Novel sampling reveals microbial changes during gill disease on Irish salmon farm

A non-lethal sampling method combined with cutting-edge molecular analysis has shed new light on microbial interactions in Atlantic salmon gills during a gill disease outbreak.

Researchers from National University of Ireland, Galway, used a new DNA extraction approach to sequence the gill microbiomes of 105 salmon, sampled at random on a fish production site over the course of a summer.

They found that before signs of gill disease became apparent in July, the bacterial genera Dyadobacter, Shewanella and Pedobacter were at their highest abundance, with Shewanella significantly more abundant before the disease episode than during. This genus could be studied more closely in further investigations into the development of gill disease, the scientists noted.

“Other bacteria associated with various gill diseases were prominent on infected gills. Those included Candidatus Branchiomonas cisticola, Piscirickettsia salmonis, Piscichlamydia sp. and Candidatus Fritschea sp., the presence of which on salmon gills during the episode may have contributed to gill damage, increasing the severity of the already existing gill lesions,” they continued.

As disease progressed, the gill microbiome of sampled salmon shifted toward lower diversity and less balance. Environmental factors such as water clarity and salinity explained 31% of the variability in microbial communities, while Neoparamoeba perurans, the bacteria which causes amoebic gill disease, explained 5%.

Gill scraping shows suitable sensitivity

The study also revealed that scraping gill mucus, a non-lethal sampling approach, provides comparable data to lethal sampling of fish gills. In particular, the technique appeared to be more reliable when targeting N. perurans.

“Bacterial communities from gill and mucus samples from this study presented very close similarities, suggesting that mucus scraping can be suitable for gill sampling for partial characterization of the whole-gill prokaryotic community,” the researchers said.

“Future research comparing these two sampling types can provide further evidence in this topic.”

Much research on gill disease has been conducted in laboratories, the researchers noted, and the combination of results from laboratory and field trials should improve overall understanding of this highly prevalent disease among farmed salmon.




Read the full article in the journal Scientific Reports.