Promise and progress in environmental genomics: a status report on the applications of gene expression-based microarray studies in ecologically relevant fish species

The advent of any new technology is typically met with great excitement. So it was a few years ago, when the combination of advances in sequencing technology and the development of microarray technology made measurements of global gene expression in ecologically relevant species possible. Many of the review papers published around that time promised that these new technologies would revolutionize environmental biology as they had revolutionized medicine and related fields. A few years have passed since these technological advancements have been made, and the use of microarray studies in non‐model fish species has been adopted in many laboratories internationally. Has the relatively widespread adoption of this technology really revolutionized the fields of environmental biology, including ecotoxicology, aquaculture and ecology, as promised? Or have these studies merely become a novelty and a potential distraction for scientists addressing environmentally relevant questions? In this review, the promises made in early review papers, in particular about the advances that the use of microarrays would enable, are summarized; these claims are compared to the results of recent studies to determine whether the forecasted changes have materialized. Some applications, as discussed in the paper, have been realized and have led to advances in their field, others are still under development.     

Pathogenesis of gram-negative bacterial infections in warmwater fish

Knowledge concerning the pathogenesis of many bacterial diseases in fish is limited, especially in those diseases that occur in warmwater species. This limited knowledge base is due to the relative recent emergence of warmwater fish culture as a major industry in many parts of the world, and to the previous economic insignificance of warmwater aquaculture and the bacterial pathogens affecting warmwater species. This article is an overview of the important gram-negative pathogens of warmwater fish, including members of the genera Aeromonas, Edwardsiella, Pasteurella, Pseudomonas, and Vibrio. The current knowledge of the pathogenesis of these organisms is emphasized, including: the source of the pathogen, its preferred site and method for attaching to and penetrating the host, its adaptations for surviving the host immune system, and its strategies for obtaining nutrients required for proliferation and growth. Although information for many of these pathogens is limited, the intent of this article is to provide a baseline for the development of future research projects. Increases in worldwide aquaculture production will result in a demand for knowledge about the pathogenesis of bacterial pathogens in warmwater fish, because of its importance in making health management decisions, in deciding on treatment regimens, and in the development of vaccines.     

Application of 16s rDNA and cytochrome <Emphasis Type="Italic">b</Emphasis> ribosomal markers in studies of lineage and fish populations structure of aquatic species

The most economically important form of aquaculture is fish farming, which is an industry that accounts for an ever increasing share of world fishery production. Molecular markers can be used to enhance the productivity of the aquaculture and fish industries to meet the increasing demand. Molecular markers can be identified via a DNA test regardless of the developmental stage, age or environmental challenges experienced by the organism. The application of 16s and cytochrome b markers has enabled rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification and the construction of high resolution genetic linkage maps for aquaculture fisheries. In this review, the advantages of principles and potential power tools of 16s and cytochrome b markers are discussed. Main findings in term of trend, aspects and debates on the reviewed issue made from the model of aquatic species for the benefit of aquaculture genomics and aquaculture genetics research are discussed. The concepts in this review are illustrated with various research examples and results that relate theory to reality and provide a strong review of the current status of these biotechnology topics.     

Cloning of fish enzymes and other fish protein genes

Fish metabolism needs special enzymes that have maximum activity at very different conditions than their mammalian counterparts. Due to the differences in activity, these enzymes, especially cold-adapted proteases, could be used advantageously for the production of some foods. In addition to the enzymes, this review describes some other unique fish polypeptides such as antifreeze proteins, fluorescent proteins, antitumor peptides, antibiotics, and hormones, that have already been cloned and used in food processing, genetic engineering, medicine, and aquaculture. Recombinant DNA technology, which allows these biological molecules to be cloned and overexpressed in microorganisms is also described, highlighting innovative applications. The expected impact of cloning fish proteins in different fields of technology is discussed.     

