Rearing background and exposure environment together explain higher survival of aquaculture fish during a bacterial outbreak

Heterogeneity of the rearing environment enhances diversity of microbial communities in intensive farming

Heterogeneity of the rearing environment in farmed animals can improve welfare and stocking success by enhancing natural behaviours, reducing stress, and decreasing pathogen occurrence. Although microbial diversity is often associated with well-being, their direct and indirect effects on health of farmed animals remain underexplored. We examined the impact of structural heterogeneity of aquaculture tanks on microbial communities in tank biofilm and fish gut microbiome. Enrichment (stones and shelters) significantly promoted microbial diversity and community homogeneity in tank biofilm. However, diversity of gut microbiome did not depend on rearing treatment or microbial composition of the environment. Fish in enriched tanks exhibited greater compositional variation in gut microbiome than those in standard tanks. Tanks without enrichments had higher occurrence of potentially pathogenic bacterial families (Corynebacteriaceae and Staphylococcaceae), while enriched tanks had more beneficial gut microbes (Lactobacillus). Microbial diversity in tank biofilm was negatively associated with fish mortality during a natural epidemic of Flavobacterium columnare, suggesting a protective effect of diverse microbial communities. These findings support environmental enrichment in mitigating disease outbreaks through enhanced microbial diversity, providing important implications for disease control and sustainable health management in aquaculture.

Feeding predictability as a cognitive enrichment protects brain function and physiological status in rainbow trout: a multidisciplinary approach to assess fish welfare

Cognitive enrichment is a promising but understudied type of environmental enrichment that aims to stimulate the cognitive abilities of animals by providing them with more opportunities to interact with (namely, to predict events than can occur) and to control their environment. In a previous study, we highlighted that farmed rainbow trout can predict daily feedings after two weeks of conditioning, the highest conditioned response being elicited by the combination of both temporal and signalled predictability. In the present study, we tested the feeding predictability that elicited the highest conditioned response in rainbow trout (both temporal and signalled by bubbles, BUBBLE + TIME treatment) as a cognitive enrichment strategy to improve their welfare. We thus analysed the long-term effects of this feeding predictability condition as compared with an unpredictable feeding condition (RANDOM treatment) on the welfare of rainbow trout, including the markers in the modulation of brain function, through a multidisciplinary approach. To reveal the brain regulatory pathways and networks involved in the long-term effects of feeding predictability, we measured gene markers of cerebral activity and plasticity, neurotransmitter pathways and physiological status of fish (oxidative stress, inflammatory status, cell type and stress status). After almost three months under these predictability conditions of feeding, we found clear evidence of improved welfare in fish from BUBBLE + TIME treatment. Feeding predictability allowed for a food anticipatory activity and resulted in fewer aggressive behaviours, burst of accelerations, and jumps before mealtime. BUBBLE + TIME fish were also less active between meals, which is in line with the observed decreased expression of transcripts related to the dopaminergic system. BUBBLE + TIME fish tented to present fewer eroded dorsal fin and infections to the pathogen Flavobacterium psychrophilum. Decreased expression of most of the studied mRNA involved in oxidative stress and immune responses confirm these tendencies else suggesting a strong role of feeding predictability on fish health status and that RANDOM fish may have undergone chronic stress. Fish emotional reactivity while isolated in a novel-tank as measured by fear behaviour and plasma cortisol levels were similar between the two treatments, as well as fish weight and size. To conclude, signalled combined with temporal predictability of feeding appears to be a promising approach of cognitive enrichment to protect brain function via the physiological status of farmed rainbow trout in the long term.

