Processes of collating a European fisheries database to meet the objectives of the European Union Water Framework Directive

Abstract  FIsh Database of European Streams, a common database for the FAME project, was merged using existing data on electric fishing and environmental data. FIsh Database of European Stream is a relational database with eight tables. Metrics based on classification of fish species into guilds were calculated, and provided in separate tables. FIsh Database of European Stream contained information about 150 freshwater fish species, from 12 countries, 17 ecoregions, 40 main river regions, 2651 rivers and 8228 sites. Examples of data coverage and use are given. Relationships between environmental variables were illustrated using principal component analysis, which resulted in three environmental components – latitude, size and altitude. Environmental component scores were correlated with fish metrics used in the European Fish Index. Results exemplify how fish guilds reflect gradients in environmental variation. Benefits and problems concerning standardisation and data availability at the global level are discussed.     

Giants' shoulders 15 years later: lessons,challenges and guidelines in fisheries meta‐analysis

Meta‐analysis has been an integral tool for fisheries researchers since the late 1990s. However, there remain few guidelines for the design, implementation or interpretation of meta‐analyses in the field of fisheries. Here, we provide the necessary background for readers, authors and reviewers, including a brief history of the use of meta‐analysis in fisheries, an overview of common model types and distinctions, and examples of different goals that can be achieved using meta‐analysis. We outline the primary challenges in implementing meta‐analyses, including difficulties in discriminating between alternative hypotheses that can explain the data with equal plausibility, the importance of validating results using multiple lines of evidence, the trade‐off between complexity and sample size and problems associated with the use of model output. For each of these challenges, we also provide suggestions, such as the use of propensity scores for dealing with selection bias and the use of covariates to control for confounding effects. These challenges are then illustrated with examples from diverse subfields of fisheries, including (i) the analysis of the stock–recruit relationship, (ii) fisheries management, rebuilding and population viability, (iii) habitat‐specific vital rates, (iv) life‐history theory and (v) the evaluation of marine reserves. We conclude with our reasons for believing that meta‐analysis will continue to grow in importance for these and many other research goals in fisheries science and argue that standards of practice are therefore essential.     

Development and application of molecular methods (PCR) for detection of Tasmanian Atlantic salmon reovirus

Molecular (PCR) diagnostic tests for the detection and identification of aquareovirus in general, and Tasmanian Atlantic salmon reovirus (TSRV) specifically, were developed, and their diagnostic sensitivity and specificity were determined and compared with virus isolation in cell culture. Intralaboratory and interlaboratory comparison of PCR (conventional hemi‐nested RT‐PCR & RT‐qPCR) and virus isolation in cell culture using finfish cell lines, CHSE‐214 and EPC, was carried out for the detection and identification of TSRV using field samples of farmed Atlantic salmon Salmo salar, L. from various aquaculture sites around Tasmania. The interlaboratory comparison of diagnostic methods was carried out between two laboratories, AAHL‐CSIRO and DPIPWE‐Tasmania. A total of 144 fish from nine sites (12–33 fish per site) were sampled from two regions of Tasmania (Tamar River estuary in the north and Huon River estuary in the south‐east) during late spring to early summer of 2009, and the data were analysed using different statistical approaches. The prevalence of TSRV ranged from 6% to 22% in both regions. All the diagnostic methods (data from both laboratories) had high specificity, while the estimated sensitivity varied between tests with RT‐qPCR being the most sensitive (95.2%) method followed by virus isolation and then conventional hemi‐nested RT‐PCR.     

Tissue composition,blood biochemistry and histology of digestive organs in Senegalese sole (Solea senegalensis) juveniles fed diets containing different plant protein ingredients

The aim of this study was to determine the impact of diets with different plant protein ingredients on proximate composition, tissue metabolites and tissue fatty acid composition, as well as hepatic and intestinal histological modifications in Senegalese sole (Solea senegalensis). Fish (21.5 ± 2.8 g body weight) were fed six isonitrogenous and isoenergetic diets during 11 weeks. A control diet containing fish meal as the main protein source was compared with five experimental diets replacing 30% fish meal protein by different plant protein sources: soybean meal (SBM), soybean protein concentrate (SPC), soybean protein isolate (SPI), wheat gluten meal (WGM) or pea protein concentrate (PPC). The inclusion of different plant protein did not significantly affect growth and proximate composition of fish. The hepatosomatic index was not significantly different to the control group; however, utilization of WGM significantly increased hepatocyte size. Plasma protein values and muscle triglycerides were influenced by the inclusion of SBM and WGM in the diets respectively. Feeding fish on SBM, WGM and PPC diets significantly enhanced n‐6 fatty acid levels in muscle, particularly linoleic acid. None of the plant protein ingredient used in the diets decreased arachidonic, eicosapentaenoic as well as docosahexaenoic acid values in liver and muscle. Overall, histological studies did not reveal the existence of any intestinal alterations induced by the inclusion of different plant proteins. Despite moderate changes produced by SBM, SPC and WGM, inclusion of dietary plant protein ingredients has no major impact on growth, tissue and blood biochemistry, fatty acid profile and gut integrity of Senegalese sole juveniles.     

