Aquaculture pathogen outbreaks pose a significant spillover risk to wild populations, demanding the development of early detection mechanisms. We applied an eDNA-based qPCR assay to inflow, rearing, and outflow waters of two independent rainbow trout (Oncorhynchus mykiss) farms to detect and quantify Flavobacterium psychrophilum, a highly infective salmonid pathogen, and identify potential spillovers into local waterways. F. psychrophilum was detected at both facilities, even in the absence of individuals displaying clinical signs of infection, with significantly higher F. psychrophilum copy numbers detected in rearing and outflow water compared with inflow water (Farm 1 mean copies: inflow = 9 f 11, rearing = 2662 f 1882, outflow = 314 f 216; Farm 2 mean copies: inflow = 24 f 26, rearing = 200 f 245, outflow = 66 f 71), indicating potential spillover. We show that eDNA-qPCR constitutes a sensitive tool for F. psychrophilum detection and quantification in the absence of clinical signs, enabling early-warning monitoring for outbreak prevention and spillover mitigation.

The emergence of antimicrobial resistance has encouraged a reappraisal of bacteriophage therapy for the mitigation of bacterial diseases in different environmental settings, including aquaculture. Here, we review aquaculture applications of phage therapy by considering its efficacy and potential for broader host-associated effects, including host immunity, microbiome composition and behaviour. The advantages of phage therapy for aquaculture include the natural abundance and diversity of phages in water, and their self-propagation, host specificity, low environmental impact and diverse administration routes. Although the efficacy of phage therapy in controlling the prevalence of bacterial pathogens across various aquaculture species is well demonstrated, the diversity of phage administration methods, experimental conditions, target strains and host physiologies have prevented a clear consensus being reached regarding the suitability of phage therapy for aquaculture. The application of phage therapy as an antimicrobial strategy induces gentler immune modulation compared to antibiotics and disinfectants, which often induce dysbiosis in host microbiomes by eliminating beneficial or commensal bacteria. However, there are divergent results regarding the influence of phage administration upon host microbiome composition and dynamics, with potentially important health implications that require further research. How phage immunogenicity may influence the host immune response is also unclear. Additional concerns include phage-neutralising antibody production, phage-resistant bacteria and horizontal gene transfer of antimicrobial resistance. Together, these represent areas warranting further research in aquaculture, along with the development of suitable fish models that demonstrate the broad applicability of phage therapy across multiple species.

Global warming remains a neglected environmental challenge for the sustainability of primary production, particularly aquaculture, which is highly susceptible to the spread of established pathogens and the induction of emerging infectious diseases under warming conditions. Over the past decade, Europe has experienced dramatically high temperatures that may impact both farmed fish and their pathogens in a largely unpredictable manner. While, in general, warming may boost the rate of disease transmission and its virulence by increasing pathogens' fitness in weakened hosts, some diseases characteristic of cooler environments may become rare. Field data is still largely fragmented, but in vitro experiments reveal that almost 28 microbial diseases in European finfish farming could be facilitated by climate warming. Innovative mitigation tools, such as fish selective breeding, epigenetic programming, the development of new vaccines, and alternative treatments, may prove essential in coping with the effects of rising water temperatures on fish diseases in Europe.

Early-life exposure to stressors can alter responses to later-life stress in either positive or negative ways, potentially mediated by multiple mechanisms, including changes in transcriptomic pathways and/or host-associated microbial communities. We investigated whether early-life stress conditioning during embryonic development influences later-life stress responses and how it differs between ploidies. Diploid and triploid rainbow trout ( Oncorhynchus mykiss ) embryos were exposed to a controlled cold shock (early-life conditioning) and then challenged with acute and chronic crowding stressors 15 weeks later (juvenile stage). Long-term stress response was assessed using transcriptome and microbiota profiling. We found that conditioned fish exposed to acute and chronic crowding stress showed a pronounced reduction in transcriptional stress response compared with unconditioned fish and responses were ploidy dependent. In contrast, microbiota analysis revealed that early-life conditioning and crowding stress altered microbial community structure independently, but that early-life conditioning did not influence subsequent microbiota response to later life stress. Overall, our results show that early-life conditioning induced long lasting effects on the later life stress responses, although the transcriptome and gut microbiota responded in different ways.

