Over 200,000 kilometers of free-flowing river habitat in Europe is altered due to impoundments

European rivers are disconnected by more than one million man-made barriers that physically limit aquatic species migration and contribute to modification of freshwater habitats. Here, a Conceptual Habitat Alteration Model for Ponding is developed to aid in evaluating the effects of impoundments on fish habitats. Fish communities present in rivers with low human impact and their broad environmental settings enable classification of European rivers into 15 macrohabitat types. These classifications, together with the estimated fish sensitivity to alteration of their habitat are used for assessing the impacts of six main barrier types (dams, weirs, sluices, culverts, fords, and ramps). Our results indicate that over 200,000 km or 10% of previously free-flowing river habitat has been altered due to impoundments. Although they appear less frequently, dams, weirs and sluices cause much more habitat alteration than the other types. Their impact is regionally diverse, which is a function of barrier height, type and density, as well as biogeographical location. This work allows us to foresee what potential environmental gain or loss can be expected with planned barrier management actions in rivers, and to prioritize management actions

Using eDNA Metabarcoding to Monitor Changes in Fish Community Composition After Barrier Removal

Artificial instream barriers are a major cause of habitat fragmentation that reduce population connectivity and gene flow by limiting fish movements. To mitigate their impacts, obsolete barriers are increasingly been removed worldwide, but few barrier removal projects are monitored. We employed a powerful Before-After-Downstream-Upstream (BADU) approach using environmental DNA (eDNA) metabarcoding to examine the effects on fish community composition of removing a weir in the river Lugg (England) that had been suggested to have a detrimental effect on salmonid migration. We found no change in fish community diversity or relative abundance after the removal above or below the weir, but detected an important effect of sampling season, likely related to the species' life cycles. eDNA detected nine fish species that were also identified by electrofishing sampling and one additional species (Anguilla anguilla) that was missed by traditional surveys. Our results suggest that monitoring of barrier removal projects should be carried out to ensure that any ecological benefits are properly documented and that eDNA metabarcoding is a sensitive technique to monitor the effects of barrier removal

Benefits of the microalgae Spirulina and Schizochytrium in fish nutrition: a meta-analysis

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

Understanding and Reducing Conflict over the Recreational Use of Rivers

The societal benefits of having greater access to rivers are numerous, but conflict sometimes ensues between recreational users. Using Wales as a case example, we conducted a survey to better understand the underlying beliefs and emotions of different river users in relation to river access. Sixty per cent of respondents felt there was conflict over river access, but perceptions differed with age and river usage. Most boaters wanted greater access to rivers, in stark contrast to anglers. Greater dialogue was highlighted as a necessary step to reduce conflict, but support for specific management actions such as usage tariffs, spatial or temporal zoning, or limiting the number of users were much less popular. River users differed in cooperativeness and assertiveness but consistently flagged water pollution as the most important factor detracting from their enjoyment of rivers. Sentiment analysis indicated that “trust” was the dominant emotion shared by all river users

Data on optimisation of a multiplex HRM-qPCR assay for native and invasive crayfish as well as the crayfish plague in four river catchments

The data presented here corresponds to the research paper “Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague using environmental DNA”. A crayfish-specific assay was designed and optimised using three real-time PCR supermixes (SYBR™ Green, SsoFast™ EvaGreen® and HOT FIREPol® EvaGreen®). Diagnostic high resolution melt (HRM) data from direct application of assay on both ex-situ eDNA water samples and field samples from four catchments (two in Wales, two in England) is presented in this article, displaying positive HRM profiles for invasive signal crayfish (Pacifastacus leniusculus), native white-clawed crayfish (Austropotamobius pallipes) and crayfish plague causal agent (Aphanomyces astaci). Keywords: Pacifastacus leniusculus, Austropotamobius pallipes, Crayfish plague, HRM-qPCR, eDN

Immune-Related Transcriptional Responses to Parasitic Infection in a Naturally Inbred Fish: Roles of Genotype and Individual Variation