Research Before Policy: Identifying Gaps in Salmonid Welfare Research That Require Further Study to Inform Evidence-Based Aquaculture Guidelines in Canada

Aquaculture is a growing industry worldwide and Canadian finfish culture is dominated by marine salmonid farming. In part due to increasing public and stakeholder concerns around fish welfare protection, the first-ever Canadian Code of Practice for the Care and Handling of Farmed Salmonids was recently completed, following the National Farm Animal Care Council's (NFACC) rigorous Code development process. During this process, both the Scientific (responsible for reviewing existing literature and producing a peer-reviewed report that informs the Code) and Code Development (a diverse group of stakeholders including aquaculture producers, fish transporters, aquaculture veterinarians, animal welfare advocates, food retailers, government, and researchers) Committees identified research gaps in tandem, as they worked through the literature on salmonid physiology, health, husbandry, and welfare. When those lists are combined with the results of a public "top-of-mind" survey conducted by NFACC, they reveal several overlapping areas of scientific, stakeholder, and public concern where scientific evidence is currently lacking: (1) biodensity; (2) health monitoring and management, with a focus on sea lice infection prevention and management; (3) feed quality and management, particularly whether feed restriction or deprivation has consequences for welfare; (4) enclosure design, especially focused on environmental enrichment provision and lighting design; and (5) slaughter and euthanasia. For each of these five research areas, we provide a brief overview of current research on the topic and outline the specific research gaps present. The final section of this review identifies future research avenues that will help address these research gaps, including using existing paradigms developed by terrestrial animal welfare researchers, developing novel methods for assessing fish welfare, and the validation of new salmonid welfare indices. We conclude that there is no dearth of relevant research to be done in the realm of farmed salmonid welfare that can support crucial evidence-based fish welfare policy development.

The effects of environmental enrichment on hatchery-performance, smolt migration and capture rates in landlocked Atlantic salmon

Enrichment of rearing environment with natural elements has been suggested to improve the welfare and post-release survival of cultured fish. We studied the combined effects of shelter structures, periodical water flow and water level changes on pre- and post-release performance of critically endangered landlocked Atlantic salmon (Salmo salar m. sebago). Relative to standard (plain) rearing tanks, provision of enrichment improved fish condition factor and survival during the first year of rearing when most mortality was attributable to parasitic and bacterial infections. The consequent higher density in enriched tanks probably induced greater growth variation and more dorsal fin damages than found in fish of standard tanks. Possibly this was partly due to the applied changes in water level. Experimentally determined smolt migration tendency at age 3 did not differ, on average, between the rearing groups, but enriched-reared fish showed clearly less variation in total movement activity than standard-reared fish. Experimental angling in earthen ponds did not suggest divergent vulnerability between the differentially reared fish at age 3, but decreased condition during the preceding growth season increased vulnerability to fishing. Based on long-term post-stocking tag returns in large-lake fisheries, fish length at release but not rearing method affected the capture rates of fish released at age 2. When released at age 3 the fish grown in enriched environment had a higher risk to be captured with stationary gears and earlier by hook and line gears compared to standard-reared conspecifics. Earlier time of maximal smolt migration activity was associated with an increased risk of being captured. We suggest that environmental enrichment may modulate growth- and behavior-related qualities that indirectly increased the vulnerability to fishing in natural conditions but not in experimental setting. The favorable effects of enrichment on early survival encourages adopting enriched rearing practices in supportive breeding of landlocked salmon.

Physical enrichment research for captive fish: Time to focus on the DETAILS

Growing research effort has shown that physical enrichment (PE) can improve fish welfare and research validity. However, the inclusion of PE does not always result in positive effects and conflicting findings have highlighted the many nuances involved. Effects are known to depend on species and life stage tested, but effects may also vary with differences in the specific items used as enrichment between and within studies. Reporting fine-scale characteristics of items used as enrichment in studies may help to reveal these factors. We conducted a survey of PE-focused studies published in the last 5 years to examine the current state of methodological reporting. The survey results suggest that some aspects of enrichment are not adequately detailed. For example, the amount and dimensions of objects used as enrichment were frequently omitted. Similarly, the ecological relevance, or other justification, for enrichment items was frequently not made explicit. Focusing on ecologically relevant aspects of PE and increasing the level of detail reported in studies may benefit future work and we propose a framework with the acronym DETAILS (Dimensions, Ecological rationale, Timing of enrichment, Amount, Inputs, Lighting and Social environment). We outline the potential importance of each of the elements of this framework with the hope it may aid in the level of reporting and standardization across studies, ultimately aiding the search for more beneficial types of PE and the development of our understanding and ability to improve the welfare of captive fish and promote more biologically relevant behaviour.

