HatchR: A toolset to predict when fish hatch and emerge

A comparative analysis of multi-biomarker responses to environmental stress: Evaluating differences in landfill leachate and pathogenic oomycete effects between wild and captive Salmo trutta

Disease interaction and pathogens exchange between wild and farmed fish populations with special reference to Norway

![Figure][1] Fish farming is flourishing along coastlines in many countries. But the United States is turning instead to the open ocean for aquaculture expansion. The National Oceanic and Atmospheric Administration (NOAA), a unit within the U.S. Department of Commerce, justifies this move on several grounds: America's seafood appetite continues to grow, ocean waters are overfished, and marine fish farming near the shore is limited by state regulations. As a result, the United States faces a large and growing seafood deficit, now around $8 billion annually. With technology such as submersible cages with robotic surveillance becoming available for open-ocean farming, why not move aquaculture into the high seas? After all, the United States has the largest exclusive economic zone (EEZ) in the world, amounting to roughly 1.5 times the landmass of the lower 48 states. Facilitating aquaculture development in federal waters of the EEZ (3 to 200 miles offshore) could result in substantial commercial benefits. But at what cost to sustainable fisheries, wild fish populations, and marine ecosystems remain sticky questions for legislation. On 8 June 2005, Commerce Committee Co-Chairmen Senators Ted Stevens (R-AK) and Daniel Inouye (D-HI) introduced the National Offshore Aquaculture Act of 2005 (S. 1195). This bill, crafted by NOAA, establishes a permitting process for offshore aquaculture development within the federal waters of the EEZ and encourages private investment in aquaculture operations, demonstrations, and research. It gives the Secretary of Commerce the authority and broad discretion to promote offshore aquaculture—in consultation with other relevant federal agencies, but without firm environmental requirements apart from existing laws. Just how much NOAA should be promoting versus overseeing aquaculture development is debatable, particularly because many of the needed environmental safeguards are missing. Without a clear legal standard for environmental and resource protection within the bill, marine fisheries and ecosystems are vulnerable to further decline. Ample evidence from near-shore systems indicates major environmental risks from fish farming: The escape of farmed fish from ocean cages can have detrimental effects on wild fish populations through competition and interbreeding, parasites and diseases can spread from farmed to wild fish, there is damaging nutrient and chemical effluent discharge from farms, and the use of wild pelagic fish for feed can deplete the low end of the marine food web in certain locations. Species targeted for offshore systems, such as halibut and cod, are also caught in the wild, so commercial fishing interests worry about the economic as well as ecological consequences. Most existing open-ocean systems are experimental. They experience predator attacks, escapes, and high use of wild fish for feed, and the full ecological impact of commercial-scale offshore aquaculture remains unknown. ![Figure][1] CREDIT: MICHAEL POLE/CORBIS Since the introduction of S. 1195, environmental and fishing groups have worked hard to stop the legislation. The bill was roundly criticized before a Senate committee in June 2006 and has yet to reach the House. In the likely event that S. 1195 resurfaces in the next legislative session, stakeholders and the public should be attentive to three points. First, states have an important role to play. For example, California's recent Sustainable Oceans Act (SB 201) sets high environmental standards for marine finfish production in state waters and could help shape national legislation. An amendment to S. 1195 also permits states to opt out of aquaculture development in federal waters off their shores. Second, industry leaders whose business strategy strongly incorporates environmental and social stewardship should contribute to the bill's revision. Positive participation by the industry would help move the legislative process forward. Finally, the revised legislation must permit firms operating in U.S. federal waters to be internationally competitive. This will only happen if the bill is crafted in an international context, with sound environmental standards adopted in all countries with marine aquaculture, whether near shore or offshore. Commerce is eyeing the global picture. So too should the global environmental community. [1]: pending:yes

Wild foods are primary components of traditional and Indigenous food systems that are valued for food security while being vulnerable to global change. This case study examines practices, experiences, and perceptions associated with wild food environments through a household survey in the rural American state of Montana. Findings highlight that wild food environments contribute to cultural identity, sense of place, food security, and dietary quality of surveyed households while being vulnerable to loss of traditional ecological knowledge as well as climate and land-use change. Of the 182 informants, 80% hunt, 83% fish, and 68% forage wild botanicals. More than half of the informants agreed that wild food procurement is part of their cultural identity (66%). Collectively, informants procure more than 172 wild food species with the most prevalent being deer, waterfowl, elk, trout, bass, a range of berries, mushrooms, and botanicals used medicinally. Participants have a multidimensional value system where wild food procurement is valued for diets, recreation, family time, spirituality, and connection to the environment. The majority of participants agreed that the consumption of wild foods contributes to the nutritional quality (87%) and diversity (82%) of their diets while lowering food costs (59%). At least half of the informants reported observing changes in climate patterns over the past decade including increased temperature (50%) and more extreme and variable weather patterns (38%) that they perceive are impacting wild food environments including shifts in wild game, fish, and edible plant populations. Based on findings, we support that wild food environments and associated bio-cultural resources are a critical place to understand, conserve, and promote for nutrition. We thus advance the concept of “conservation for nutrition”. Community engagement, education, and policy plans are called for to promote wild food environments toward supporting sustainable diets and planetary health.