稻渔综合种养的科学范式

21世纪是渔业的世纪。中国和世界水产业历经数十年的发展为人类应对食品危机做出了巨大贡献。然而,我国传统的水产业对产量的片面追求导致养殖环境日趋恶化,养殖生态系统不断退化,养殖业的可持续发展受到限制。传统稻田其氮素的流失亦是导致农业面源污染的主要原因之一。我国当前的环境问题源于复合生态系统演化进程的缺陷,解决当前的环境问题,必须从优化复合生态系统演化进程着眼。采用优化的生态循环水产养殖模式,如综合水产养殖则可以大大提高氮、磷等养分物质的利用率。稻渔综合种养是一种科学的复合生态模式,可以概括为三种模式,一种是在我国传统稻田养鱼的基础上,逐步发展起来的一种稻渔共生模式,可采取稻鱼、稻蟹、稻虾等多种共作形式;二是稻田作为湿地用于处理水产养殖尾水的模式,属于异位处理形式;三是将稻渔共生和水产养殖相耦合的模式,尤其是与多种水产养殖形式结合或与复合水产养殖系统相结合,甚至是与农牧系统相结合。这第三种稻渔共作模式又称为陆基生态渔场,具有高产、高品质、高生态可持续性等特点,应加强对该创新养殖模式中有机碳、氮、磷等营养收支平衡和循环利用的相关机制以及复合生态系统对外源营养输入的整体响应机制开展研究。概括而...     

Review: Assessing fish welfare in research and aquaculture,with a focus on European directives

The number of farmed fish in the world has increased considerably. Aquaculture is a growing industry that will in the future provide a large portion of fishery products. Moreover, in recent years, the number of teleost fish used as animal models for scientific research in both biomedical and ecological fields has increased. Therefore, it is increasingly important to implement measures designed to enhance the welfare of these animals. Currently, a number of European rules exist as requirements for the establishment, care and accommodation of fish maintained for human purposes. As far as (teleost) fish are concerned, the fact that the number of extant species is much greater than that of all other vertebrates must be considered. Of further importance is that each species has its own specific physical and chemical requirements. These factors make it difficult to provide generalized recommendations or requirements for all fish species. An adequate knowledge is required of the physiology and ecology of each species bred. This paper integrates and discusses, in a single synthesis, the current issues related to fish welfare, considering that teleosts are target species for both aquaculture and experimental models in biological and biomedical research. We first focus on the practical aspects, which must be considered when assessing fish welfare in both research and aquaculture contexts. Next, we address husbandry and the care of fish housed in research laboratories and aquaculture facilities in relation to their physiological and behavioural requirements, as well as in reference to the suggestions provided by European regulations. Finally, to evaluate precisely which parameters described by Directive 2010/63/EU are reported in scientific papers, we analysed 82 articles published by European researchers in 2014 and 2015. This review found that there is a general lack of information related to the optimal environmental conditions that should be provided for the range of species covered by this directive.     

Aquaculture: a newly emergent food production sector—and perspectives of its impacts on biodiversity and conservation

The fisheries sector in the course of the last three decades have been transformed from a developed country to a developing country dominance. Aquaculture, the farming of waters, though a millennia old tradition during this period has become a significant contributor to food fish production, currently accounting for nearly 50?% of global food fish consumption; in effect transforming our dependence from a hunted to a farmed supply as for all our staple food types. Aquaculture and indeed the fisheries sector as a whole is predominated in the developing countries, and accordingly the development strategies adopted by the sector are influenced by this. Aquaculture also being a newly emerged food production sector has being subjected to an increased level of public scrutiny, and one of the most contentious aspects has been its impacts on biodiversity. In this synthesis an attempt is made to assess the impacts of aquaculture on biodiversity. Instances of major impacts on biodiversity conservation arising from aquaculture, such as land use, effluent discharge, effects on wild populations, alien species among others are highlighted and critically examined. The influence of paradigm changes in development strategies and modern day market forces have begun to impact on aquaculture developments. Consequently, improvements in practices and adoption of more environmentally friendly approaches that have a decreasing negative influence on biodiversity conservation are highlighted. An attempt is also made to demonstrate direct and or indirect benefits of aquaculture, such as through being a substitute to meet human needs for food, particularly over-exploited and vulnerable fish stocks, and for other purposes (e.g. medicinal ingredients), on biodiversity conservation, often a neglected entity.     