Systematic review of the status of veterinary epidemiological research in two species regarding the FAIR guiding principles

Background

The FAIR (Findable, Accessible, Interoperable, Reusable) principles were proposed in 2016 to set a path towards reusability of research datasets. In this systematic review, we assessed the FAIRness of datasets associated with peer-reviewed articles in veterinary epidemiology research published since 2017, specifically looking at salmonids and dairy cattle. We considered the differences in practices between molecular epidemiology, the branch of epidemiology using genetic sequences of pathogens and hosts to describe disease patterns, and non-molecular epidemiology.

Results

A total of 152 articles were included in the assessment. Consistent with previous assessments conducted in other disciplines, our results showed that most datasets used in non-molecular epidemiological studies were not available (i.e., neither findable nor accessible). Data availability was much higher for molecular epidemiology papers, in line with a strong repository base available to scientists in this discipline. The available data objects generally scored favourably for Findable, Accessible and Reusable indicators, but Interoperability was more problematic.

Conclusions

None of the datasets assessed in this study met all the requirements set by the FAIR principles. Interoperability, in particular, requires specific skills in data management which may not yet be broadly available in the epidemiology community. In the discussion, we present recommendations on how veterinary research could move towards greater reusability according to FAIR principles. Overall, although many initiatives to improve data access have been started in the research community, their impact on the availability of datasets underlying published articles remains unclear to date.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02971-1.

Gaussian Distribution Model for Detecting Dangerous Operating Conditions in Industrial Fish Farming

The development of better monitoring technologies, the early combat of outbreaks, massive mortality, and promoting sustainability are challenges that the aquaculture industry still faces, and the development of solutions for this is an open problem. In this paper, focusing our attention on monitoring technologies as a promising solution to these issues, we report a Gaussian distribution model for detecting dangerous operating conditions in industrial fish farming. This approach allows us to indicate through a 2D image visualization when fish production is under normal, warning, or dangerous operating conditions. Furthermore, our proposed method has promising possibilities for application in the most varied fields of science, given that the mathematical procedure described allows us to discover the fundamental statistical structure of physical, chemical, and biological systems governed by laws of a probabilistic nature.

Quantity and Quality of Aquaculture Enrichments Influence Disease Epidemics and Provide Ecological Alternatives to Antibiotics

Environmental heterogeneity is a central component influencing the virulence and epidemiology of infectious diseases. The number and distribution of susceptible hosts determines disease transmission opportunities, shifting the epidemiological threshold between the spread and fadeout of a disease. Similarly, the presence and diversity of other hosts, pathogens and environmental microbes, may inhibit or accelerate an epidemic. This has important applied implications in farming environments, where high numbers of susceptible hosts are maintained in conditions of minimal environmental heterogeneity. We investigated how the quantity and quality of aquaculture enrichments (few vs. many stones; clean stones vs. stones conditioned in lake water) influenced the severity of infection of a pathogenic bacterium, Flavobacterium columnare, in salmonid fishes. We found that the conditioning of the stones significantly increased host survival in rearing tanks with few stones. A similar effect of increased host survival was also observed with a higher number of unconditioned stones. These results suggest that a simple increase in the heterogeneity of aquaculture environment can significantly reduce the impact of diseases, most likely operating through a reduction in pathogen transmission (stone quantity) and the formation of beneficial microbial communities (stone quality). This supports enriched rearing as an ecological and economic way to prevent bacterial infections with the minimal use of antimicrobials.