A growing body of literature suggests that adult salmon produced by artificial culture are not as reproductively successful as wild fish when they spawn under natural conditions. Behavioral, morphological, and physiological divergences have been observed between hatchery and wild fish. These disparities are the likely proximate causes of the differences seen in the reproductive success of hatchery and wild salmonids. Two evolutionary paradigms have been proposed to explain why salmonids cultured in hatcheries are genetically and phenotypically different from wild cohorts. The first proposes that natural selection has been significantly relaxed in hatcheries. Consequently, fish that normally would have perished because of the possession of unsuitable traits are able to survive. If these traits have a genetic basis, they may become established in a hatchery population and cause its productivity to be less than expected if the fish are once again exposed to natural selection pressures. The second theorizes that environmental and social conditions in hatcheries are less variable than in the natural environment and that these conditions will remain relatively constant from one generation to the next. In this circumstance, selection for genetic traits that adapt fish to artificial culture will become prevalent in the population. Such traits may be mal-adaptive under natural conditions. Many of the studies that have compared the reproductive success (RS) of hatchery and wild fish, however, have used non-local hatchery fish that have experienced multiple generations of hatchery culture. Few efforts have been made where both the hatchery and wild fish have originated from the same population. When such studies have been performed differences in the competency of the fish to produce offspring have not been detected or are not as great as those expressed when non-local hatchery fish have been used. The hatchery spring Chinook produced by the Yakima Fisheries Project originated from wild fish returning to the upper Yakima River. When they return as adults, almost all of them will spawn naturally in the Yakima River. The offspring they produce are expected to augment the Yakima spring Chinook population. Whether such an increase will occur or how great it may be depends on two factors, the ability of hatchery fish to reproduce under natural conditions and the capacity of their offspring to survive to maturity. One of the objectives of the Yakima Fisheries Project is to determine whether the hatchery-origin adults produced by the project have experienced any reduction in their ability to reproduce under natural conditions. To accomplish that objective an observation stream was built in 2000 on the grounds of the Cle Elum Supplementation and Research Facility. Beginning in 2001 hatchery and wild spring Chinook from the upper Yakima River stock have been introduced into the stream and allowed to reproduce. Microsatellite DNA is used to establish the genetic relationships between the adults placed into the stream and fry that are produced by each population. Six populations consisting of mixtures of wild and hatchery fish have been placed into the stream. Pedigree assessments have been completed on five of them. These assessments have shown that the reproductive success in males is often twice as variable as that experienced by females. In the five populations so far examined; wild males (age 4 and 5) produced the most offspring. The success of comparable hatchery males relative to wild males ranged from 37% to 113%. Hatchery and wild males maturing as 3-yr-olds (jacks) and as 1- and 0-yr-olds (precocious males) were also used in the study populations. They were not as successful at producing offspring as the larger hatchery and wild males. During 2001 and 2002 two populations of hatchery and wild fish were placed into the observation stream each year. Each one occupied about half of the structure. In these populations wild females exhibited a superior capacity to deposit eggs. In addition, their eggs survived to the fry stage at higher rates. This survival advantage ranged from 1.9 to 11.7%. In 2003 the entire observation stream was made available to a single population of fish in an effort to reduce intrasexual competition among the females for redd locations. In this year, hatchery females were better at depositing eggs (12.5%) and their buried eggs also achieved a higher egg-to-fry survival rate (3.4%). This suggests that at low population levels hatchery females were as competent as wild fish in burying eggs and in producing fry. Although variation in the reproductive success of females was lower than that seen in males it could be quite variable. For example, coefficient of variation values calculated on female RS ranged from 34 to 77% in the populations we examined. Numerous factors may affect RS in females.

