Zebrafish as a model organism for nutrition and growth: towards comparative studies of nutritional genomics applied to aquacultured fishes

Zebrafish (Danio rerio) is a common research model in fish studies of toxicology, developmental biology, neurobiology and molecular genetics; it has been proposed as a possible model organism for nutrition and growth studies in fish. The advantages of working with zebrafish in these areas are their small size, short generation time (12–14 weeks) and their capacity to produce numerous eggs (100–200 eggs/clutch). Since a wide variety of molecular tools and information are available for genomic analysis, zebrafish has also been proposed as a model for nutritional genomic studies in fish. The detailed study of every species employed as a model organism is important because these species are used to generalize how several biological processes occur in related organisms, and contribute considerably toward improving our understanding of the mechanisms involved in nutrition and growth. The objective of this review is to show the relevant aspects of the nutrition and growth in zebrafish that support its utility as a model organism for nutritional genomics studies. We made a particular emphasis that gene expression and genetic variants in response to zebrafish nutrition will shed light on similar processes in aquacultured fish.     

Selection for Adaptation to Dietary Shifts: Towards Sustainable Breeding of Carnivorous Fish

Genetic adaptation to dietary environments is a key process in the evolution of natural populations and is of great interest in animal breeding. In fish farming, the use of fish meal and fish oil has been widely challenged, leading to the rapidly increasing use of plant-based products in feed. However, high substitution rates impair fish health and growth in carnivorous species. We demonstrated that survival rate, mean body weight and biomass can be improved in rainbow trout (Oncorhynchus mykiss) after a single generation of selection for the ability to adapt to a totally plant-based diet (15.1%, 35.3% and 54.4%, respectively). Individual variability in the ability to adapt to major diet changes can be effectively used to promote fish welfare and a more sustainable aquaculture.     

Family of Tc1-like elements from fish genomes and horizontal transfer

The involvement of horizontal transfer (HT) in the evolution of vertebrate transposable elements (TEs) is a matter of an ongoing debate. The phylogenetic relationships between Tc1 TEs, based on limited dataset have been previously used to infer a case of Tc1 HT between the genomes of fish and frogs. Here this hypothesis has been critically evaluated by the experimental approach including comparative data on the range of fish species available today. The distribution of a Tc1 subfamily of TE in selected fish species was investigated by PCR with a single primer complementary to ITRs and showed that they are widespread in the studied 17 fish species. They belong to five different subfamilies of Tc1 TEs, as revealed by the comparison with current genomic data for fish and amphibians. The original hypothesis would get much weaker support from the current data, although at least one novel potential and more convincing case of HT was identified between genomes of Perciformes fish. An interesting case of recombination-driven mobilisation of a degenerated TE by distantly related TE from different subfamily was discovered in the genome of pike. The occurrence of such cases widens the range of TE elements identifiable with the employed experimental approach. Further similar studies would help to explain the evolution of the multiple Tc1 lineages including species for which full genome sequences will not be available soon.     

Transposable elements in medaka fish

DNA-based transposable elements appear to have been nearly or completely inactivated in vertebrates. Therefore the elements of the medaka fish Oryzias latipes that still have transposition activity provide precious materials for studying transposition mechanisms, as well as the evolution, of transposable elements in vertebrates. Fortunately, the medaka fish has a strong background for genetic and evolutionary studies. The advantages of this host species and their elements, together with results so far obtained, are here described.     

