenylbutyric acid). However, the execution of this method in the context of health monitoring is challenging due to the variability of the protocols, the recoveries obtained with these protocols, and the important matrix effects associated with the method. The objectives of this study were i) to optimize an existing protocol of chemical oxidation "Lemieux1" on fresh fish fillet matrices, ii) to compare two existing protocols ("Lemieux1" and "Lemieux2"), and iii) apply Lemieux oxidation to fish fillets and livers naturally contaminated with MCs-producing cyanobacteria and to freshwater mussels contaminated with MCs in laboratories. Optimization of the "Lemieux1" protocol, in particular in the oxidation and SPE (solid phase extraction) steps improved the method's yields on the fresh fish fillet matrix (from <5 % to around 40 %). Moreover, several quantification methods have been compared through various calibration techniques (solvent calibration curve, matrix-matched calibration curve, oxidized MC-LR calibration curve and also by testing the addition of d3-MMPB as an internal standard). Comparison with the "Lemieux2" protocol showed the best results on the same matrix, with yields of around 65 %. MMPB was analyzed using this "Lemieux 2" protocol, in livers of carps sampled during an episode of cyanobacteria proliferation, at concentrations ranging from 17.9 to 27.5 µg/kg MMPB and at concentrations ranging from 50 to 2890 µg/kg MMPB in freshwater mussels laboratory contaminated to MCs.