Michele De Noia

Lacking a peptidoglycan cell wall, mycoplasmas are the smallest self-replicating life forms. Members of this bacterial genus are known to parasitise a wide array of metazoans including vertebrates. Whilst much research has been significant targeted at parasitic mammalian mycoplasmas, very little is known about their role in other vertebrates. In the current study, we aim to explore the biology and evolution of Mycoplasma in salmonids, including cellular niche, genome size structure and gene content. Using Fluorescence in-situ hybridisation (FISH), mycoplasmas were identified in epithelial tissues across the digestive tract (stomach, pyloric caecum and midgut) during the developmental stages (eggs, parr, subadult) of farmed Atlantic salmon ( Salmo salar ), showing a high abundance in acidic compartments. With high throughput sequencing from subadults farmed Atlantic salmon, we assembled a nearly complete genome (~0.57 MB) via shotgun-metagenomics. The phylogenetic inference from the recovered genome revealed successful taxonomic proximity to Mycoplasma penetrans (~1.36 Mb) from the recovered genome. Although, no significant correlation between genome size and its phylogeny was observed, we recovered functional signatures, especially, riboflavin encoding genes pathway and sugars transporters, suggesting a symbiotic relationship between Mycoplasma and the host. Though 247 strains of Mycoplasma are available in public databases, to the best of our knowledge, this is the first study to demonstrate ecological and functional association between Mycoplasma and Salmo salar which delineates symbiotic reductive evolution and genome erosion primarily and also serves as a proxy for salmonid health in aquaculture processes (cell lines, in vitro gut models).

Anguillicoloides crassus is an invasive nematode parasite of the European eel, Anguilla anguilla , and one of the primary drivers of eel population collapse. The presence of the parasite has been shown to impact many features of eel physiology and life history. Early detection of the parasite is vital to limit the spread of A. crassus . However, until recently, accurate diagnosis of infection could only be achieved via terminal dissection. To support A. anguilla fisheries management in the context of A. crassus we developed a rapid non-lethal and non-invasive environmental DNA method to detect the presence of the parasite in the swim bladder. Screening of 131 wild eels was undertaken between 2017 and 2019 Ireland and UK to validate the procedure. DNA extractions and PCR were conducted using both a Qiagen Stool kit at Glasgow University and in situ using Whatman qualitative filter paper No. 1 and a miniPCR DNA Discovery System™. Primers were specifically designed from the cytochrome oxidase mtDNA gene region. In situ extraction and amplification takes approx. 3h for up to 16 individuals with higher specificity and sensitivity compare to the laboratory Qiagen kit extraction. The local diagnostic procedure demonstrated Positive Predictive Values at 96% and Negative Predictive Values at 87%. Our method will be a powerful tool in the hands of fisheries managers to help protect this iconic but critically endangered species. It will allow a non-invasive monitoring of the A. crassus dispersion across the European waters.

The soft-shell clam Mya arenaria is one of the most ancient invaders of European coasts and is present in many coastal ecosystems, yet little is known about its genetic structure in Europe. We collected 266 samples spanning a latitudinal cline from the Mediterranean to the North Sea and genotyped them at 12 microsatellite loci. In parallel, geometric morphometric analysis of shell outlines was used to test for associations between shell shape, latitude and genotype, and for a selection of shells we measured the thickness and organic content of the granular prismatic (PR), the crossed-lamellar (CL) and the complex crossed-lamellar (CCL) layers. Strong population structure was detected, with Bayesian cluster analysis identifying four groups located in the Mediterranean, Celtic Sea, along the continental coast of the North Sea and in Scotland. Multivariate analysis of shell shape uncovered a significant effect of collection site but no associations with any other variables. Shell thickness did not vary significantly with either latitude or genotype, although PR thickness and calcification were positively associated with latitude, while CCL thickness showed a negative association. Our study provides new insights into the population structure of this species and sheds light on factors influencing shell shape, thickness and microstructure.