The effect of GH overexpression on GHR and IGF-I gene regulation in different genotypes of GH-transgenic zebrafish

Most biological actions of growth hormone (GH) are mediated by the insulin-like growth factor I (IGF-I) that is produced after the interaction of the hormone with a specific cell surface receptor, the GH receptor (GHR). Even though the GH excess on fish metabolism is poorly known, several species have been genetically engineered for this hormone in order to improve growth for aquaculture. In some GH-transgenic fish growth has been dramatically increased, while in others high levels of transgene expression have shown inhibition of the growth response. In this study, we used for the first time different genotypes (hemizygous and homozygous) of a GH-transgenic zebrafish (Danio rerio) lineage as a model for studying the GH resistance induced by different GH transgene expression levels. The results obtained here demonstrated that homozygous fish did not grow as expected and have a lower condition factor, which implies a catabolic state. These findings are explained by a decreased IGF-I and GHR gene expression as a consequence of GH resistance. Together, our results demonstrated that homozygous GH-transgenic fish showed similar characteristics to the starvation-induced fish and could be an interesting model for studying the regulation of the GH/GHR/IGF-I axis in fish.     

Expression and promoter activity of endogenous retroviruses in the Olive flounder (<Emphasis Type="Italic">Paralichthys olivaceus</Emphasis>)

Olive flounder (Paralichthys olivaceus) is regarded as one of economical fish species in the world. Genome information of Olive flounder has been revealed by next generation sequencing. Endogenous retroviruses (ERVs) as a member of transposable elements have been involved in functional roles of various genes in variety organisms. In this study, we identified an Olive flounder ERV (OF-ERV5) using RepeatMasker program, and examined expression pattern of pol gene of OF-ERV5, which indicated the high expression in two kidney samples (head kidney and body kidney). In addition, the 5′LTR sequences of OF-ERV5 are cloned into pGL4.11 vectors to confirm promoter activity. Luciferase assay indicated that the OF-ERV5_LTR showed promoter activity in both HepG2 and HINAE cell lines. These data could be of great use for further study to understand biological function of transposable elements in Oliver flounder.     

Vigour-related traits and immunity in hybrids of evolutionary divergent cyprinoid species: advantages of hybrid heterosis?

Hybrid advantage, described as the superiority of hybrids in some traits over their parents and termed the “heterosis effect,” is widely documented in the case of reciprocal crosses of parental species (i.e., hybrids representing the F1 generation). In fish, high survival, fast growth and better health status have been widely documented in F1 hybrids. Nonetheless, the effects of interspecific hybridization on vigour, physiology and immunity-related traits in fish are largely unknown, especially concerning native systems of coexisting parental and hybrid genomes in the same habitat. The present study examined the potential physiological and immune aspects of hybrid heterosis by comparing condition status (measured especially by indexes), haematological profile, glucose concentration and selected parameters of non-specific and specific immunity between the evolutionarily divergent non-congeneric cyprinoid species Abramis brama and Rutilus rutilus and their hybrids representing the F1 generation, all of them caught in nature. Clear differences were documented for vigour-related, physiological and immune parameters between the two divergent species. Hybrids generally tended to express intermediate characters of the measured traits, likely generated by the evolutionary divergence of the hybridizing species; nonetheless, for some traits, hybrids exhibited a character that was more similar to one parental species than to the other. This was interpreted as the heterozygote advantage for F1 hybrids. It is suggested that a maternally inherited genetic background may potentially influence the expression of some branches of non-specific immunity or other aspects related to the fish health status.     

Genome evolution and biodiversity in teleost fish

Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre- and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates.     

Intergenerational effects of CO2‐induced stream acidification in the Trinidadian guppy (Poecilia reticulata)

Rising atmospheric carbon dioxide levels are driving decreases in aquatic pH. As a result, there has been a surge in the number of studies examining the impact of acidification on aquatic fauna over the past decade. Thus far, both positive and negative impacts on the growth of fish have been reported, creating a disparity in results. Food availability and single‐generation exposure have been proposed as some of the reasons for these variable results, where unrealistically high food treatments lead to fish overcoming the energetic costs associated with acclimating to decreased pH. Likewise, exposure of fish to lower pH for only one generation may not capture the likely ecological response to acidification that wild populations might experience over two or more generations. Here we compare somatic growth rates of laboratory populations of the Trinidadian guppy (Poecilia reticulata) exposed to pH levels that represent the average and lowest levels observed in streams in its native range. Specifically, we test the role of maternal acclimation and resource availability on the response of freshwater fishes to acidification. Acidification had a negative impact on growth at more natural, low food treatments. With high food availability, fish whose mothers were acclimated to the acidified treatment showed no reduction in growth, compared to controls. Compensatory growth was observed in both control–acidified (maternal–natal environment) and acidified–control groups, where fish that did not experience intergenerational effects achieved the same size in response to acidification as those that did, after an initial period of stunted growth. These results suggest that future studies on the effects of shifting mean of aquatic pH on fishes should take account of intergenerational effects and compensatory growth, as otherwise effects of acidification may be overestimated.     