Non‐invasive fast real‐time PCR assay for detection of the enteric parasite Enteromyxum scophthalmi in cultured turbot (Scophthalmus maximus L.)

Enteromyxum scophthalmi is a myxozoan parasite that causes severe parasitic diseases in cultured turbot affecting mainly the intestine of the host. It is characterized by producing acute enteritis, starvation and eventually death. Current diagnosis of E. scopthalmi use traditional techniques, based on the identification of the morphology of the parasite. These techniques take extended time to be carried out and do not favour the adoption of control measure at turbot farms and require the sacrifice of fish. This study develops a fast real‐time PCR molecular tool for the detection of E. scophthalmi in infected farmed turbot. This methodology is applicable for routine controls on the farm at every stage of the parasite infection. Results of the study demonstrate the robustness, specificity, efficiency and reliability of the technique. In addition, this study also provides a non‐invasive procedure of sampling through swaps. This allows control, prevention and diagnosis of the parasite infection at turbot farms while maintaining the welfare of the cultivated fish and avoiding sacrifice of the fish sampled.     

Spat availability of commercial bivalve species recruited on artificial collectors from the northern Gulf of California. Seasonal changes in species composition

This study reports a year‐round recruitment of spat of four commercial bivalve species; Pteria sterna, Euvola vogdesi, Pinctada mazatlanica and Pinna rugosa collected in the region of Puerto Peñasco, north‐eastern coast of the Gulf of California. Bimonthly recruitment of commercial bivalve spat on netlon^® collectors was evaluated for six sites from June 2007 to August 2008. To describe spat recruitment abundances with environmental parameters, sea surface temperature (°C) and surface chlorophyll a concentration (mg m^?3) were characterized by means of monthly Aqua/MODIS satellite data. For each species a repeated measures anova was used to evaluate differences in the number of spat between months, sites and depths. Maximum sea surface temperature was recorded in August–September (~31.5°C) and the minimum in January–February (~15°C), while the minimum surface chlorophyll a was observed in June–September (mean range = 1.5–2 mg m^?3) and the maximum in January–March (mean range = 2–5 mg m^?3). Spat recruitment showed distinct patterns; P. sterna can be characterized as having a Winter–Spring pattern, E. vogdesi a winter pattern, while P. mazatlanica and P. rugosa a summer spat recruitment pattern. This information constitutes part of the fundamental data needed for the development of aquaculture and conservation initiatives in the region based on wild spat supply.     

Minerals content of extruded fish feeds containing cricket ( Acheta domesticus ) and black soldier fly larvae ( Hermetia illucens ) fractions

Animal food sources provide human beings with minerals considerably in adequate quantities. Fish is an indispensable reliable source of nutrients, as aquaculture is a sector that is fast growing and which provides 50% of the world’s fish production. However, fish production is hampered by the increasing costs of feeds due to the ever rising cost of fish meal, an integral component of fish feeds. Substituting fish meal with cheap, yet highly nutritious ingredients in fish feeds is therefore paramount. This study investigated the effects of substituting fish meal with adult cricket meal (ACM) and black soldier fly meal (BSFM) on minerals content of extruded fish feeds, where four levels of substitution (0, 25, 50 and 75%) were used. The effect of feed moisture content on minerals was also studied where 20 and 30% feed moisture levels were used. Leaching effects of the pellets were studied as well. The results showed a significant increase (P < 0.05) in the levels of phosphorus and potassium as the level of fish meal substitution increased from 0 to 75%. On the other hand, iron and sodium levels reduced significantly (P < 0.05) as the level of fish meal substitution increased. Magnesium content increased with increasing level of substitution with BSFM, but decreased with increasing level of substitution with ACM. Copper, zinc and manganese were not greatly influenced by levels of fish meal substitution. Diets that had zero substitution showed higher leaching effect for most minerals than diets that were substituted with 75% ACM or BSFM. This study found that both ACM and BSFM can be used to substitute fish meal in fish feeds and obtain adequate mineral profile and low leaching effect.     