Conservation plans for declining species often rely on contemporary genetic/genomic data to infer historical population structure and evolutionary history of the species. However, modern samples alone may not accurately reflect historical genetic variation, especially after severe population declines or intensive management, and need reference baseline data prior to anthropogenic impact. We analysed whole-genome sequences dating to 18,800-16,700 years ago from Atlantic salmon (Salmo salar), that experienced major declines over the past century. Comparing Paleolithic and modern genomes, we found that ancient salmon from the Iberian glacial refugium were genetically closer to present-day northern European populations than to modern Iberian salmon, consistent with southward displacement of northern lineages during glacial periods, postglacial decline of Iberian populations and contemporary human impacts. We identified ancient SNPs linked to reproduction and age at maturation in modern salmon populations, while high ancient mitochondrial effective population size suggests greater prehistorical female lineage diversity. These genetic discontinuities between ancient and modern Iberian salmon, not evident in modern samples alone, highlight the value of ancient genomics in conservation.

The fragmentation of river systems by artificial barriers is contributing to the global decline of migratory fish species. In response, many barriers are now being considered for removal or mitigation to restore connectivity, but the effectiveness of such interventions is unclear due to a lack of monitoring before and after mitigation. We used two complementary monitoring methods based on environmental DNA (eDNA) analysis, detection (determined by number of positive qPCRs) and abundance (based on the analysis of copy numbers), to assess the response of two migratory fish (the European eel, Anguilla anguilla, and the Atlantic salmon Salmo salar) as well as the (predominantly) potadromous brown trout (Salmo trutta) to the partial or full removal of twelve barriers in five Welsh rivers. We observed species-specific responses, and differences based on the assessment method (detection or abundance) and mitigation type (easement or removal). Trout detection and abundance increased following barrier mitigation, while salmon and eel detection declined, with salmon abundance remaining the same. Analysis using the number of copies offered higher resolution than relying on qPCR positives alone, indicating that eDNA monitoring which relies solely on detection may obscure subtle changes in populations following barrier mitigation. Our abundance estimates comparing the removal and easement of small weirs indicate that full barrier removal leads to an increase in trout abundance one year after mitigation when compared to easement, but even small mitigation interventions of in-stream barriers influence both migratory and resident fish populations, which may benefit from increasing habitat availability and connectivity.

The gut microbiome is an important regulator of nutrition and immunity in fish, but it is highly sensitive to common aquaculture stressors (such as temperature shocks and air exposure during handling and transport) and influenced by host genetic factors, including immune function and mucus production. Triploid fish are commonly produced in aquaculture as they are sterile and have potentially higher growth rates. However, compared with their diploid counterparts, triploids have differences in morphology and susceptibility to stress, which could be related to the composition and diversity of the gut microbiome. Here, we exposed diploid and triploid rainbow trout (Oncorhynchus mykiss) to an early life stressor (cold shock) and assessed its effects on the composition and diversity of the gut microbiome five months later, through 16S rRNA sequencing. We found substantial differences in baseline microbiome diversity and composition between diploid and triploid fish, as well as in the microbiota's response to stress. Triploidy was associated with significantly reduced microbial richness and phylogenetic diversity, potential reduction in lactic acid producing bacteria, increased abundance of facultative pathogenic taxa from the family Enterobacteriaceae and elevated mortality. Early life acute stress caused shifts in microbiome communities in later life, promoting an increase in the relative abundance of Enterobacteriaceae and a reduction of potential probiotic taxa, which are more evident in triploids. Our results indicate that early life stress has long term consequences for the gut microbiome composition of rainbow trout, with disproportionately greater effects in triploids compared with diploids.

Environmental DNA (eDNA) combined with quantitative PCR analysis is a fast and accurate alternative to more costly and laborious physical methods to detect the highly invasive zebra mussel (Dreissena polymorpha). We have developed, in collaboration with the managing authorities of an artificial reservoir, a cost-effective eDNA qPCR-High resolution melt (HRM) assay for zebra mussel which we used for a pilot monitoring of spatial-temporal fluctuations in density across the reservoir. Zebra mussel eDNA densities varied significantly across sampling locations and months, being lower in the winter (when zebra mussel growth is slower) and the highest in April (about a month ahead of the reproductive peak). Temperature was a significant predictor of eDNA concentration. We hypothesise that extreme temperatures might have triggered early reproduction, highlighting the need to plan regular monitoring exercises considering environmental variation, particularly in years with extreme variations. Establishing fast, accurate and affordable methods for regular zebra mussel monitoring is particularly relevant in relation to climate change and may allow prediction of reproductive peaks or distribution shifts. The collaboration with the managing authorities is essential for the regular monitoring of aquatic invasive species such as the zebra mussel.

Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their plasticity in co-occurring native and invasive species across urban-rural gradients. Here, we explored gut microbiomes of four sympatric small mammal species along an urban-rural ecotone in Borneo, one of the planet's oldest rainforest regions experiencing recent urban expansion. Host species identity was the strongest determinant of microbiome composition, while land use and spatial proximity shaped microbiome similarity within and among the three rat species. The urban-dwelling rat Rattus rattus had a microbiome composition more similar to that of the native, urban-adapted rat Sundamys muelleri (R. rattus' strongest environmental niche overlap), than to the closely related urban-dwelling R. norvegicus. The urban-dwelling shrew Suncus murinus presented the most distinct microbiome. The microbiome of R. norvegicus was the most sensitive to land use intensity, exhibiting significant alterations in composition and bacterial abundance across the ecotone. Our findings suggest that environmental niche overlap among native and invasive species promotes similar gut microbiomes. Even for omnivorous urban-dwellers with a worldwide distribution like R. norvegicus, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes, influencing the way in which native and invasive species are able to exploit novel environments.

ABSTRACTIncreasing consideration of welfare in aquaculture has prompted interest in non‐invasive methods of monitoring that avoid unnecessary stress and handling. Machine vision (MV) provides a potential solution to these needs, as it can be used for non‐invasive monitoring of animal health and welfare in real‐time. We examined the practical applications of MV for welfare monitoring in aquaculture, the hardware and algorithms used for automated data collection, and the main challenges and solutions for data processing and analysis. The most common application of MV has been the estimation of size‐related metrics (growth, biomass) in fish, but key aspects of welfare, such as monitoring of parasites and disease or detection of stress‐related behaviours, are lagging behind. Numerous camera setups have been used, ranging from single to stereoscopic cameras and from emersed to submerged cameras, but these have often been used under optimal conditions that may not always reflect those prevalent in industry (high densities, low visibility), likely overestimating performance. Object detection algorithms, such as YOLO, have been the approach of choice for most MV applications in aquaculture, but our review has identified an increasing number of alternatives that can help circumvent some of the challenges posed by high densities and poor lighting typical of commercial farms. MV has the potential to transform welfare monitoring in aquaculture, but there are still important challenges that need to be overcome before it can become mainstream, namely the ability to detect ectoparasites and diseases, identify abnormal behaviours, and work across taxa, particularly in crustaceans.

Diet characterisation is important for understanding trophic roles of animals across space and time, including in response to climate change. This has led to the development of a large range of dietary analysis techniques, from centuries-old morphological stomach analysis to recent molecular techniques. Given the difficulties and limitations of direct analysis in marine animals, here we review DNA-based methods of marine vertebrate diet analysis, examining the proliferation of studies over the last two decades. We identify a keystone taxon, sea turtles, where DNA-based approaches have had limited use, but offer great potential for characterising diet across species, life stages and regions. We show that contemporary molecular techniques can overcome some limitations of traditional methods based on morphological identification, such as the ability to identify rapidly digested food items. We report on the development of DNA metabarcoding protocols that enable simultaneous identification of many diet item sequences from heterogeneous samples. DNA metabarcoding can increase taxonomic resolution, improve the identification of certain items (e.g., gelatinous organisms), and increase the comprehensiveness of diet characterisation, particularly in combination with other techniques. However, careful methodological development and finer optimisation of metabarcoding protocols (e.g., appropriate primer selection, blocking of host DNA amplification) are necessary to improve results. Combination approaches to sea turtle dietary analysis and further experimentation with metabarcoding methodology will help to characterise variations and effectively monitor shifts in diet composition in response to environmental changes such as rising sea temperatures and displacement to alternative foraging grounds.

