**1. Introduction**

Aquaculture, the so-called blue biotechnology of the future [1], is the fastest growing food production sector and should continue expanding and diversifying to fulfill the need for good-quality protein of the ∼8.5 billion people that will populate the earth by 2030. Such ascending trajectory of aquaculture will also help to achieve some of the United Nations (UN) sustainable developmental goals (SDGs) [2] that seek a better, less unequal, and more sustainable future for humanity by 2030, specifically in relation to food security, improved nutrition, and poverty alleviation in rural communities in particular. Therefore, aquaculture growth and management of aquatic genetic resources should be done in a sustainable manner, a goal that requires maximizing ecosystem goods and services in line with the Blue Growth Initiative of the Food and Agriculture Organization (FAO) [2]. Aquaculture has expanded at a rate of 5.8% annually (2001–2016), totalizing ~ 80 million of tons

in 2016, worth USD 231.6 billion (mainly finfish, crustacea, mollusk) [2]. Yet, the potential for expansion and diversification is immense considering the diversity of existing marine species [3]. For example, the total number of commercially farmed species increased in the last 10 years from 472 (2006) to 598 (2016) [2]. However, the sustainable aquaculture expansion is currently hampered by the impact of detrimental diseases causing high mortality and economic loss to the sector [4], together with the indiscriminate and inefficient use of antibiotics and chemicals to control them, which causes a negative ecosystem impact [5, 6]. To reevaluate this approach is the challenge ahead, and a good start is the ban imposed to the use of antibiotics by international organizations and consumers, which have stimulated the search for alternative microbial control strategies, like the use of probiotics [6]. Chile is a well-known and competitive salmon and trout producer. In fact, it's the world's second producer of salmon following Norway, and recently it has become a relevant mussel producer [2]. According to the FAO, in 2016 Chile ranked fourth among the world producers of marine and coastal finfish with 726.9 thousand tons (live weight) and the fourth marine mollusk producer (307.4 thousand tons [2]). The relevant aquaculture species are shown in **Figure 1**, with a total of 2162 centers distributed between the so-called Lake District (administrative region X); the northern part of Patagonia, where the salmon boom began; and the Magellan and Antarctic Region (XII). Region X is full of lakes that are intensively exploited as hatcheries for smolt production and also has protected coastal bays, fjords, and estuaries ideal for completing the marine phase of salmonid life cycle, not so far away from hatcheries. This region has 666 registered fish and 1171 mollusk centers. However, due to the ecosystem and disease consequences of the intensive salmon farming (high densities of fish per water volume) [7], the activity has moved to Region XI, with a total of 767 fish centers. In total (fish and mollusk), these centers harvested 1219.739 tons in 2016 [8].

One striking aspect of the farming of exotic salmonid species in Chile is the impressive expansion from the initial 80,000 tons harvested in the early 1990s to the 688,000 tons in 2004 and 900,000 tons in 2014 according to official statistics of the national service of fisheries, SERNAPESCA. In 2017 the production leveled at 791.103 tons with the following production figures by species (2017, tons): Atlantic salmon (*Salmo salar*) 582,350; coho salmon (*Oncorhynchus kisutch*), 134,235; and rainbow trout *(Oncorhynchus mykiss*) 74,518. Such successful story dates back to the last part of the twentieth century with the introduction of rainbow and brown trout

#### **Figure 1.**

*Main species produced by Chilean aquaculture. According to production figures (2017), farming of salmon and trout is by far the main aquaculture activity in Chile, followed by the Chilean mussel (Mytilus chilensis). Others correspond to seaweeds and the Chilean scallop.*

#### *Application of Metagenomics to Chilean Aquaculture DOI: http://dx.doi.org/10.5772/intechopen.86302*

and other salmonids, initially for recreational fisheries and later for aquaculture [9]. However, the industry almost collapsed in 2006–2007 by the outbreak of the deadly virus responsible of the infectious salmon anemia (ISA), a problem that some anticipated due to the unlimited expansion of the industry in an ecosystem with limited carrying capacity [10]. This has raised serious concerns on the environmental standards of an industry making intensive use of coastal, estuaries, and lakes that are shared by multiple users and due to the high rate of antibiotic consumption (0.53 Kg per ton harvested in 2016), one of the highest in the world [7]. The interaction between host (fish), microbiota, and environmental microorganisms could be a key factor to develop rational strategies to improve the productivity by increasing the resistance to infection and reducing the use of antibiotic**s** and the environmental impact of aquaculture. However, in the production scale, the intensive use of water and the utilities of the sector does not match with the lack of scientific research available to deal with the problems caused.

This chapter focuses on Chilean aquaculture to evaluate how metagenomics, a recently developed genomic subdiscipline, is actually contributing, or could potentially contribute, to develop more efficient aquaculture practices in relation to disease control and the environmental burden such practices have brought about. Metagenomics has made possible and cheaper the analysis of the complex genomes of microbial communities to unravel their diversity, dynamics, and functioning in different environments. The application of this tool to the aquaculture microcosm in particular has been reviewed by Martinez-Porchas and Vargas-Albores [11]. One of the benefits of metagenomics is to provide access to unculturable species, the vast majority of diseaserelated microbes in aquaculture whose diversity and function were unknown so far. We first provide an overview of Chilean aquaculture, the microbiological threats faced by the salmon farming industry, mainly the symbiotic and antagonist interrelationship between microbes and farmed animals. The focus is placed on how the gut microbiota of farmed and native species contribute to their fitness and overall performance in production-related traits like disease or stress resistance. Finally, we seek to evaluate the application of metagenomics to monitoring environmental biodiversity and microbial dynamics in a scenario of climate oscillations and other ecosystem perturbations such as the development of harmful algal blooms.