The interaction of pathogens between wild and farmed aquatic animal populations is a concern that remains unclear and controversial. Ichthyophthirius multifiliis, a ciliated protozoan parasite, is a pathogen of freshwater finfish species with geographic and host range that causes significant economic losses in aquaculture. Flow-through farming systems may facilitate the transfer of such a parasite with free-living stages between farmed and wild stocks. Here, experimental and field study infection data are used to describe the infection dynamics of Ichthyophthirius multifiliis in rainbow trout using a simple macroparasite model by including host resistance. The study considered flow-through farming systems with a single or two age-class compartments and simulated the transfer of the parasite between farmed and wild fish populations. Results suggest that aquaculture can promote the prevalence of the resistance in wild stocks by increasing the parasite population in the wild environment. At the same time, acquired resistance in the farmed fish population may protect the wild fish population from lethal effects of the parasite by reducing the total parasite population. This study offers a promising mathematical basis for understanding the effects of freshwater aquaculture in disease spread in wildlife, developing risk assessment modeling, and exploring new ways of aquaculture management.

Fish, genes and genomes: contributions to ecology, evolution and management.

Effects of metformin on wild fathead minnows (Pimephales promelas) using in-lake mesocosms in a boreal lake ecosystem

The scombrids (Family Scombridae), commonly known as tunas, bonitos, Spanish mackerels, and mackerels, play an important role as predators and prey in coastal and oceanic marine ecosystems, and sustain some of the most important fisheries in the world. Knowledge of their basic biology and life history traits, such as growth, age, and maturity, is fundamental to sustainably manage these species, and maintain their critical role in marine ecosystems. Given the economic and social importance of their fisheries in many regions throughout the world, numerous life history studies have been conducted in the last century. Despite efforts to create global repositories of life history parameters, e.g., FishBase, many life history studies remain scattered and not readily accessible. Here, we compiled 667 life history studies published between 1933 and 2012 describing the growth, age, and reproductive biology of the 51 species of scombrids distributed around the world and create a standardized life history data set including maximum size, longevity, growth, maturity, fecundity, spawning season and frequency, and egg size information. We created this data set to promote the best use of the existing life history information and with the intention of providing a data resource suitable to test large‐scale ecological hypotheses on life history strategies and life history evolution, as well as support the management and conservation of this important group of commercially exploited species. We envisage the large repository of standardized life history data compiled will make this endeavor more effective and robust by providing a valuable resource that can help address many research questions.

Red sea bream iridovirus (RSIV) causes substantial economic damage to aquaculture. In the present study, RSIV in wild fish near aquaculture installations was surveyed to evaluate the risk of wild fish being an infection source for RSIV outbreaks in cultured fish. In total, 1102 wild fish, consisting of 44 species, were captured from 2 aquaculture areas in western Japan using fishing, gill nets, and fishing baskets between 2019 and 2022. Eleven fish from 7 species were confirmed to harbor the RSIV genome using a probe-based real-time PCR assay. The mean viral load of the RSIV-positive wild fish was 101.1 ± 0.4 copies mg-1 DNA, which was significantly lower than that of seemingly healthy red sea bream Pagrus major in a net pen during an RSIV outbreak (103.3 ± 1.5 copies mg-1 DNA) that occurred in 2021. Sequencing analysis of a partial region of the major capsid protein gene demonstrated that the RSIV genome detected in the wild fish was identical to that of the diseased fish in a fish farm located in the same area in which the wild fish were captured. Based on the diagnostic records of RSIV in the sampled area, the RSIV-infected wild fish appeared during or after the RSIV outbreak in cultured fish, suggesting that RSIV detected in wild fish was derived from the RSIV outbreak in cultured fish. Therefore, wild fish populations near aquaculture installations may not be a significant risk factor for RSIV outbreaks in cultured fish.

Polychlorinated biphenyls (PCBs) are widespread persistent anthropogenic contaminants that can accumulate in tissues of fish. The toxicity of PCBs and their transformation products has been investigated for nearly 50 years, but there is a lack of consensus regarding the effects of these environmental contaminants on wild fish populations. The objective of this review is to critically examine these investigations and evaluate publicly available databases for evidence of effects of PCBs in wild fish. Biological activity of PCBs is limited to a small proportion of PCB congeners [e.g., dioxin-like PCBs (DL-PCBs)] and occurs at concentrations that are typically orders of magnitude higher than PCB levels detected in wild fish. Induction of biomarkers consistent with PCB exposure (e.g., induction of cytochrome P450 monooxygenase system) has been evaluated frequently and shown to be induced in fish from some environments, but there does not appear to be consistent reports of damage (i.e., biomarkers of effect) to biomolecules (i.e., oxidative injury) in these fish. Numerous investigations of endocrine system dysfunction or effects on other organ systems have been conducted in wild fish, but collectively there is no consistent evidence of PCB effects on these systems in wild fish. Early life stage toxicity of DL-PCBs does not appear to occur at concentrations reported in wild fish embryos, and results do not support an association between PCBs and decreased survival of early life stages of wild fish. Overall, there appears to be little evidence that PCBs have had any widespread effect on the health or survival of wild fish.

