Application of Metagenomics to Chilean Aquaculture

Abstract

Aquaculture is a rapidly expanding food production sector, facing the challenge of growth both increasing its efficiency and reducing its negative impact on the environment. Metagenomics is an emerging tool in aquaculture that helps to understand the complex host (fish-shellfish)-microbiota-pathogen-environment relationship underlying disease outbreaks, monitoring the dynamics of microbial diversity in farmed animals subject to different environmental conditions or perturbations. As Chile takes an important share of world aquaculture market, this chapter reviews the actual and potential applications of metagenomics to support a sustainable expansion and diversification of Chilean aquaculture. The focus is on (i) the role and function of the gut microbiota in the proper immunostimulation and disease control and (ii) the role of metagenomics in monitoring environmental microbial biodiversity and dynamics in relation to disease persistence and ecosystem stability. We conclude that despite the importance of the aquaculture sector in Chile, the application of metagenomics to deal with disease control and ecosystem preservation is still an emerging field of study. Understanding host (fish-shellfish)microbiota-pathogen-environment diversity of interactions in a more holistic view, i.e., the holobiome approach, could be key to develop rational strategies to improve productivity by increasing resistance to diseases and reducing the use of antibiotics and their negative environmental impact.

Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective

“…This interaction implies induction of gene expression and protein synthesis on both sides, and an infectious process may develop in the host, leading ultimately to death, if the host response or defense system fails to combat the pathogenic challenge [ 171 ]. However, a wider perspective on host-pathogen interactions may be undertaken [ 172 ], spanning these interactions to the associated microbial populations e.g., the host microbiome, known as the “holobiome” approach [ 173 ]. Indeed, it has been demonstrated that the microbiota may play a critical role in the immune response of organisms [ 174 ].…”

“…Indeed, it has been demonstrated that the microbiota may play a critical role in the immune response of organisms [ 174 ]. The “holobiome” approach on the study of fish host-pathogen interactions i.e., between the fish host, its microbiome, the pathogen, and other environmental microorganisms, has been pointed as a critical aspect for further development of rational strategies aiming at fish disease prevention and resistance [ 172 ]. Moreover, this holistic knowledge of fish host-pathogen interactions could contribute to promote sustainability in aquaculture, by reducing the use of antibiotics, responsible for a negative environmental impact of this industry [ 172 ].…”

“…Metagenomics and metaproteomics are among the most powerful and emerging high-throughput tools in marine/ocean environments to disclose the genome and proteome, of the associated microbial communities [ 172 , 175 , 176 , 177 ]. These methodologies are still scarce on aquaculture research, although it might be extremely useful in the study of microbial populations inherent to the farmed fish surrounding environment.…”

“…Furthermore, metagenomics and metaproteomics approaches enable the characterization of the microbiota associated to fish skin mucous or fish gut, thus unravelling key genes or proteins in the immune function, that may act as the whole biosystem through complex networks during fish host-pathogen interactions. An additional and major benefit of these tools is the possibility of accessing to unculturable species, the vast majority of disease-related microbes in aquaculture, whose identity and function would otherwise remain unknown [ 172 ].…”

Hypersaline Lagoons from Chile, the Southern Edge of the World

“…One evident expression of this interaction is that Artemia gets energy grazing on bacteria [58][59][60], which also provide enzymes to digest the algae and yeasts that are also Artemia food items. Additionally, environmental bacteria colonize and establish in the Artemia gut conforming the microbiota, which is known to provide multiple functional benefits to the host such as protection against pathogens, energy balance, immunological enhancement, and behavior [61]. Thus, imbalances (i.e., reduced diversity) in the microbiota composition due to environmental or other factors such as pathogens seriously affect the performance of the host in a given environment.…”