Fish transposons and their potential use in aquaculture

A large part of repetitive DNA of vertebrate genomes have been identified as transposon elements (TEs) or mobile sequences. Although TEs detected to date in most vertebrates are inactivated, active TEs have been found in fish and a salmonid TE has been successfully reactivated by molecular genetic manipulation from inactive genomic copies (Sleeping Beauty, SB). Progress in the understanding of the dynamics, control and evolution of fish TEs will allow the insertion of selected sequences into the fish genomes of germ cells to obtain transgenics or to identify genes important for growth and/or of somatic cells to improve DNA vaccination. Expectations are high for new possible applications to fish of this well developed technology for mammals. Here, we review the present state of knowledge of inactive and active fish TEs and briefly discuss how their possible future applications might be used to improve fish production in aquaculture.     

An analysis of temporal variability in abundance, diversity and growth rates within the coastal ichthyoplankton assemblage of South Georgia (sub-Antarctic)

The study of spatial and temporal distribution and diversity of ichthyoplankton (fish eggs and larvae) can provide fisheries-independent information on the population dynamics and recruitment processes of marine fish species. Ichthyoplankton studies in the Southern Ocean have to date been largely constrained to the summer months. We analysed ichthyoplankton data collected from a year round, long term (2002–2008), plankton trawl sampling programme in a large fjord system (Cumberland Bay) at South Georgia, sub-Antarctic (54.25°S, 36.5°W) to assess temporal changes in larval fish diversity and abundance. Larvae of 22 species, representing nine families, were identified although three, Krefftichthys anderssoni (Myctophidae), Lepidonotothen nudifrons/Trematomus hansoni (Nototheniidae) and Champsocephalus gunnari (Channichthyidae), dominated abundance in all years. Significant seasonal and interannual differences in the larval fish assemblage were revealed by multivariate analyses. Estimates of larval growth are provided for five abundant species. Considerable inter-specific differences in relative larval growth rate were recorded but interannual variability within species was small. However, in the commercially important C. gunnari, multiple larval cohorts, representing a protracted spawning season, were observed to grow at different rates, and this may be related to temperature and/or food availability. A comparison with historical growth data from South Georgia suggests there has been little change in growth rate for the main species over the last three decades.     

Habitat structure and body size distributions: cross‐ecosystem comparison for taxa with determinate and indeterminate growth

Habitat structure across multiple spatial and temporal scales has been proposed as a key driver of body size distributions for associated communities. Thus, understanding the relationship between habitat and body size is fundamental to developing predictions regarding the influence of habitat change on animal communities. Much of the work assessing the relationship between habitat structure and body size distributions has focused on terrestrial taxa with determinate growth, and has primarily analysed discontinuities (gaps) in the distribution of species mean sizes (species size relationships or SSRs). The suitability of this approach for taxa with indeterminate growth has yet to be determined. We provide a cross‐ecosystem comparison of bird (determinate growth) and fish (indeterminate growth) body mass distributions using four independent data sets. We evaluate three size distribution indices: SSRs, species size–density relationships (SSDRs) and individual size–density relationships (ISDRs), and two types of analysis: looking for either discontinuities or abundance patterns and multi‐modality in the distributions. To assess the respective suitability of these three indices and two analytical approaches for understanding habitat–size relationships in different ecosystems, we compare their ability to differentiate bird or fish communities found within contrasting habitat conditions. All three indices of body size distribution are useful for examining the relationship between cross‐scale patterns of habitat structure and size for species with determinate growth, such as birds. In contrast, for species with indeterminate growth such as fish, the relationship between habitat structure and body size may be masked when using mean summary metrics, and thus individual‐level data (ISDRs) are more useful. Furthermore, ISDRs, which have traditionally been used to study aquatic systems, present a potentially useful common currency for comparing body size distributions across terrestrial and aquatic ecosystems.     

