To determine the optimum indispensable (I) amino acid (AA) balance in Atlantic salmon (Salmo salar L.) fry, a single protocol established for the pig was adapted. The balance was calculated from the reduction in N gain after replacing about 45 % of a single IAA by a mixture of dispensable AA in isonitrogenous diets. We confirmed that the mixture of AA simulating the AA pattern of cod-meal protein and gelatine (46:3, w/w) was used with the same efficiency as cod-meal protein and gelatine. From the deletion experiment an optimum balance between the IAA was derived. Expressed relative to lysine ¼ 100, the optimal balance was: arginine 76 (SE 0·2), histidine 28 (SE 2·2), methionine þ cystine 64 (SE 1·7), phenylalanine þ tyrosine 105 (SE 1·6), threonine 51 (SE 2·4), tryptophan 14 (SE 0·7), valine 59 (SE 1·7). No estimates were made for isoleucine and leucine. Expressed as g/16 g N, the optimal balance was: arginine 4·0 (SE 0·0), histidine 1·5 (SE 0·1), lysine 5·3 (SE 0·2), methionine þ cystine 3·4 (SE 0·1), phenylaline þ tyrosine 5·6 (SE 0·1), threonine 2·7 (SE 0·1), tryptophan 0·7 (SE 0·0), valine 3·1 (SE 0·1). This AA composition is close to that of the Atlantic salmon whole-body, but using it as an estimation of the IAA requirements may lead to an overestimation of the branched-chain AA requirements and an underestimation of aromatic and S-containing AA requirements. The results are discussed in accordance with the key assumptions associated with the model used (brokenline model, IAA efficiencies and maintenance requirements).

Effective conservation of species and ecosystems requires the understanding of important ecological traits, such as dietary habits, food webs, and trophic niches. In diet studies, the visual identification of partially digested prey has been enhanced with the recent more powerful and accurate technique, DNA barcoding. Here, we summarize the contribution of this recent methodology to the investigation of both terrestrial and aquatic taxa diet, and compare the level of novelty uncovered through the use of this technique regarding species' ecology. From a total of 150 studies analyzed, focusing on more than 250 vertebrate wild species, seven domesticated taxa, and humans, we suggest that barcoding has led to more significant findings for aquatic taxa and ecosystems, where direct observations of feeding events and consequent trophic niche understanding are typically limited. Finally, we introduce the term dietary DNA (dDNA) to describe environmental approaches that use DNA extracted from gut, stomach, or fecal contents, aiming to assess both species dietary habits and describe local biodiversity. Particularly, we highlight the complementarity of environmental DNA (eDNA) and dDNA as a new tool for biodiversity assessments in remote areas, including most of the aquatic realm.

tcsBU is available on-line at http://cibio.up.pt/software/tcsBU/. The source code is freely available from https://github.com/sairum/tcsbu/ under a standard MIT license.

The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens. Infectious diseases are one of the main constraints to aquaculture growth leading to huge economic losses. Despite their negative impacts on microbial diversity and overall fish health, antibiotics are still the method of choice to treat many such diseases. Here, we use 16 rRNA V4 metataxonomics to study over a 6 week period the dynamics of the gill and skin microbiomes of farmed seabass before, during and after a natural disease outbreak and subsequent antibiotic treatment with oxytetracycline. Photobacterium damselae was identified as the most probable causative agent of disease. Both infection and antibiotic treatment caused significant, although asymmetrical, changes in the microbiome composition of the gills and skin. The most dramatic changes in microbial taxonomic abundance occurred between healthy and diseased fish. Disease led to a decrease in the bacterial core diversity in the skin, whereas in the gills there was both an increase and a shift in core diversity. Oxytetracycline caused a decrease in core diversity in the gill and an increase in the skin. Severe loss of core diversity in fish mucosae demonstrates the disruptive impact of disease and antibiotic treatment on the microbial communities of healthy fish.

