The Influence of Behavioral, Social, and Environmental Factors on Reproducibility and Replicability in Aquatic Animal Models

A simple semi-automated home-tank method and procedure to explore classical associative learning in adult zebrafish

The zebrafish is a laboratory species that gained increasing popularity the last decade in a variety of subfields of biology, including toxicology, ecology, medicine, and the neurosciences. An important phenotype often measured in these fields is behaviour. Consequently, numerous new behavioural apparati and paradigms have been developed for the zebrafish, including methods for the analysis of learning and memory in adult zebrafish. Perhaps the biggest obstacle in these methods is that zebrafish is particularly sensitive to human handling. To overcome this confound, automated learning paradigms have been developed with varying success. In this manuscript, we present a semi-automated home tank-based learning/memory test paradigm utilizing visual cues, and show that it is capable of quantifying classical associative learning performance in zebrafish. We demonstrate that in this task, zebrafish successfully acquire the association between coloured-light and food reward. The hardware and software components of the task are easy and cheap to obtain and simple to assemble and set up. The procedures of the paradigm allow the test fish to remain completely undisturbed by the experimenter for several days in their home (test) tank, eliminating human handling or human interference induced stress. We demonstrate that the development of cheap and simple automated home-tank-based learning paradigms for the zebrafish is feasible. We argue that such tasks will allow us to better characterize numerous cognitive and mnemonic features of the zebrafish, including elemental as well as configural learning and memory, which will, in turn, also enhance our ability to study neurobiological mechanisms underlying learning and memory using this model organism.

Beyond compliance: harmonising research and husbandry practices to improve experimental reproducibility using fish models

Reproducibility in animal research is impacted by the environment, by husbandry practices in the laboratory and by the animals' provenance. These factors, however, are often not adequately considered by researchers. A disconnect between researchers and animal care staff can result in inappropriate housing and husbandry decisions for scientific studies with those animals. This is especially the case for the research in neuro-behaviour, epigenetics, and the impact of climate change, as heritable phenotypic, behavioural or physiological changes are known to result from the animals' environmental housing, husbandry, provenance and prior experience. This can lead to greater variation (even major differences) in data outcomes among studies, driving scientific uncertainties. Herein, we illustrate some of the endpoints measured in fish studies known to be intrinsically linked to the environment and husbandry conditions and assess the significance of housing and husbandry practice decisions for research adopting these endpoints for different fish species. We highlight the different priorities and challenges faced by researchers and animal care staff and how harmonising their activities and building greater understanding of how husbandry practices affect the fish will improve reproducibility in research outcomes. We furthermore illustrate how improving engagement between stakeholders, including regulatory bodies, can better underpin fish husbandry decisions and where researchers could help to drive best husbandry practices through their own research with fish models.

Novel Husbandry Practices Result in Rapid Rates of Growth and Sexual Maturation Without Impacting Adult Behavior in the Blind Mexican Cavefish

Animal model systems are dependent on the standardization of husbandry protocols that maximize growth and reduce generation time. The Mexican tetra, Astyanax mexicanus, exists as eyed surface and blind cave dwelling populations. The opportunity for comparative approaches between independently evolved populations has led to the rapid growth of A. mexicanus as a model for evolution and biomedical research. However, a slow and inconsistent growth rate remains a major limitation to the expanded application of A. mexicanus. Fortunately, this temporal limitation can be addressed through husbandry changes that accelerate growth rates while maintaining optimal health outcomes. Here, we describe a husbandry protocol that produces rapid growth rates through changes in diet, feeding frequency, growth sorting and progressive changes in tank size. This protocol produced robust growth rates and decreased the age of sexual maturity in comparison to our previous protocol. To determine whether changes in feeding impacted behavior, we tested fish in exploration and schooling assays. We found no difference in behavior between the two groups, suggesting that increased feeding and rapid growth will not impact the natural variation in behavioral traits. Taken together, this standardized husbandry protocol will accelerate the development of A. mexicanus as a genetic model.