Stochastic population dynamics and life-history variation in marine fish species

Abstract We examined whether differences in life-history characteristics can explain interspecific variation in stochastic population dynamics in nine marine fish species living in the Barents Sea system. After observation errors in population estimates were accounted for, temporal variability in natural mortality rate, annual recruitment, and population growth rate was negatively related to generation time. Mean natural mortality rate, annual recruitment, and population growth rate were lower in long-lived species than in short-lived species. Thus, important species-specific characteristics of the population dynamics were related to the species position along the slow-fast continuum of life-history variation. These relationships were further associated with interspecific differences in ecology: species at the fast end were mainly pelagic, with short generation times and high natural mortality, annual recruitment, and population growth rates, and also showed high temporal variability in those demographic traits. In contrast, species at the slow end were long-lived, deepwater species with low rates and reduced temporal variability in the same demographic traits. These interspecific relationships show that the life-history characteristics of a species can predict basic features of interspecific variation in population dynamical characteristics of marine fish, which should have implications for the choice of harvest strategy to facilitate sustainable yields.     

Changes in growth rates of oral jaw elements produce evolutionary novelty in bahamian pupfish

To understand the origins of novelty and the evolution of biological diversity, it is important to investigate the processes that generate phenotypic variation from genotypic variation. A number of path‐breaking studies have revealed the genetic basis for phenotypic differences between distantly related taxa, but how qualitative change is produced during the early stages of divergence is largely unexplored. Here, we focus on striking differences in jaw morphology exhibited by three closely related sympatric pupfish species (genus Cyprinodon) from San Salvador Island, Bahamas as a basis for investigating the genetic sources of morphological variation in recently diverged species. San Salvador Island pupfish are trophically diverse and display derived jaw morphologies distinct from any other species in the genus. We illustrate these qualitative morphological differences between species with 3D‐reconstructed CT‐images and camera lucida drawings of the skulls of wild‐caught fish. Quantitative data representing the size of individual bony skull elements in wild fish show how qualitatively novel morphologies arise as a consequence of changes to the size and shape of individual skull elements, particularly the dentary, premaxilla, and maxilla bones associated with the oral jaws. Consistent with these comparative data is that the growth rate of individual bony skull elements, measured on a developmental time series of lab‐reared fish, differs between species. Our data provide a critical foundation for future studies developing San Salvador Cyprinodon pupfishes as a model system to understand the evolution and development of novel morphologies at the species level. J. Morphol. 277:935–947, 2016. © 2016 Wiley Periodicals, Inc.     

Nature versus nurture? Consequences of short captivity in early stages

Biological changes occurring as a consequence of domestication and/or captivity are not still deeply known. In Atlantic salmon (Salmo salar), endangered (Southern Europe) populations are enhanced by supportive breeding, which involves only 6 months of captive rearing following artificial spawning of wild‐collected adults. In this work, we assess whether several fitness‐correlated life‐history traits (migratory behavior, straying rate, age at maturity, and growth) are affected by early exposure to the captive environment within a generation, before reproduction thus before genetic selection. Results showed significant differences in growth and migratory behavior (including straying), associated with this very short period of captivity in natural fish populations, changing even genetic variability (decreased in hatchery‐reared adults) and the native population structure within and between rivers of the species. These changes appeared within a single generation, suggesting very short time of captivity is enough for initiating changes normally attributed to domestication. These results may have potential implications for the long‐term population stability/viability of species subjected to restoration and enhancement processes and could be also considered for the management of zoo populations.     