Towards more efficient longline fisheries: fish feeding behaviour,bait characteristics and development of alternative baits

Better knowledge of food search behaviour in fish is essential for studies that aim to improve longline fishing, particularly through bait development. This review provides an overview of our understanding of how fish detect and locate sources of food odour, focusing on the stimuli and sensory modalities involved, and on factors that affect feeding activity. Studies that identify feeding attractants and efforts to develop alternative longline baits are presented. The review reveals that such studies are few in number, and that to date there are no alternatives to traditional baits in commercial longlining despite the growing demand for these resources, which are also used for human consumption. The chemical compounds that elicit food search behaviour differ from species to species, and species selectivity could be improved by incorporating specific feeding attractants in manufactured baits. The unique properties of chemical stimuli and odour dispersal form the basis for improving longline efficiency through the development of a long-lasting bait. Vision is important in prey capture, and manufactured baits can be made more visible than natural baits by increasing the contrast (e.g. via fluorescent or polarising coatings) and creating motion through buoyancy. Physical properties such as size, shape, texture and strength can also be manipulated in a manufactured bait to improve catch efficiency. Knowledge obtained from studies of various aspects of food search behaviour is of paramount importance for future research aimed at alternative bait development and improving longline fishing.     

How can plant genetic engineering contribute to cost-effective fish vaccine development for promoting sustainable aquaculture?

Aquaculture, the fastest growing food-producing sector, now accounts for nearly 50 % of the world’s food fish (FAO in The state of world fisheries and aquaculture. FAO, Rome, 2010). The global aquaculture production of food fish reached 62.7 million tonnes in 2011 and is continuously increasing with an estimated production of food fish of 66.5 million tonnes in 2012 (a 9.4 % increase in 1 year, FAO, www.fao.org/fishery/topic/16140). Aquaculture is not only important for sustainable protein-based food fish production but also for the aquaculture industry and economy worldwide. Disease prevention is the key issue to maintain a sustainable development of aquaculture. Widespread use of antibiotics in aquaculture has led to the development of antibiotic-resistant bacteria and the accumulation of antibiotics in the environment, resulting in water and soil pollution. Thus, vaccination is the most effective and environmentally-friendly approach to combat diseases in aquaculture to manage fish health. Furthermore, when compared to >760 vaccines against human diseases, there are only about 30 fish vaccines commercially available, suggesting the urgent need for development and cost-effective production of fish vaccines for managing fish health, especially in the fast growing fish farming in Asia where profit is minimal and therefore given high priority. Plant genetic engineering has made significant contributions to production of biotech crops for food, feed, valuable recombinant proteins etc. in the past three decades. The use of plants for vaccine production offers several advantages such as low cost, safety and easy scaling up. To date a large number of plant-derived vaccines, antibodies and therapeutic proteins have been produced for human health, of which a few have been made commercially available. However, the development of animal vaccines in plants, especially fish vaccines by genetic engineering, has not yet been addressed. Therefore, there is a need to exploit plant biotechnology for cost effective fish vaccine development in plants, in particular, edible crops for oral fish vaccines. This review provides insight into (1) the current status of fish vaccine and vaccination in aquaculture, (2) plant biotechnology and edible crops for fish vaccines for oral administration, (3) regulatory constraints and (4) conclusions and future perspectives.     

The biological role of pituitary adenylate cyclase‐activating polypeptide (PACAP) in growth and feeding behavior in juvenile fish

To date, many technologies have been developed to increase efficiency in aquaculture, but very few successful biotechnology molecules have arrived on the market. In this context, marine biotechnology has an opportunity to develop products to improve the output of fish in aquaculture. Published in vivo studies on the action of the pituitary adenylate cyclase‐activating polypeptide (PACAP) in fish are scarce. Recently, our group, for the first time, demonstrated the biological role of this neuropeptide administrated by immersion baths in the growth and development of larval fish. In this work, we have evaluated the effects of recombinant Clarias gariepinus PACAP administration by intraperitoneal injection on growth performance and feeding behavior in juvenile fish. Our results showed the physiological role of this peptide for growth control in fish, including the juvenile stage, and confirm that its biological functions are well conserved in fish, since C. gariepinus PACAP stimulated growth in juvenile tilapia Oreochromis niloticus. In addition, we have observed that the growth‐promoting effect of PACAP in juvenile tilapia was correlated with higher GH concentration in serum. With regard to the neuroendocrine regulation of growth control by PACAP, it was demonstrated that PACAP stimulates food intake in juvenile tilapia. In general, PACAP appears to act in the regulation of the growth control in juvenile fish. These findings propose that PACAP is a prominent target with the potential to stimulate fish growth in aquaculture. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Genetic basis and biotechnological manipulation of sexual dimorphism and sex determination in fish