Structural environmental enrichment and the way it is offered influence cognitive judgement bias and anxiety-like behaviours in zebrafish

Environmental enrichment in zebrafish generally reduces anxiety-related behaviours, improves learning in maze trials and increases health and biological fitness. However, certain types of enrichment or certain conditions induce the opposite effects. Therefore, it is essential to study the characteristics of environmental enrichment that modulate these effects. This study aims to investigate if structural environmental enrichment and the way it is offered influence cognitive judgement bias and anxiety-like behaviours in adult zebrafish. The fish were assigned to six housing manipulations: constant barren, constant enrichment, gradual gain of enrichment, gradual loss of enrichment, sudden gain of enrichment and sudden loss of enrichment. We then transposed the cognitive judgment bias paradigm, formerly used in studies on other animals to measure the link between emotion and cognition, to objectively assess the impact of these manipulations on the zebrafish's interpretation of ambiguous stimuli, considering previous experiences and related emotional states. We used two battery tests (light/dark and activity tests), which measured anxiety-related behaviours to check if these tests covariate with cognitive bias results. The fish with a sudden gain in enrichment showed a pessimistic bias (interpreted ambiguous stimuli as negative). In addition, the fish that experienced a sudden gain and a gradual loss in enrichment showed more anxiety-like behaviours than the fish that experienced constant conditions or a gradual gain in enrichment. The data provide some proof that structural environmental enrichment and the way it is presented can alter zebrafish's cognitive bias and anxiety-like behaviours.

A FELASA Working Group Survey on Fish Species Used for Research, Methods of Euthanasia, Health Monitoring, and Biosecurity in Europe, North America, and Oceania

Simple Summary

An international survey was conducted regarding species used for research, methods of euthanasia, health monitoring, and biosecurity in fish laboratories. A total of 145 facilities from 23 countries contributed. Over 80 different species were reported to be used for research, of which zebrafish (Danio rerio) was the most common by far. Anesthetic overdose was the preferred method for euthanasia for adults, fry, and larvae not capable of independent feeding. For all developmental stages, the most popular anesthetic compound was tricaine. Around half of the respondents did not perform a completion method to ensure death. One-quarter of the responding facilities did not have a health monitoring system in place. Only a small fraction reported quarantine routines to ensure reliable biological barriers. There was little consensus amongst facilities in how to perform biosecurity measures.

Abstract

An international survey was conducted regarding species used for research, methods of euthanasia, health monitoring, and biosecurity in fish laboratories. A total of 145 facilities from 23 countries contributed. Collectively, over 80 different species (or groups of species) were reported to be used for research, of which zebrafish (Danio rerio) was the most common by far. About half of the participating laboratories used multiple species. Anesthetic overdose was the preferred method for euthanasia for adult, fry (capable of independent feeding), and larval (not capable of independent feeding) fish. For all developmental stages, the most popular anesthetic compound was tricaine (MS-222), a substance associated with distress and aversion in several species. Moreover, around half of the respondents did not perform a completion method to ensure death. One-quarter of the responding facilities did not have a health monitoring system in place. While most respondents had some form of quarantine process for imported fish, only a small fraction reported quarantine routines that ensure reliable biological barriers. Furthermore, less than one in five screened fish for pathogens while in quarantine. In sum, there was little consensus amongst facilities in how to perform biosecurity measures. Regarding euthanasia, health monitoring, and biosecurity processes, there is a need for updated and universal guidelines and for many laboratories to adjust their practices.

What do male and female zebrafish prefer? Directional and color preference in maze tasks

Studies regarding the animals' innate preferences help elucidate and avoid probable sources of bias and serve as a reference to improve and develop new behavioral tasks. In zebrafish research, data obtained in behavioral assessments are often not replicated between research groups or even inside the same laboratory raising huge concerns about replicability and reproducibility. Among the potential causes that are not well considered, sexual differences can be a probable source of bias. Thus, this study aimed to investigate the male and female zebrafish directional and color preferences in the plus-maze and T-maze behavioral tasks. Experiment 1 evaluated directional preference and experiment 2 evaluated color preference in a plus-maze task; experiment 3 evaluated preference between black or white in a T-maze task. Individual preferences were expressed as the percentage of time spent in each zone. Our results showed that male and female zebrafish demonstrated no difference in directional preference in the plus-maze task. Surprisingly, male and female zebrafish showed color preference differences in the plus-maze task; males did not show any color preference, while female zebrafish demonstrated a red preference compared to white, blue, and yellow colors. Moreover, both male and female zebrafish demonstrated a strong black color preference compared to the white color in the T-maze task. Our findings characterized the spontaneous preference of male and female zebrafish for direction and color, identifying possible biases, and providing insights that contribute to the standardization of future protocols.

