Background Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome. Results The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members. Conclusions Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research.
Gelatinous plankton present a challenge to marine fish aquaculture that remains to be addressed. Shifting plankton distributions, suggested by some to be a result of factors such as climate change and overfishing, appear to be exacerbated by anthropogenic factors linked directly to aquaculture. Fish health can be negatively influenced by exposure to the cnidarian hydrozoan and scyphozoan life stages commonly referred to as “jellyfish”. Impact is particularly pronounced in gill tissue, where three key outcomes of exposure are described; direct traumatic damage, impaired function, and initiation of secondary disease. Cnidarian jellyfish demonstrated to negatively impact fish include Cyanea capillata, Aurelia aurita, and Pelagia noctiluca. Further coelenterates have also been associated with harm to fish, including sessile polyps of species such as Ectopleura larynx. An accurate picture of inshore planktic exposure densities within the coastal environments of aquaculture would aid in understanding cnidarian species of concern, and their impact upon fish health, particularly in gill disease. This information is however presently lacking. This review summarises the available literature regarding the impact of gelatinous plankton on finfish aquaculture, with a focus on cnidarian impact on fish health. Present strategies in monitoring and mitigation are presented, alongside identified critical knowledge gaps.
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