Assessment of plastic ingestion by pole-caught pelagic predatory fish from O'ahu,Hawai'i

1. Although the frequency of occurrence of plastic ingestion in the large-sized dolphinfish and tunas taken by the Hawai'i longline fishery is very low (frequency of occurrence < 5% of sampled individuals), the ingestion of plastic in smaller-sized specimens caught with pole-and-line gear by commercial and recreational fishers has not been investigated.
2. This study examined ingestion of >0.25 mm marine plastic debris (MPD) by four predatory fish species caught by commercial fishers around the Main Hawaiian Islands, and documented ingestion in three species: 85.7% of albacore tuna (n = 7), 40.0% of skipjack tuna (n = 10) and 12.5% of dolphinfish (n = 8).
3. Yellowfin tuna (n = 10) did not contain any MPD, probably owing to the high proportion of empty stomachs (60%).
4. For skipjack tuna, the frequency of occurrence of MPD ingestion was significantly higher for the smaller-sized specimens caught with pole-and-line (40%), compared with the larger-sized specimens caught with longlines (0%).
5. For dolphinfish, the frequency of occurrence of MPD ingestion was similar for the similar-sized specimens caught with pole-and-line and with longlines.
6. The ingested MPD items were micro–meso plastics, between 1 and 25 mm. While most ingested items were fragments, albacore also ingested line and skipjack also ingested sheets.
7. The predatory fishes ingested light MPD items that float in sea water, but there were species-specific differences in their polymer composition: albacore contained more polypropylene and polyethylene, and skipjack contained more elastomers, characterized by a high percentage of ester plasticizers.
8. Altogether, these results suggest that albacore and skipjack tunas ingest plastic of different types and polymers. Yet more research is needed to understand how differences in vertical distribution, foraging ecology and diet influence the MPD sampled by these predatory fish species.

     

Science and conservation of Amazonian crocodilians: a historical review

1. Crocodilians represent one of the oldest extant vertebrate lineages. They have co-existed with humans throughout the Amazon basin for thousands of years, often having a strong cultural and economic influence on people's lives. Shifts in the socio-economic and political reality of the Amazon basin during the last century have led crocodilian populations to face large variations in their numbers according to different levels of exploitation and strategies for their conservation.
2. This article reviews the scientific knowledge obtained between 1945 and 2019 on the biology, conservation and management for the four Amazonian crocodilian (caiman) species (Caiman crocodilus, Melanosuchus niger, Paleosuchus palpebrosus and Paleosuchus trigonatus). It provides a general overview on past and current population status and research efforts involving caimans in the Amazon basin and discusses perspectives for the future.
3. The most significant studies on the ecology, genetics and management strategies are examined in more detail and this information is contextualized to provide an overview of the most relevant findings that might explain caiman population trends over the last 75 years.
4. Systems for sustainable management in the Amazon basin have been discussed for the past 20 years, but remain rarely applicable. It is necessary to develop new ways to maintain healthy caiman populations through innovative management programmes. Sustainable harvesting of wildlife has been shown to promote conservation targets, especially those initiatives based on community co-management. In this article, we propose some general guidelines for future management schemes, in the expectation that the information provided by the scientific community will be considered fully without political agendas determining the priorities.

     

In vitro markers for virulence in Yersinia ruckeri

In this study, different traits that have been associated with bacterial virulence were studied in Yersinia ruckeri. Two isolates that had been shown to cause disease and mortality in experimentally infected rainbow trout were compared with five avirulent isolates. Both virulent isolates showed high adhesion to gill and intestinal mucus of rainbow trout, whereas the majority of non‐virulent strains demonstrated significantly lower adhesion. A decrease in adherence capability following bacterial treatment with sodium metaperiodate and proteolytic enzymes suggested the involvement of carbohydrates and proteins. All strains were able to adhere to and invade chinook salmon embryo cell line (CHSE‐214), fathead minnow epithelial cell line (FHM) and rainbow trout liver cell line (R1). One non‐virulent strain was highly adhesive and invasive in the three cell lines, whereas the virulent strains showed moderate adhesive and invasive capacity. The internalization of several isolates was inhibited by colchicine and cytochalasin‐D, suggesting that microtubules and microfilaments play a role. For all strains, intracellular survival assays showed a decrease of viable bacteria in the cells 6 h after inoculation, suggesting that Y. ruckeri is not able to multiply or survive inside cultured cells. Analysis of the susceptibility to the bactericidal effect of rainbow trout serum demonstrated that virulent Y. ruckeri strains were serum resistant, whereas non‐virulent strains were generally serum sensitive.