A cross-sectional survey of Renibacterium salmoninarum infection in farmed rainbow trout (RBT) and wild fish populations was carried out in 10 farms and six river catchments, respectively, in England and Wales. The majority of the wild fish were sampled in 1998 and the farmed fish in 2000. Grayling, Thymallus thymallus, and brown trout, Salmo trutta, were the main wild species sampled. Two fish, one grayling and one salmon, Salmo salar, were R. salmoninarum culture-positive, compared with 40 confirmed polymerase chain reaction-positive wild fish. The highest prevalence of R. salmoninarum infection was found in grayling in rivers with RBT farms with a history of R. salmoninarum infection. One hundred and fifty fish were sampled from each RBT farm, but none of the fish was found to be R. salmoninarum-positive. Evidence was found, for the first time, for the presence of R. salmoninarum in an eel, Anguilla anguilla.

Beside various fields of its applications, in this study epidemiological modelling was used to understand how parasites from farmed fish may cause wild fish declines. Two separate strategic models were constructed addressing the transmission of micro-parasites and macro-parasites between farmed and wild fish: A SIR (Susceptible-Infective-Removed) model for micro-parasite infections and a compartmental density-dependent model for macro-parasite infestations. The results indicated that parasites originated in wild fish populations, after infecting farmed fish can cause epizootics. Subsequently, these parasites can be transmitted from farmed to wild fish and might have negative impact on the dynamics of wild fish populations. Sensitivity analysis of the basic model parameters in both models showed that model parameters, which are influenced by abiotic factors and allow passive manipulation, such as pathogen specific transmission rate (β), pathogen specific transmission rate between infected farmed and susceptible wild fish (δ), the rate of production of infective stages by an adult parasite (λ) and transmission rate between host and parasite infective stages (β) are more sensitive compared to model parameters which encompass chemical control and fallowing. This emphasizes the importance of the preventive medicine rather than intervention procedures in aquaculture aiming at eradicating epizootics caused by parasites and protecting wild fish stocks.

Seafood is an important resource for global nutrition and food security, with both land and marine aquaculture playing pivotal roles. High visual acuity is key for health and survival of farmed, cultured, and wild fish. Cleaner fish technology to control parasite infestation has become important in marine aquaculture and highlights the importance of visual acuity in the efficacy of cleaner fish species. New clinical diagnostic approaches towards understanding and optimising fish visual health could benefit both aquacultured and wild fish populations. Opportunities for developing and using advanced non-invasive clinical assessment and diagnosis of ocular health in wild, cultured, and experimental fish are key to more rapidly realising how threats to eye health in these animals might be better understood and mitigated. Ophthalmoscopy can rapidly and non-invasively image anatomical aspects of retinal and anterior ocular tissues and has been used in mammalian biomedicine since the turn of the 20th century. More now than ever, labour-intensive post-mortem approaches for ocular analysis such as histology are increasingly being replaced or supplemented by application of various forms of optical coherence tomography (OCT) imaging of ocular tissues in mammalian biomedicine. Advances and availability of other methodological approaches such as three-dimensional printing and computer science make instrument customisation affordable and adaptable. This review article will outline how ophthalmoscopy, OCT, and other methodologies are being applied towards understanding ocular health in teleost fish species and will describe some of the future opportunities that technological advances might afford in advancing ocular imaging in fish health and disease in general.

This report describes the viral epidemiology of wild fish adjacent to cage farms within the Tunisian coasts and is focused on viral nervous necrosis virus (VNNV). A total of 92 apparently healthy wild marine fish were collected near aquaculture facilities in five different coastal areas of Tunisia. The brains and eyes of fish were examined by quantitative real time reverse transcriptase-polymerase chain reaction (qRT-PCR) to detect the nodavirus coat protein gene of. A total of 57 out of 92 (61.9%) samples were positive for nodavirus by qRT-PCR. This finding indicates that carrier fish occur at a considerable level in populations of wild marine fish. Samples from 13 fish species were found to be positive to the virus genome: Sarpa salpa, Trachurs trachurus, Boobs boops, Sardinella aurita, Diplodus vulgaris, Diplodus puntazzo Liza aurata, Diplodue sargus, Sparus aurata, Sardina pilchardus, Spicara maena, Spondyliosoma cantharus, and Diplodus annularis. The partial sequences of the RNA2 coat protein gene of these strains were identical with RGNNV type previously identified within farmed sea bass and sea bream species in Tunisia, with a homology >97%. With respect to the proximity of the sampling sites to the coast and to rearing facilities, results analysis can suggest that these viruses may be indigenous to Tunisian coastal waters.