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Temporal Changes in the Gut Microbiota in Farmed Atlantic Cod (Gadus Morhua) Outweigh 2 the Response to Diet Supplementation with Macroalgae

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bioRxiv preprint doi: https://doi.org/10.1101/2020.08.10.222604; this version posted August 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh 2 the response to diet supplementation with macroalgae. 3 4 C. Keating1,2 Y*, M. Bolton-Warberg3 Y, J. Hinchcliffe 5, R. Davies6, S. Whelan3, A.H.L. Wan7,8, 5 R. D. Fitzgerald3†, S. J. Davies9, U. Z. Ijaz2*, C. J. Smith1,2* 6 7 1Department of Microbiology, School of Natural Sciences, National University of Ireland 8 Galway, Ireland, H91 TK33. 9 2Water and Environment Group, Infrastructure and Environment Division, James Watt School of 10 Engineering, University of Glasgow, Glasgow, United Kingdom, G12 8LT. 11 3Carna Research Station, Ryan Institute, National University of Ireland Galway, Carna, Co. 12 Galway, Ireland, H91 V8Y1. 13 5Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 14 Sweden. 15 6AquaBioTech Group, Central Complex, Naggar Street, Targa Gap, Mosta, MST 1761, Malta 16 G.C. 17 7Irish Seaweed Research Group, Ryan Institute and School of Natural Sciences, National 18 University of Ireland Galway, Ireland, H91 TK33. 19 8Aquaculture Nutrition and Aquafeed Research Unit, Carna Research Station, Ryan Institute and 20 School of Natural Sciences, National University of Ireland Galway, Carna, Co. Galway, Ireland, 21 H91 V8Y1. 22 9 Department of Animal Production, Welfare and Veterinary Science, Harper Adams University, 23 Newport, Shropshire, UK, TF10 8NB. 24 25 YThese authors contributed equally. 26 * Correspondence: 27 Joint corresponding authors: [email protected]; [email protected]; 28 [email protected] 29 Keywords: Atlantic cod1, Hindgut microbiome2, Seaweed3, Macroalgae4, Ulva rigida5, 30 Ascophyllum nodosum6, 16S rRNA Amplicon sequencing7, Aquaculture8. bioRxiv preprint doi: https://doi.org/10.1101/2020.08.10.222604; this version posted August 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 31 Abstract 32 Background: Aquaculture successfully meets global food demands for many fish species. 33 However, aquaculture production of Atlantic cod (Gadus morhua) is modest in comparison to 34 market demand. For cod farming to be a viable economic venture specific challenges on how to 35 increase growth, health and farming productivity need to be addressed. Feed ingredients play a 36 key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with 37 both health and economic benefits for terrestrial farmed animals and fish. The impact of such 38 dietary supplements to cod gut integrity and microbiota, which contribute to overall fish 39 robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic 40 cod with macroalgae and determine the impacts on fish condition and growth, gut morphology 41 and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of 42 three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum 43 nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. 44 45 Results: The results demonstrated there was no significant difference in fish condition, gut 46 morphology or hindgut microbiota between the U. rigida supplemented fish group and the control 47 group at any time-point. This contrasts with the A. nodosum treatment. Fish within this group 48 were further categorised as either ‘Normal’ or ‘Lower Growth’. ‘Lower Growth’ individuals 49 found the diet unpalatable resulting in reduced weight and condition factor combined with an 50 altered gut morphology and microbiome relative to the other treatments. Excluding this group, 51 our results show that the hindgut microbiota was largely driven by temporal pressures with the 52 microbial communities becoming more similar over time irrespective of dietary treatment. The 53 core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and 54 Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales 55 (Lachnoclostridium). 56 57 Conclusions: Our study indicates that U. rigida macroalgae can be supplemented at 10% 58 inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition 59 or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. 