A review of the influence of biogeography,riverine linkages,and marine connectivity on fish assemblages in evolving lagoons and lakes of coastal southern Africa

The Holocene evolution of eight South African coastal lakes and lagoons is examined and related to changes in fish composition over that period. Historical and current connectivity with riverine and marine environments are the primary determinants of present‐day fish assemblages in these systems. A small and remarkably consistent group of relict estuarine species have persisted in these coastal lakes and lagoons. The loss or reduction of connectivity with the sea has impacted on the diversity of marine fishes in all eight study systems, with no marine fishes occurring in those water bodies where connectivity has been completely broken (e.g. Sibaya, Groenvlei). In systems that have retained tenuous linkages with the sea (e.g., Verlorenvlei, Wilderness lakes), elements of the marine fish assemblage have persisted, especially the presence of facultative catadromous species. Freshwater fish diversity in coastal lakes and lagoons is a function of historical and present biogeography and salinity. From a freshwater biogeography perspective, the inflowing rivers of the four temperate systems reviewed here contain three or fewer native freshwater fishes, while the subtropical lakes that are fed by river systems contain up to 40 freshwater fish species. Thus, the significantly higher fish species diversity in subtropical versus temperate coastal lakes and lagoons comes as no surprise. Fish species diversity has been increased further in some systems (e.g., Groenvlei) by alien fish introductions. However, the impacts of fish introductions and translocations have not been studied in the coastal lakes and lagoons of South Africa. In these closed systems, it is probable that predation impacts on small estuarine fishes are significant. The recent alien fish introductions is an example of the growing threats to these systems during the Anthropocene, a period when human activities have had significant negative impacts and show potential to match the changes recorded during the entire Holocene.     

Shape analysis of the jaws between two minnow species over ontogeny

This study compares sand shiner (Notropis stramineus ) and silverjaw (Ericymba buccata ) minnows, in terms of the morphological shape changes of the upper, lower, and pharyngeal jaws over ontogeny. These two species of minnows initially feed on midge larvae and undergo an ontogenic prey shift. The traditional morphometrics measured—total length, snout‐to‐vent length, eye diameter, premaxilla length, lower jaw length, gape—were regressed onto total length to test for allometry. Digital pictures were processed with tpsDig and further analyzed with MorphoJ utilizing a regular geometric morphometrics procedure using principle component analyses. We examined gut contents for 16 fish of each species. For the silverjaw minnows, we found all jaw variables to exhibit positive allometric growth with increasing total length, while most of the jaw variables for the sand shiner exhibited negative allometric growth with increasing total length. This correlates with an ontogenic prey shift for both species. Sand shiner minnows have been found to be more omnivorous, feeding on algae later in life, while silverjaw minnows undergo a prey shift to larger invertebrates. These species lack oral dentition causing an increased reliance on the pharyngeal apparatus. Principle component analyses revealed elongation of pharyngeal jaw elements in the silverjaw minnows and a relative shortening and bulking of pharyngeal jaws in the sand shiner minnows. The ontogenic dietary shifts observed in these two species provide possible explanation for the morphological changes over ontogeny in jaw elements, which are likely enabling these species to occupy the same habitat with little niche overlap.     

Comparative trace element and organic growth factor requirements of five hansenula species

A comparative response of specific trace elements and organic growth factors for the growth of five Hansenula species (H. anomala, H. beijerinckii, H. ciferrii, H. polymorpha and H. sydowiorum) has been studied. Out of twenty three trace elements tested, Fe, Zn, Mn and Cu were found to be essential for the growth of all yeast species studied here, whereas the rest of the elements exhibited variable essentiality. From fifteen organic growth factors tested, thiamine, biotin, pyridoxine and inositol are the most commonly required growth factors by the yeasts, whereas the rest of the organic growth factors showed variable essentiality. All species of yeasts investigated required different concentrations of trace elements and organic growth factors for their optimum growth. Concentrations higher than the optimum have been found to be inhibitory for the growth of all the yeasts studied.