Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs

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.

Evaluation of the genotoxic potential of water impacted by acid mine drainage from a coal mine in Mpumalanga, South Africa, using the Ames test and Comet assay

Several potential genotoxins found in water samples arise from anthropogenic activities. Acid mine effluent resulting from coal mining poses serious environment concerns all over the world. The use of toxicity tests to evaluate the quality of streams add value by providing site-specific toxicological data. Treatment systems such as the use of natural wetlands (passive) or conventional physical and chemical pH-neutralised processes (active) are employed mainly to meet certain water quality guidelines. Nonetheless, potential genotoxins or residues remain which influence the quality of discharged effluents. The objective of this study was to evaluate the genotoxic potential of acid mine drainage (AMD) released into a natural stream following treatment by passive and active methods. This study aimed to identify the extent of AMD mutagenicity and genotoxicity to African Vero monkey kidney cell line and a fish gill cell line (RTgill-W1) using two assays, the Ames test, and the comet assay, as a rapid and effective screening tool. The Ames test performed without metabolic activation using Salmonella typhimurium TA98 and TA100 strains showed no indication of mutagenicity in the water samples tested. Differing results were however obtained for the comet assay using the African Vero monkey kidney cell line and a fish gill cell line (Rtgill-W1), which revealed DNA fragmentation and variations in morphologies indicative of genotoxicity in the water samples following the two treatment processes. A significant reduction in DNA damage was observed in water samples following active treatment of the AMD, evidenced by reduced damage frequency and a lowered comet score. This bioassay confirms the urgency of integrating high-throughput screening in aquatic toxicity assessment at genetic levels, giving further evidence that in-vitro bioassays can be incorporated for use in short-term genotoxicity assays. The result suggests that the comet assay proved sensitive at detecting genotoxicity, supporting the integration of this into environmental monitoring frameworks targeted at AMD-contaminated sites.

Distribution of metals in Labeo coubie (Ruppel, 1832) from a National Park river in Nigeria

This study assesses heavy metals distribution in body parts of Labeo coubie (African carp) fromRiver Oli, in Kainji Lake National Park as pollution index of the ecosystem. Fish parts samples (gills, muscles andvertebra bone) were prepared and specifically analyzed for the levels of Pb, Cr, Zn, Cu, Fe and Cd using Atomicabsorption spectrophotometry. The concentration of metals in the samples at different concentrations ranged from0.001±0.000 μg/g for Cd to 224.87±4.07 μg/g of Fe in the fish gill. There is significant (p<0.05) differences in the Pb,Zn, Cu and Fe concentrations across the different fish parts with gills accumulated the highest levels metals while Crlevels significantly (p<0.05) differed in the fish body parts and accumulated more in the muscles (10.75±0.15 μg/g).The mean concentrations of metal elements in the fish parts had shown some distinguish connection in its distributionswith Pb and Cu; Gills > Muscles > Vertebra bones, Fe and Zinc; Gills > Vertebra bones > Muscles while Cr wasdistributed in Muscles > Gill > Vertebra bones. However, it is revealed that Labeo coubie, a euryphagus fish probablyabsorb these metals through ingestion of contaminated food or absorption by the gills and bioaccumulate in differentfish parts. It is therefore established that River Oli is contaminated with heavy metals as presence of these metals infish is an indication of its immediate environment. Keywords: absorption, bioaccumulation, fish parts, heavy metals, pollution

Developing in vitro models to assess fish gill excretion of emerging contaminants

Advances in analytical methods have enabled the detection of emerging contaminants at ever lower concentrations in freshwaters. However, such measurements need to be linked to effect-based assays to identify risks....