FELASA-AALAS Recommendations for Monitoring and Reporting of Laboratory Fish Diseases and Health Status, with an Emphasis on Zebrafish (Danio Rerio)

The exchange of fish for research may expose an aquatic laboratory to pathogen contamination as incoming fish can introduce bacteria, fungi, parasites, and viruses capable of affecting both experimental results and fish and personnel health and welfare. To develop risk mitigation strategies, FELASA and AALAS established a joint working group to recommend good practices for health monitoring of laboratory fish. The recommendations address all fish species used for research, with a particular focus on zebrafish (Danio rerio). First, the background of the working group and key definitions are provided. Next, fish diseases of high impact are described. Third, recommendations are made for health monitoring of laboratory fishes. The recommendations emphasize the importance of daily observation of the fish and strategies to determine fish colony health status. Finally, report templates are proposed for historical screening data and aquatic facility description to facilitate biohazard risk assessment when exchanging fish.

Improving zebrafish laboratory welfare and scientific research through understanding their natural history

Globally, millions of zebrafish (Danio rerio) are used for scientific laboratory experiments for which researchers have a duty of care, with legal obligations to consider their welfare. Considering the growing use of the zebrafish as a vertebrate model for addressing a diverse range of scientific questions, optimising their laboratory conditions is of major importance for both welfare and improving scientific research. However, most guidelines for the care and breeding of zebrafish for research are concerned primarily with maximising production and minimising costs and pay little attention to the effects on welfare of the environments in which the fish are maintained, or how those conditions affect their scientific research. Here we review the physical and social conditions in which laboratory zebrafish are kept, identifying and drawing attention to factors likely to affect their welfare and experimental science. We also identify a fundamental lack knowledge of how zebrafish interact with many biotic and abiotic features in their natural environment to support ways to optimise zebrafish health and well-being in the laboratory, and in turn the quality of scientific data produced. We advocate that the conditions under which zebrafish are maintained need to become a more integral part of research and that we understand more fully how they influence experimental outcome and in turn interpretations of the data generated.

Understanding how stress responses and stress-related behaviors have evolved in zebrafish and mammals

Stress response is essential for the organism to quickly restore physiological homeostasis disturbed by various environmental insults. In addition to well-established physiological cascades, stress also evokes various brain and behavioral responses. Aquatic animal models, including the zebrafish (Danio rerio), have been extensively used to probe pathobiological mechanisms of stress and stress-related brain disorders. Here, we critically discuss the use of zebrafish models for studying mechanisms of stress and modeling its disorders experimentally, with a particular cross-taxon focus on the potential evolution of stress responses from zebrafish to rodents and humans, as well as its translational implications.

Different influences of anxiety models, environmental enrichment, standard conditions and intraspecies variation (sex, personality and strain) on stress and quality of life in adult and juvenile zebrafish: A systematic review

Antagonist and long-lasting environmental manipulations (EM) have successfully induced or reduced the stress responses and quality of life of zebrafish. For instance, environmental enrichment (EE) generally reduces anxiety-related behaviours and improves immunity, while unpredictable chronic stress (UCS) and aquarium-related stressors generate the opposite effects. However, there is an absence of consistency in outcomes for some EM, such as acute exposure to stressors, social enrichment and some items of structural enrichment. Therefore, considering intraspecies variation (sex, personality, and strain), increasing intervention complexity while improving standardisation of protocols and contemplating the possibility that EE may act as a mild stressor on a spectrum between too much (UCS) and too little (standard conditions) stress intensity or stimulation, would reduce the inconsistencies of these outcomes. It would also help explore the mechanism behind stress resilience and to standardise EM protocols. Thus, this review critically analyses and compares knowledge existing over the last decade concerning environmental manipulations for zebrafish and the influences that sex, strain, and personality may have on behavioural, physiological, and fitness-related responses.

The role of auditory and vibration stimuli in zebrafish neurobehavioral models

Strongly affecting human and animal physiology, sounds and vibration are critical environmental factors whose complex role in behavioral and brain functions necessitates further clinical and experimental studies. Zebrafish are a promising model organism for neuroscience research, including probing the contribution of auditory and vibration stimuli to neurobehavioral processes. Here, we summarize mounting evidence on the role of sound and vibration in zebrafish behavior and brain function, and outline future directions of translational research in this field. With the growing environmental exposure to noise and vibration, we call for more active use of zebrafish models for probing neurobehavioral and bioenvironmental consequences of acute and long-term exposure to sounds and vibration in complex biological systems.

Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration

BACKGROUND

Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to equilibrate following installation, before fish can be introduced. There is little information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium in RAS in general.

METHODS

A zebrafish housing system was monitored at multiple different system sites including tank water in six different tanks, pre- and post-particulate filter water, the fluidized bed biofilter substrate, post-carbon filter water, and water leaving the ultra-violet (UV) disinfection unit and entering the tanks. All of these samples were collected in quadruplicate, from prior to population of the system with zebrafish through 18 weeks post-population, and analyzed using both 16S rRNA amplicon sequencing and culture using multiple agars and annotation of isolates via matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. Sequencing data were analyzed using traditional methods, network analyses of longitudinal data, and integration of culture and sequence data.

RESULTS

The water microbiome, dominated by Cutibacterium and Staphylococcus spp., reached a relatively stable richness and composition by approximately three to four weeks post-population, but continued to evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter and water leaving the UV disinfection unit were distinct from water at all other sites. Core taxa detected using molecular methods comprised 36 amplicon sequence variants, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, and showed moderate agreement with sequencing data.

CONCLUSIONS

The microbiome of commercial RAS used for research zebrafish reaches a relatively stable state by four weeks post-population and would be expected to be suitable for experimental use following that time-point.

Understanding complex dynamics of behavioral, neurochemical and transcriptomic changes induced by prolonged chronic unpredictable stress in zebrafish

Stress-related neuropsychiatric disorders are widespread, debilitating and often treatment-resistant illnesses that represent an urgent unmet biomedical problem. Animal models of these disorders are widely used to study stress pathogenesis. A more recent and historically less utilized model organism, the zebrafish (Danio rerio), is a valuable tool in stress neuroscience research. Utilizing the 5-week chronic unpredictable stress (CUS) model, here we examined brain transcriptomic profiles and complex dynamic behavioral stress responses, as well as neurochemical alterations in adult zebrafish and their correction by chronic antidepressant, fluoxetine, treatment. Overall, CUS induced complex neurochemical and behavioral alterations in zebrafish, including stable anxiety-like behaviors and serotonin metabolism deficits. Chronic fluoxetine (0.1 mg/L for 11 days) rescued most of the observed behavioral and neurochemical responses. Finally, whole-genome brain transcriptomic analyses revealed altered expression of various CNS genes (partially rescued by chronic fluoxetine), including inflammation-, ubiquitin- and arrestin-related genes. Collectively, this supports zebrafish as a valuable translational tool to study stress-related pathogenesis, whose anxiety and serotonergic deficits parallel rodent and clinical studies, and genomic analyses implicate neuroinflammation, structural neuronal remodeling and arrestin/ubiquitin pathways in both stress pathogenesis and its potential therapy.

Improving Replicability, Reproducibility, And Reliability In Preclinical Research: A Shared Responsibility

Reproducible and reliable scientific investigation depends on the identification and consideration of various intrinsic and extrinsic factors that may affect the model system used. The impact of these factors must be managed during all phases of a study: planning, execution, and reporting. The value of in vivo (animal) research has come under increasing scrutiny over the past decade because of multiple reports documenting poor translatability to human studies. These failures have been attributed to various causes, including poor study design and execution as well as deficiencies in reporting. It is important to recognize that achieving reproducible and reliable preclinical research results is a joint responsibility that requires a partnership between the investigative team and the animal care and use program staff. The myriad of intrinsic factors, such as species, strain/substrain, age, sex, physiologic and health status, and extrinsic factors, including temperature, humidity, lighting, housing system, and diet, need to be recognized and managed during study planning and execution, as they can influence animal physiology and biological response. Of equal importance is the need to document and report these details. The ARRIVE and PREPARE guidelines were developed by concerned scientists, veterinarians, statisticians, journal editors, and funding agencies to assist investigative teams and scientific journals manage and report on intrinsic and extrinsic factors to improve reproducibility and reliability. This issue of the ILAR Journal will focus on the various extrinsic factors that have been recognized to confound animal research.