Cost of a deprived environment - increased intraspecific aggression and susceptibility to pathogen infections

A lack of environmental enrichment can be severely detrimental to animal welfare. For terrestrial species, including humans, barren environments are associated with reduced cognitive function and increased stress responses and pathology. Despite a clear link between increased stress and reduced immune function, uncertainty remains on how enrichment might influence susceptibility to disease. For aquatic vertebrates, we are only now beginning to assess enrichment needs. Enrichment deprivation in fish has been linked to increased stress responses, agonistic behaviour, physiological changes and reduced survival. Limited data exist, however, on the impact of enrichment on disease resistance in fish, despite infectious diseases being a major challenge for global aquaculture. Here, using a model vertebrate host-parasite system, we investigated the impact of enrichment deprivation on susceptibility to disease, behaviour and physiology. Fish in barren tanks showed significantly higher infection burdens compared with those in enriched enclosures and they also displayed increased intraspecific aggression behaviour. Infections caused hosts to have significantly increased standard metabolic rates compared with uninfected conspecifics, but this did not differ between enriched and barren tanks. This study highlights the universal physiological cost of parasite infection and the biological cost (increased susceptibility to infection and increased aggression) of depriving captive animals of environmental enrichment.

Purinergic signaling and gene expression of purinoceptors in the head kidney of the silver catfish Rhamdia quelen experimentally infected by Flavobacterium columnare

The head kidney is a lymphoid immune organ that plays a key role in the immune and inflammatory responses of teleost fish. It is associated with immunoglobulin G production and differentiation of B cells. The presence of a multi-enzymatic complex found anchored in the plasma membrane makes the head kidney an important purinergic-dependent tissue. Purinergic signaling has been associated with these responses under pathological conditions via regulation of extracellular adenosine triphosphate (ATP), the main damage molecular associated pattern agent released during bacterial infections. The aim of this study was to determine whether purinergic signaling is a pathway associated with impairment of immune responses in silver catfish (Rhamdia quelen) experimentally infected by Flavobacterium columnare, as well as to evaluate the role of P2 purine receptors in this response. Triphosphate diphosphohydrolase (NTPDase) activity in the head kidney was significantly lower in silver catfish experimentally-infected F. columnare 72 h post-infection (hpi) than in the control group, while no significant difference was observed with respect NTPDase activity on adenosine diphosphate, as well as on 5'-nucleotidase and adenosine deaminase activities. Extracellular ATP levels were significantly higher in the head kidney of experimentally-infected fish than in the control group at 72 hpi. Finally, p2ry11 and p2rx3 purine receptor levels were significantly higher in experimentally-infected fish than in the control group at 72 hpi. We conclude that purinergic signaling in the head kidney of silver catfish infected by F. columnare creates a pro-inflammatory profile that may contribute to impairment of immune and inflammatory responses via reduction of ATP hydrolysis and its accumulation in the extracellular milieu, accompanied by upregulation of p2ry11 and p2rx3 purine receptors, leading to pro-inflammatory status.

Sequential infection can decrease virulence in a fish-bacterium-fluke interaction: Implications for aquaculture disease management

Hosts are typically infected with multiple strains or genotypes of one or several parasite species. These infections can take place simultaneously, but also at different times, i.e. sequentially, when one of the parasites establishes first. Sequential parasite dynamics are common in nature, but also in intensive farming units such as aquaculture. However, knowledge of effects of previous exposures on virulence of current infections in intensive farming is very limited. This is critical as consecutive epidemics and infection history of a host could underlie failures in management practices and medical intervention of diseases. Here, we explored effects of timing of multiple infections on virulence in two common aquaculture parasites, the bacterium Flavobacterium columnare and the fluke Diplostomum pseudospathaceum. We exposed fish hosts first to flukes and then to bacteria in two separate experiments, altering timing between the infections from few hours to several weeks. We found that both short-term and long-term differences in timing of the two infections resulted in significant, genotype-specific decrease in bacterial virulence. Second, we developed a mathematical model, parameterized from our experimental results, to predict the implications of sequential infections for epidemiological progression of the disease, and levels of fish population suppression, in an aquaculture setting. Predictions of the model showed that sequential exposure of hosts can decrease the population-level impact of the bacterial epidemic, primarily through the increased recovery rate of sequentially infected hosts, thereby substantially protecting the population from the detrimental impact of infection. However, these effects depended on bacterial strain-fluke genotype combinations, suggesting the genetic composition of the parasite populations can greatly influence the degree of host suppression. Overall, these results suggest that host infection history can have significant consequences for the impact of infection at host population level, potentially shaping parasite epidemiology, disease dynamics and evolution of virulence in farming environments.