The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis. Diseases and antibiotic administration are known to cause dysbiosis in farmed fish. Pathogen infections greatly affect the production of gilthead seabream, and antibiotic treatment is still frequently required. Here, we employed a 16S rRNA high-throughput metataxonomics approach to characterize changes in the gut, skin, and gill microbiomes occurring due to infection with Photobacterium damselae subsp. piscicida and subsequent antibiotic treatment with oxytetracycline (OTC), as well as during recovery. Although microbiota response differed between studied tissues, overall changes in composition, diversity, structure, and predicted function were observed in all mucosae. The skin and gill microbiomes of diseased fish became largely dominated by taxa that have been frequently linked to secondary infections, whereas in the gut the genus Vibrio, known to include pathogenic bacteria, increased with OTC treatment. The study highlights the negative impacts of disease and antibiotic treatment on the microbiome of farmed fish. Our results also suggest that fish transportation operations may have profound effects on the fish microbiome, but further studies are needed to accurately evaluate their impact.

Monogenean capsalids of the genus Neobenedenia are widespread parasites of wild and farmed marine fish, and represent a potential threat to mariculture due to their pathogenicity and ability to cause mortality in fish maintained in controlled conditions. The identification of Neobenedenia species and, consequently, the definition of their host specificity is often problematic due to their highly conserved morphology; therefore, in order to establish their specific identity, microscopic observation should be complemented with molecular analysis. The present work aims at characterizing Neobenedenia specimens infecting the skin of cage reared gilthead seabream Sparus aurata from Portugal. Parasite samples obtained from caged fish were processed for morphological analysis, through observation in light and scanning electron microscopy, and for molecular analysis, through amplification and sequencing of 28S rDNA and cytB, aimed at identifying them to the species level. Our results showed that the collected parasites belonged to the species Neobenedenia girellae; the susceptibility of S. aurata towards this pathogenic capsalid monogenean highlighted in the present work represents an important risk in the farming of this valuable fish species.

Routine aquaculture practices such as capture, transportation, and handling can disrupt the relationship between commensal and opportunistic bacteria in the fish skin microbiome. Anesthetic baths are a common welfare practice in aquaculture to reduce stress during handling. However, to date, no studies assessed the effect of anesthetics on bacterial communities in fish skin mucus. This study is the first to evaluate the influence of benzocaine, a widely used anesthetic, on the skin mucus bacterial microbiome of Atlantic salmon reared in a recirculating aquaculture system (RAS). Using Illumina high-throughput 16S rRNA gene sequencing, we found that bacterial richness and diversity were significantly reduced in skin mucus samples from fish with anesthesia (ANE) when compared with those without anesthesia (CTR). The predominant bacterial classes in both groups were Gammaproteobacteria (54.1–62.6%) and Betaproteobacteria (22.6–22.9%). However, significant dissimilarities in beta diversity were observed between the bacterial community structure of salmon skin mucus samples from ANE and CTR. These findings demonstrate that benzocaine exposure alters skin mucus microbiome of Atlantic salmon potentially leading to dysbiosis. This study also provides baseline information on the bacterial communities of Atlantic salmon skin mucus microbiome in an RAS. As no temporal resampling was performed, the duration and persistence of these changes remain unknown and warrant further investigation.