Aquaculture has made an enormous contribution to the world food production,especially to the sustainable supply of animal proteins.The utility of diverse reproduction strategies in fish,such as the exploiting use of unisexual gynogenesis,has created a typical case of fish genetic breeding.A number of fish species show substantial sexual dimorphism that is closely linked to multiple economic traits including growth rate and body size,and the efficient development of sex-linked genetic markers and sex control biotechnologies has provided significant approaches to increase the production and value for commercial purposes.Along with the rapid development of genomics and molecular genetic techniques,the genetic basis of sexual dimorphism has been gradually deciphered,and great progress has been made in the mechanisms of fish sex determination and identification of sex-determining genes.This review summarizes the progress to provide some directive and objective thinking for further research in this field.     

池养大口胭脂鱼鱼种的食性

池养大口胭脂鱼鱼种的食性研究表明 ,大口胭脂鱼鱼种为浮游动物尺寸选择性鱼类 ,其选食行为主要受鱼体及水体中浮游动物的个体大小影响 ,与浮游动物的种类、逃跑能力、运动方式等关系不明显。并初步探讨了 3种浮游生物食性鱼类 (大口胭脂鱼、鲢、鳙 )的食物关系。     

Feeding and trapping fish withPiper auritum

The “natives” at Rio Indio, on the central Caribbean slope of Panama, trap the river fishBrycon chagrensis using leaves ofPiper auritum as bait in feeders. The people use this technique because the fish tastes like the leaf after it has fed regularly on the leaf. This technique has potential use in aquaculture. The plant could also be cultivated for marketing as a food-flavoring condiment and fish food.     

Structured modeling of fish physiology.

The use of models in simulation and state estimation has proved useful in diverse applications, especially in industrial process control. The project presented here looked into the modeling of fish physiology for applications in fish physiology research and aquaculture. The models deal with gastric evacuation, metabolism, kidneys, gills, the cardiovascular system, and feeding behavior and are based on data from the literature. Model responses are mostly in accord with real responses in principle, but, as with most models of complex biological systems, the numerical accuracy is low in several cases. However, these structured models enable researchers to test hypotheses by altering the submodels and parameters.     

Matrix metalloproteinases in fish biology and matrix turnover

Matrix metalloproteinases have important functions for tissue turnover in fish, with relevance both for the fish industry and molecular and cellular research on embryology, inflammation and tissue repair. These metalloproteinases have been studied in different fish types, subjected to both aquaculture and experimental conditions. This review highlights studies on these metalloproteinases in relation to both fish quality and health and further, the future importance of fish for basic research studies.     

Generation of viable fish from cryopreserved primordial germ cells

An increasing number of wild fish species are in danger of extinction, often as a result of human activities. The cryopreservation of gametes and embryos has great potential for maintaining and restoring threatened species. The conservation of both paternal and maternal genetic information is essential. However, although this technique has been successfully applied to the spermatozoa of many fish species, reliable methods are lacking for the long-term preservation of fish eggs and embryos. Here, we describe a protocol for use with rainbow trout (Oncorhynchus mykiss) primordial germ cells (PGCs) and document the restoration of live fish from gametes derived from these cryopreserved progenitors. Genital ridges (GRs), which are embryonic tissues containing PGCs, were successfully cryopreserved in a medium containing 1.8 M ethylene glycol (EG). The thawed PGCs that were transplanted into the peritoneal cavities of allogenic trout hatchlings differentiated into mature spermatozoa and eggs in the recipient gonads. Furthermore, the fertilization of eggs derived from cryopreserved PGCs by cryopreserved spermatozoa resulted in the development of fertile F1 fish. This PGC cryopreservation technique represents a promising tool in efforts to save threatened fish species. Moreover, this approach has significant potential for maintaining domesticated fish strains carrying commercially valuable traits for aquaculture purposes.