There is substantial evidence showing that the microbiome of teleosts plays a key role in host health and wellbeing. Aquaculture practices increase the risk of dysbiosis (i.e. microbial imbalance), which is known to facilitate pathogen infections. The skin and gills are the primary defense organs against pathogens, thus, characterizing their microbiome composition in farmed fish is pivotal for detecting potential alterations that may lead to disease susceptibility.Here, we assessed the skin and gill microbiomes of two of the most important adult fish species farmed in southern Europe, the seabass and the seabream, during winter months. We coupled next-generation sequencing (MiSeq) of the 16S rRNA V4 region with the DADA2 bioinformatic pipeline to assess microbial composition and structure. Variation in microbial alpha-diversity (intra-sample) and taxa proportions were assessed using analysis of variance. Differences in beta-diversity (between-sample) were tested using permutational multivariate analysis of variance. Microbiomes of both tissues (n=30 per species) identified 19 bacteria phyla, dominated by the phyla Proteobacteria (44 -68%) andBacteroidetes (15 -37%); the families Flavobacteriaceae (11 -28%), Rhodobacteraeae (4 -8%) and Vibrionaceae (2 -17%); and the genera Rubritalea (4 -13%), Pseudomonas (4 -8%) and the NS3a marine group (4 -12%). Mean relative proportion of these taxa, some alpha-diversity indices and all beta-diversity distances varied significantly between tissues within and between species. ASVs belonging to the genera Polaribacter and Vibrio, which include several species that are pathogenic, were detected in the core microbiomes of seabass or seabream.

1. The European eel Anguilla anguilla is a critically endangered fish species as a result of human activities and climate change in river and oceanic ecosystems. Restocking using glass eels in continental freshwater areas is a potential conservation measure for enhancing local eel stocks and for conserving the species in aquatic habitats, where it may otherwise disappear. However, little is known about the fate of these restocked individuals and the early ecological behaviour of the young eels translocated in rivers. 2.A portable radio-frequency identification (RFID) telemetry system and 12-mm tags were used to track restocked eels for a duration of 4 years. The aim was to understand the early movement, behavioural traits, dispersal, and habitat use of elvers after restocking performed in 2013 with glass eels in a shallow riverine environment.3. From the 241 tagged eels (total length, Q 50 = 152 mm), 85% were detected in 1968 positions during a period of 4 years, beginning in 2014. Clear seasonality in eel activity was observed, with higher mobility in summer when the water temperature was high (above 12°C). Dispersal was slowed by numerous artificial obstacles and the high carrying capacity of habitats. There was a negative relationship between the body size of eels at tagging and their mobility. Five behavioural categories of mobility patterns were identified: ascending, descending, oscillating with an upstream trend, oscillating with a downstream trend, and stationary. The first four categories depleted with time, in favour of stationary individuals that displayed a highly sedentary lifestyle.4. This study provides new knowledge of the long-term dispersal behaviour of restocked eels and the influence of seasons, barriers, and habitats on their colonization strategy changing with time. The results contribute to a better understanding of the issue of uncommon restocking practices in upland rivers.

The ocean sunfish (Mola mola) is the world’s heaviest bony fish reaching a body mass of up to 2.3 tonnes. However, the prey M. mola consumes to fuel this prodigious growth remains poorly known. Sunfish were thought to be obligate gelatinous plankton feeders, but recent studies suggest a more generalist diet. In this study, through molecular barcoding and for the first time, the diet of sunfish in the north-east Atlantic Ocean was characterised. Overall, DNA from the diet content of 57 individuals was successfully amplified, identifying 41 different prey items. Sunfish fed mainly on crustaceans and teleosts, with cnidarians comprising only 16% of the consumed prey. Although no adult fishes were sampled, we found evidence for an ontogenetic shift in the diet, with smaller individuals feeding mainly on small crustaceans and teleost fish, whereas the diet of larger fish included more cnidarian species. Our results confirm that smaller sunfish feed predominantly on benthic and on coastal pelagic species, whereas larger fish depend on pelagic prey. Therefore, sunfish is a generalist predator with a greater diversity of links in coastal food webs than previously realised. Its removal as fisheries’ bycatch may have wider reaching ecological consequences, potentially disrupting coastal trophic interactions.

No abstract