Prevalence of six amoeba species colonising the gills of farmed Atlantic salmon with amoebic gill disease (AGD) using qPCR

Amoebic gill disease (AGD) is the primary health concern for Atlantic salmon Salmo salar farmed in Tasmania, Australia. Neoparamoeba perurans is the aetiological agent of AGD; however, a diversity of other amoebae colonise the gills, and their role in AGD is unknown. Previous studies which document these accompanying amoebae on AGD-affected farmed Atlantic salmon relied on culture-based techniques which do not accurately determine the prevalence and abundance of these species nor whether they correlate with AGD pathology. Drawing on our previous culture-based study, here we develop and apply 5 new Taqman quantitative PCR (qPCR) assays to profile the prevalence of multiple amoeba species on the gills of AGD-affected Atlantic salmon held at 2 Tasmanian farm sites over a 1 yr period. The prevalence and abundance of N. perurans was also assessed using a previously established qPCR method. N. perurans was the dominant species, and its abundance positively correlated with the progression of gross gill pathology. Only a small number of sporadic detections of Pseudoparamoeba and Vannellida species were observed. Nolandella spp. was the notable exception, as it was the most prevalent amoeba (92 %) at 1 site at 1 sample time, during which no N. perurans were detected on gills but low levels of gross gill pathology were observed. N. perurans is the predominant species and primary pathogen of AGD; however, there were instances when they were not detected on diseased gills and Nolandella spp. were highly prevalent. The significance of Nolandella spp. in relation to AGD is not yet understood.