60 nodosum is not a suitable feed supplement in a farmed cod diet. 61 62 Background 63 Sustainable food production is gaining increased attention from consumers, farmers, and 64 policymakers. This is spurred on by concerns on the impact of climate change, consumer 65 awareness, and the growing global food demand [1]–[3]. Currently, 151 million tonnes of fish are 66 produced annually for human consumption [4]. Wild fish stocks cannot sustain further increases 67 in demand. Several wild fish populations have collapsed or are in danger of critical decline from 68 over-fishing and habitat damage. A significant depletion in 4 European cod stocks (Kattegat, 69 North Sea, West of Scotland and Irish Sea) by the early 2000s led to wild stock enhancement 70 initiatives, such as the European Union’s Cod Recovery Plan (EC No 1342/2008; [5], and 71 ultimately included enforced catch quotas. However, despite their initial recovery, The 72 International Council for the Exploration of the Sea (ICES) have advised that the North Sea, 73 Celtic Sea, Irish Sea and West of Scotland cod stocks are in decline once more [6]–[9]. The cause 74 of this decline is unclear, with climate change, destruction of nearshore cod nurseries by trawling, bioRxiv preprint doi: https://doi.org/10.1101/2020.08.10.222604; this version posted August 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 75 grey seal predation and fisheries management being implicated [10]–[12]. The precarious 76 condition of these wild cod stocks means this is simply not a sustainable option to meet consumer 77 demand for this fish. 78 Commercial aquaculture has successfully met the market demand for a range of fish species, 79 including Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), gilt-head 80 seabream (Sparus aurata), and seabass (Dicentrarchus labrax), thereby alleviating demand on 81 wild resources [4]. Despite the popularity of cod as a food fish, aquaculture production of farmed 82 cod is a business that has waxed and waned since the 1970’s. Currently, only 2.5% of the total 83 Atlantic cod produced for food is through aquaculture [3]-[4]. The economic viability of a 84 commercial cod farming operation presents a number of challenges including a consistent high- 85 quality broodstock, reducing high mortality, disease susceptibility, market pricing and high costs 86 associated with aquafeeds [13]–[15]. Developing novel feed ingredients and alternatives to 87 marine by-products in formulated diets not only could improve the economic viability of 88 commercial cod farming but could also have implications in the sustainability status of cod 89 farming and consumer perception of farmed cod. 90 One potential solution is to supplement the diet of farmed cod with high-quality functional 91 ingredients that provide health benefits, nutrition and are environmentally sustainable and low 92 cost. The use of macroalgae (also known as seaweeds) as a potential feed supplement could 93 further this sustainability agenda. The biomass can often be grown or sustainably harvested at 94 quantities that would meet commercial aquafeed demand. Dietary supplementation of macroalgae 95 has been trialled in many farmed fish species including Atlantic salmon (S. salar, [16], rainbow 96 trout (O. mykiss, [17], European seabass (D. labrax, [18], carp (C. carpio, [19]), and tilapia (O. 97 niloticus, [20]. Some studies have advocated that macroalgae could partially replace protein 98 constituents in formulated diets [21], [22]. However, the lower algal protein content (up to 27%) 99 in comparison to highly proteinaceous fishmeal (e.g. LT94 fish meal, ~ 67 %) and plant by- 100 products (e.g. soy protein concentrates, ~76%) typically used in formulated diets, indicate it 101 would be better to exploit algal meal as a functional feed supplement instead [23]. As a functional 102 feed supplement macroalgae can be used to supply trace metals, carotenoids, long-chain omega-3 103 polyunsaturated fatty acids, and vitamins that potentially benefit the growing farmed fish [24]. In 104 general, the inclusion of macroalgae into formulated fish diets without causing decreased growth 105 performance is approximately 10% [23]. However, the dietary macroalgae inclusion level that 106 fish can tolerate is dependent on the algal species and fish species, i.e. carnivorous versus 107 omnivorous fish, brown versus green macroalgae or indeed morphological differences in the fish 108 gastrointestinal tract [25]. 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.10.222604; this version posted August 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 109 There is a wealth of evidence outside of fish research showing that the gut microbiota is 110 intrinsically linked to digestive function, metabolism, immune support and general health as 111 shown in dogs [26] and rats [27] for example. For fish gut microbiota these links are less clearly 112 defined, though this is the focus of intensive research efforts in Atlantic salmon (S.
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