Aquaculture is the fastest-growing food-producing sector. With an annual growth rate of 6%, this industry aims to reduce human dependency on natural resources from the oceans. However, maintaining a low footprint on the environment through sustainable and yet profit farming is complex. Towards this goal, farms must keep water of high quality and free from harmful pathogens, use environmentally friendly ingredients in the aquafeeds, and verify that discharged effluents contain only minimal loads of nutrients and other contaminants such as antibiotics and hormones.
Microbes in the water and cultured species have tremendous and immediate impacts on farm and animals' condition and performances which often tip the balance between farm profit and failure as in the case of fish infection by undesirable pathogens. Interactions of microbes with each other and with host and ecosystem are of major concern towards improving aquaculture sustainability. Recent advances in genomic-based methods and bioinformatics opened the door toward this direction with studies performed on various set-ups and cultured species.
In the realm of Global Health concepts towards sustainability in aquaculture, contemporary studies are in favour of environmental biodiversity that encourages more diverse microbiomes, thus eventually resulting in a more resilient system and healthier cultured species. Different set-ups of the culture systems, as in monoculture versus multi-trophic systems, the rate of organic loads, and other environmental forces have been proposed to determine microbial community diversity but knowledge concerning the outputs in terms of performances and functioning is still needed. This includes studies of germ-free models of aquaculture species that arose to better understand the circumstances in which the structure and traits of the microbial community improve growth, health, or other phenotypes of the cultured species. Furthermore, augmentation of antimicrobial and antiparasitic agents in aquaculture impacts the resident microbiota and may be acute if supplemented during larval rearing when the development of the gut microbiome is rapid alongside with frequent occurrence of undesired pathogens that take the advantage of this sensitive phase. Disease control via the use of antibiotics and antiparasitics enlarges the capacity of the aquaculture resistome with antimicrobial resisting genes and peptides which are further transferred to the aquaculture-related environment by the withstanding microbiota.
The major aim of this Research Topic is to share novel scientific knowledge that will allow improvement of the sustainability of aquaculture through discussion of the outputs from changes in aquaculture-related microbiomes, and therefore a broader understanding of the aquaculture ecosystem as a holobiome. A broad range of aspects will be covered to address differences between the selected experimental approaches and tools, as well as between the different examined set-ups and organisms. Furthermore, the novel knowledge is expected to allow identification of the methodologies that will lead future research in this area and to provide microbial management protocols that can be further developed and examined with respect to their efficacy for improving aquaculture sustainability and performances of cultured species.
We welcome authors to contribute articles in the form of original research, review, and mini-review that will focus on, but are not limited to, the following themes:
• Microbe-host interactions in aquaculture and the influences on host traits and performances.
• Forces influencing microbial communities, their diversity, and functioning in the aquaculture environment.
• Managing microbial diversity in the hypertrophic aquaculture towards improving microbes services in disease controlling, increasing water quality, and improving performances and traits of the cultured species.
• Consequences of antibiotics administration in the aquaculture on microbial diversity, functioning, and antimicrobial resistance within the system and in aquaculture-related ecosystems.
• Advanced methods for pathogens controlling in aquaculture including target-specific probiotics, microbes-microbes interaction, microbial maturation, microbial-derived metabolites, quorum-sensing, and bacteriophages.
• Improvements in the development of microbial-based feeds and prebiotics for various uses in aquaculture.
Aquaculture is the fastest-growing food-producing sector. With an annual growth rate of 6%, this industry aims to reduce human dependency on natural resources from the oceans. However, maintaining a low footprint on the environment through sustainable and yet profit farming is complex. Towards this goal, farms must keep water of high quality and free from harmful pathogens, use environmentally friendly ingredients in the aquafeeds, and verify that discharged effluents contain only minimal loads of nutrients and other contaminants such as antibiotics and hormones.
Microbes in the water and cultured species have tremendous and immediate impacts on farm and animals' condition and performances which often tip the balance between farm profit and failure as in the case of fish infection by undesirable pathogens. Interactions of microbes with each other and with host and ecosystem are of major concern towards improving aquaculture sustainability. Recent advances in genomic-based methods and bioinformatics opened the door toward this direction with studies performed on various set-ups and cultured species.
In the realm of Global Health concepts towards sustainability in aquaculture, contemporary studies are in favour of environmental biodiversity that encourages more diverse microbiomes, thus eventually resulting in a more resilient system and healthier cultured species. Different set-ups of the culture systems, as in monoculture versus multi-trophic systems, the rate of organic loads, and other environmental forces have been proposed to determine microbial community diversity but knowledge concerning the outputs in terms of performances and functioning is still needed. This includes studies of germ-free models of aquaculture species that arose to better understand the circumstances in which the structure and traits of the microbial community improve growth, health, or other phenotypes of the cultured species. Furthermore, augmentation of antimicrobial and antiparasitic agents in aquaculture impacts the resident microbiota and may be acute if supplemented during larval rearing when the development of the gut microbiome is rapid alongside with frequent occurrence of undesired pathogens that take the advantage of this sensitive phase. Disease control via the use of antibiotics and antiparasitics enlarges the capacity of the aquaculture resistome with antimicrobial resisting genes and peptides which are further transferred to the aquaculture-related environment by the withstanding microbiota.
The major aim of this Research Topic is to share novel scientific knowledge that will allow improvement of the sustainability of aquaculture through discussion of the outputs from changes in aquaculture-related microbiomes, and therefore a broader understanding of the aquaculture ecosystem as a holobiome. A broad range of aspects will be covered to address differences between the selected experimental approaches and tools, as well as between the different examined set-ups and organisms. Furthermore, the novel knowledge is expected to allow identification of the methodologies that will lead future research in this area and to provide microbial management protocols that can be further developed and examined with respect to their efficacy for improving aquaculture sustainability and performances of cultured species.
We welcome authors to contribute articles in the form of original research, review, and mini-review that will focus on, but are not limited to, the following themes:
• Microbe-host interactions in aquaculture and the influences on host traits and performances.
• Forces influencing microbial communities, their diversity, and functioning in the aquaculture environment.
• Managing microbial diversity in the hypertrophic aquaculture towards improving microbes services in disease controlling, increasing water quality, and improving performances and traits of the cultured species.
• Consequences of antibiotics administration in the aquaculture on microbial diversity, functioning, and antimicrobial resistance within the system and in aquaculture-related ecosystems.
• Advanced methods for pathogens controlling in aquaculture including target-specific probiotics, microbes-microbes interaction, microbial maturation, microbial-derived metabolites, quorum-sensing, and bacteriophages.
• Improvements in the development of microbial-based feeds and prebiotics for various uses in aquaculture.