Parasites are strong drivers of evolutionary change and the genetic variation of both host and parasite populations can co-evolve as a function of parasite virulence and host resistance. The role of transcriptome variation in specific interactions between host and parasite genotypes has been less studied and can be confounded by differences in genetic variation. We employed two naturally inbred lines of a self-fertilizing fish to estimate the role of host genotype in the transcriptome response to parasite infection using RNA-seq. In addition, we targeted several differentially expressed immune-related genes to further investigate the relative role of individual variation in the immune response using RT-qPCR, taking advantage of the genomic uniformity of the self-fertilizing lines. We found significant differences in gene expression between lines in response to infection both in the transcriptome and in individual gene RT-qPCR analyses. Individual RT-qPCR analyses of gene expression identified significant variance differences between lines for six genes but only for three genes between infected and control fish. Our results indicate that although the genetic background plays an important role in the transcriptome response to parasites, it cannot fully explain individual differences within genetically homogeneous lines, which can be important for determining the response to parasites

Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague pathogen using environmental DNA

Aquatic Invasive Species (AIS) are important vectors for the introduction of novel pathogens which can, in turn, become drivers of rapid ecological and evolutionary change, compromising the persistence of native species. Conservation strategies rely on accurate information regarding presence and distribution of AIS and their associated pathogens to prevent or mitigate negative impacts, such as predation, displacement or competition with native species for food, space or breeding sites. Environmental DNA is increasingly used as a conservation tool for early detection and monitoring of AIS. We used a novel eDNA high-resolution melt curve (HRM) approach to simultaneously detect the UK endangered native crayfish (Austropotamobius pallipes), the highly invasive signal crayfish (Pacifastacus leniusculus) and their dominant pathogen, Aphanomyces astaci, (causative agent of crayfish plague). We validated the approach with laboratory and field samples in areas with known presence or absence of both crayfish species as well as the pathogen, prior to the monitoring of areas where their presence was unknown. We identified the presence of infected signal crayfish further upstream than previously detected in an area where previous intensive eradication attempts had taken place, and the coexistence of both species in plague free catchments. We also detected the endangered native crayfish in an area where trapping had failed. With this method, we could estimate the distribution of native and invasive crayfish and their infection status in a rapid, cost effective and highly sensitive way, providing essential information for the development of conservation strategies in catchments with populations of endangered native crayfish

Improving Species Distribution Modelling of freshwater invasive species for management applications

Freshwater ecosystems rank among the most endangered ecosystems in the world and are under increasing threat from aquatic invasive species (AIS). Understanding the range expansion of AIS is key for mitigating their impacts. Most approaches rely on Species Distribution Models (SDMs) to predict the expansion of AIS, using mainly environmental variables, yet ignore the role of human activities in favouring the introduction and range expansion of AIS. In this study, we use five SDM algorithms (independently and in ensemble) and two accuracy measures (TSS, AUC), combined with a null modelling approach, to assess the predictive performance of the models and to quantify which predictors (environmental and anthropogenic from the native and introduced regions) best explain the distribution of nine freshwater invasive species (including fish, arthropods, molluscs, amphibians and reptiles) in a large island (Great Britain), and which species characteristics affect model performance. Our results show that the distribution of invasive species is difficult to predict by SDMs, even in cases when TSS and AUC model accuracy values are high. Our study strongly advocates the use of null models for testing SDMs performance and the inclusion of information from the native area and a variety of both human-related and environmental predictors for a more accurate modelling of the range expansion of AIS. Otherwise, models that only include climatic variables, or rely only on standard accuracy measures or a single algorithm, might result in mismanagement of AIS

Colour plasticity in response to social context and parasitic infection in a self-fertilizing fish

Many animal species rely on changes in body coloration to signal social dominance, mating readiness and health status to conspecifics, which can in turn influence reproductive success, social dynamics and pathogen avoidance in natural populations. Such colour changes are thought to be controlled by genetic and environmental conditions, but their relative importance is difficult to measure in natural populations, where individual genetic variability complicates data interpretation. Here, we studied shifts in melanin-related body coloration in response to social context and parasitic infection in two naturally inbred lines of a self-fertilizing fish to disentangle the relative roles of genetic background and individual variation. We found that social context and parasitic infection had a significant effect on body coloration that varied between genetic lines, suggesting the existence of genotype by environment interactions. In addition, individual variation was also important for some of the colour attributes. We suggest that the genetic background drives colour plasticity and that this can maintain phenotypic variation in inbred lines, an adaptive mechanism that may be particularly important when genetic diversity is low