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.

Deep-water sharks exhibit species-specific reproductive strategies, which include segregation by sex, size and reproductive stage. However, due to the wide spatial distribution of most species, available information, usually collected at a regional scale, is usually not adequate to infer species reproductive spatial dynamics. This study draws together information on the distribution of reproductive stages of three species of squaliform sharks: Portuguese dogfish Centroscymnus coelolepis (Somniosidae), leafscale gulper shark Centrophorus squamosus (Centrophoridae) and birdbeak dogfish Deania calcea (Centrophoridae), gathering data from several geographical areas from the Atlantic, Indian and Pacific Oceans. For each species we analysed the sex ratio and the spatial patterns of reproductive stages within regions, considering the influence of geographical area, depth, season, temperature and Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site 2 salinity. The combination of statistical methods used in this study successfully identified a number of life history patterns which reflect different use of habitats by sex and life cycle stage. Pregnant females of the three species are spatially segregated, inhabiting shallower and/or warmer waters. In the case of the leafscale gulper shark this segregation might be associated with large scale migrations. In contrast, in Portuguese dogfish all adult maturity stages occur in the same geographical area. Pregnant female birdbeak dogfish were rare in all samples. Larger immature specimens of all the three species distribute deeper than the remaining maturity stages in most of the regions analysed. Mature males of leafscale gulper shark and birdbeak dogfish were more broadly distributed than mature females, supporting the possibility of sex-biased dispersal. Neonates and small sized specimens were scarce in the Northeast Atlantic potentially explained by their concentration in nurseries, and/or by gear selectivity. Management measures will benefit from considering the geographic scale of demographic variation between species. However, standardized collaborative approaches will be needed for comprehensive assessment.

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Actinospores released from the marine oligochaete Limnodriloides agnes inhabiting a Southern Portuguese fish farm are molecularly recognized as developmental stages of the life cycle of Ortholinea auratae, a myxosporean parasite that infects the urinary bladder of Sparus aurata. The molecular analysis of the 18S rRNA gene reveals a similarity of 99.9 to 100 % of the actinospores analyzed to the myxospores of O. auratae. The actinospores belong to the triactinomyxon morphotype and occur in groups of eight within pansporocysts that develop in the intestinal epithelium of the oligochaete host. This is the first record of a myxosporean using an oligochaete as its invertebrate host in the marine environment.