The aquaculture microbiome at the centre of business creation

Twelve per cent of the world’s population is currently securing their livelihood partly, or fully, through the fisheries and aquaculture sector (FAO Fisheries and Aquaculture Department, 2016). Most people occupied in this sector rely on wild catches; however, fish stocks are becoming depleted with 90% of stocks being fully or overexploited (FAO Fisheries and Aquaculture Department, 2016). A more productive and sustainable aquaculture sector is needed to meet the sustainable development goals (SDGs) of the UN number 2, 12 and 14 and supply a growing world population, which is expected to reach 10 individuals in approximately 30 years (United Nations, Department of Economic and Social Affairs, Population Division, 2015), with high-quality protein. The aquaculture sector has, within the past few years, surpassed wild catches in the production of seafood (fish and plants combined; Bentzon-Tilia et al., 2016), and overall employment in the fisheries sector has decreased by approximately one million individuals from 2010 to 2014, while the aquaculture sector saw an increase of 0.1 million individuals. In general, a shift has been seen from 1990, where 83% were employed in fisheries and 17% in aquaculture, to 2014 where 67% were employed in fisheries and 33% in aquaculture (FAO Fisheries and Aquaculture Department, 2016). The sector is projected to increase its output from 74 million tons in 2014 to 102 million tons by 2025, and up to 121 million tons by 2030 (FAO Fisheries and Aquaculture Department, 2016). Furthermore, it was recently suggested that the global biological production potential for marine aquaculture is more than 100 times the current global seafood consumption, thus suitable habitats do not seem to be a limiting factor in the growth of the sector (Gentry et al., 2017). Consequently, the industry is faced with a need to significantly increase productivity while at the same time securing both livelihoods and sustainability. Controlling the microorganisms that are associated with aquaculture systems (i.e. the aquaculture microbiome) has always been essential in high-intensity rearing of fish. Disease outbreaks caused by pathogenic bacteria are believed to be one of the most serious challenges faced by the aquaculture industry (Meyer, 1991), and consequently, extensive measures are taken to limit the introduction and proliferation of such bacteria in the aquaculture systems. Furthermore, microbial activity in these naturally eutrophied systems may produce unwanted toxic metabolites such as hydrogen sulphide (H2S), which is formed when microorganisms reduce sulphate (SO4 ) in anaerobic respiration and which interferes with mammalian respiration. However, microbes may also serve as a solution to an array of these very challenges. In the agriculture industry, microbiome-based products such as seed coatings that increase nutrient uptake in crops, and which antagonize plant pathogenic soil organisms, are becoming increasingly popular tools to improve productivity in a sustainable manner, and microbiome-based products may reach a market size comparable to that of chemical agro-chemicals within a few years (Singh, 2017). The very same technologies that have facilitated this development, for example advances in high-throughput sequencing and synthetic biology, have been proposed to be key in the sustainable development of the aquaculture industry in the coming years as well (Bentzon-Tilia et al., 2016). However, with a few exceptions, such as studies on recirculating aquaculture systems and fish-associated microbial communities (van Kessel et al., 2011; Llewellyn et al., 2014), the aquaculture microbiome has not been characterized to the same degree as its terrestrial counterpart. In contrast, most studies concerning the aquaculture microbiome relies on bacterial isolation and PCR-based approaches. Hence, the implementation of microbiomebased products is in its infancy and many practices are still of a ‘hope for the best’ fertilization-based nature (Moriarty, 1997), where specific functional groups of the aquaculture microbiome are enriched for by adding, for example carbon-rich substrates. This is the case for most ‘biofloc’ approaches where molasses or an equivalent C-rich fertilizer is added as a means to increase the