The gut microbiota influences human and animal cognition and behaviour through its effects on the endocrine and immune systems. The microbiome–behaviour relationship may be especially relevant for fish, due to their diverse evolutionary history and potential implications for farming and conservation. Yet, there is limited research on the interaction between gut microbiome and behaviour in non-model fish. We manipulated the rearing environment and diet of fish from two inbred strains of the self-fertilizing mangrove killifish (Kryptolebias marmoratus) and assessed the effects on the gut microbiome and its interactions with anxiety-like behaviours. We found that microbiota composition and alpha diversity were significantly influenced by host genetics (strain), hatching mode (naturally or artificial dechorionation) and diet, but not by environmental enrichment. Fish activity level and inspections of a novel object were strongly associated with microbiota community composition and alpha diversity. The microbial taxa associated with differences in behaviour were dominated by Bacteroidales, potentially related to the production of metabolites affecting neural development. We suggest that the association between microbiome and fish behaviour could be an indirect effect of the modulation of the gut microbiota by host genetics and early rearing conditions, which could be affecting the production of microbial metabolites that interact with the fish physiology.

Background The gut microbiota influences human and animal cognition and behaviour through its effects on the endocrine and immune systems, but the relationship between host genetics, environmental factors and the microbiota, and their joint effect on the host cognitive behaviour has not been determined. The microbiome-behaviour relationship may be especially relevant for fish, due to their diverse evolutionary history and potential applications for farming and conservation. Yet, there is limited research of the interaction between gut microbiome and behaviour in fish, apart from using zebrafish as a model for human applications. We manipulated the rearing environment and diet of fish from two highly inbred strains of the self-fertilising mangrove killifish (Kryptolebias marmoratus) and assessed their effects on the gut microbiome (based on 16S rRNA sequencing) and the potential interactions with behaviour (based on a novel object test). Results We found that the microbiome composition and alpha diversity were significantly influenced by strain, hatching mode and diet, but not by environmental enrichment. We also identified a strong association between fish gut microbiota (community composition and alpha diversity measured as Chao1 and Faith phylogenetic diversity) and behaviour (activity level and inspections of a novel object), but no significant influence of strain, diet, environment or hatching mode on behaviour. The particular taxa influenced by host genetics and environmental factors were not the same as those associated with the behaviour, but in both cases were dominated by Bacteroidales, potentially related to the production of SCFAs and neurodevelopment. Conclusion We suggest thatthe observed association between microbiome and fish behaviour could be an indirect effect of the modulation of the ecological conditions of the gut microbiota by the host genetics and rearing conditions (hatching and diet), which could be affecting the production of microbial metabolites that interact with the fish physiology.

AbstractMicroalgae offer a sustainable source of omega − 3 fatty acids that can replace fish oil in aquafeeds, but the nutritional benefits are not always clear, particularly when microalgae are used as complete oil replacements in starter feeds. We compared the survival, growth, omega − 3 deposition and composition of the gut microbiota of juvenile mixed‐sex Nile tilapia (Oreochromis niloticus) that had been fed over a 3‐month period on six isonitrogenous, isolipidic and isocaloric aquafeeds that varied only on the contribution of fish oil, soya oil and microalgae (Schizochytrium) oil as lipid sources. Survival was not affected by diet, but fish fed a diet where the entire oil component (5%) was replaced by microalgae oil grew twice as fast as fish fed plant oil or a mixture of plant and fish oil. Dietary omega − 3 content was strongly correlated with omega − 3 deposition in the fish fillet. Complete replacement of fish oil by plant oil caused a significant decrease in the abundance of Peptostreptococcaceae and an increase in the abundance of Aeromonadaceae which is often associated with an inflammatory response in the fish gut. In contrast, when fish and soya oil in the reference diet were replaced by 100% microalgae oil, an increase in Mycobacteriaceae was observed. Our study indicates that Schizochytrium oil can be used to improve the growth of Nile tilapia and increase its omega − 3 content without any of the detrimental effects on the gut microbiome typically associated with some plant oil replacements.

Inland navigation is one of the most sustainable transport alternatives to help decarbonise the world economy. However, the likely impacts of intensifying inland navigation on freshwater ecosystems are difficult to predict. A global map of knowledge that considers both abiotic and biotic responses to increasing shipping traffic and developing infrastructures is lacking. Deriving general evidence-based assessments is challenging, because most studies on inland navigation impacts are merely descriptive and either consist of local case studies, or address single navigation stressors or specific taxa only. We conducted a systematic mapping of the published literature (1908-2021) to provide a global synthesis of the effects of inland navigation on the biotic and abiotic components of freshwater ecosystems. We show that only half of the reported navigation-related impacts were statistically tested. Navigation itself (vessel operation) had mainly negative effects on native taxa (57%), followed by waterway management (40%), and navigation infrastructures (35%). Navigation has direct negative impacts caused by physical disturbances such as vessel-induced waves, and indirect impacts that facilitate the spread of aquatic invasive species, and altering the abiotic habitat conditions. Thirty percent of the tested relationships showed non-significant impacts on the biotic environment, while in 10% of cases impacts were context-dependent. We identified the main gaps of knowledge, namely (i) impacts of waterway management on communities, (ii) underlying processes of navigation impacts on river ecosystems; and (iii) interactions between multiple navigation factors and cascading effects on multi-taxa responses. These future research directions should improve the diagnosis, mitigate the negative impacts of navigation on rivers and provide guidelines for improving navigated river management.

Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity. Species with low genetic diversity have limited capacity to adapt to environmental change. This study finds that the skin microbiome and non-genetic (epigenetic) modifications of the DNA represent additional sources of variation that could help low diversity fish survive environmental challenges.

In marine species with large populations and high dispersal potential, large-scale genetic differences and clinal trends in allele frequency can provide insight into the evolutionary processes that shape diversity. Lumpfish, Cyclopterus lumpus, is found throughout the North Atlantic and has traditionally been harvested for roe and more recently used as a cleaner fish in salmon aquaculture. We used a 70 K SNP array to evaluate trans-Atlantic differentiation, genetic structuring, and clinal variation across the North Atlantic. Basin-scale structuring between the Northeast and Northwest Atlantic was significant, with enrichment for loci associated with developmental/mitochondrial function. We identified a putative structural variant on chromosome 2, likely contributing to differentiation between Northeast and Northwest Atlantic Lumpfish, and consistent with post-glacial trans-Atlantic secondary contact. Redundancy analysis identified climate associations both in the Northeast (N = 1269 loci) and Northwest (N = 1637 loci), with 103 shared loci between them. Clinal patterns in allele frequencies were observed in some loci (15%-Northwest and 5%-Northeast) of which 708 loci were shared and involved with growth, developmental processes, and locomotion. The combined evidence of trans-Atlantic differentiation, environmental associations, and clinal loci, suggests that both regional and large-scale potentially-adaptive population structuring is present across the North Atlantic.

The killifish genus Kryptolebias currently contains seven recognized species found in freshwater and mangrove microhabitats in South and Central America, the Caribbean, and Florida. Kryptolebias species have several unique features. Beyond its amphibious nature, two of the Kryptolebias species (K. marmoratus and K. hermaphroditus sensu Costa 2011) are the only known vertebrates capable of self-fertilization. Although reference genomes for self-fertilizing species are readily available, a complete understanding of the genomic basis leading to the transition in mating systems in the genus requires more genomic resources at a broader taxonomic level. Here, we present the complete genome sequences for three Kryptolebias species from Brazil: the endangered freshwater species Kryptolebias brasiliensis and Kryptolebias gracilis and the androdiecious but obligate outcrossing Kryptolebias ocellatus (sensu Costa 2011). The raw data and assembled genomes are available in GenBank.

Use of microalgae in fish nutrition can relieve pressure on wild fish stocks, but there is no systematic quantitative evaluation of microalgae benefits. We conducted a metanalysis on the nutritional benefits of Spirulina and Schizochytrium as replacements of fishmeal and fish or plant oil, respectively. We reviewed 50 peer-reviewed studies involving 26 finfish species and 144 control vs microalgae replacement comparisons. Inclusion of Spirulina in the fish diet significantly improved growth compared to controls (SMD = 1.21; 95% CI 0.71–1.70), while inclusion of Schizochytrium maintained the content of omega-3 PUFA of the fish fillet compared to fish fed on fish or plant oils (SMD = 0.62; 95% CI − 0.51–1.76). Benefits were apparent at replacement levels as low as 0.025% in the case of Spirulina and 10% in the case of Schizochytrium oil. Dose-dependent effects were found for Spirulina replacement on growth, but not for Schizochytrium on omega-3 fillet content. Subgroup analysis and meta-regression revealed that ~ 24–27% of variation in effect sizes can be accounted by variation between fish families, the rest likely reflecting variation in experimental conditions. Overall, the evidence indicates that Spirulina and Schizochytrium replacement in aquafeeds can be used to improve fish growth and maintain fillet quality, respectively, but considerable uncertainty exists on the predicted responses. To reduce uncertainty and facilitate the transition towards more sustainable aquafeeds, we recommend that feeding trials using microalgae are conducted under commercially relevant conditions and that greater care is taken to report full results to account for sources of heterogeneity.