Skin and Blood Microbial Signatures of Sedentary and Migratory Trout (Salmo trutta) of Kerguelen Islands

Abstract

Our understanding of how microbiome signatures are modulated in wild fish populations remains poorly known and has, until now, mostly been inferred from studies in commercial and farmed fish populations. Here, we have studied for the first time changes in the skin and blood microbiomes of the Salmo trutta population of the volcanic Kerguelen archipelago located at the northern limit of the Antarctic Ocean. Kerguelen is a natural framework of population expansion and a likely situation under further climate change in distribution areas. Our results showed that S. trutta of Kerguelen has a microbiome signature distinct from those of salmonids of the Northern Hemisphere. Our study also revealed that the skin and blood microbiomes differ between sedentary and migratory S. trutta. While 18 phyla were shared between both groups of trout, independent of the compartment, six phyla were unique to migratory trout. Further analyses showed that microbiome signatures undergo significant site-specific variations that correlate, in some cases, to the peculiarity of specific ecosystems. Our study also revealed the presence of potential pathogens at particular sites and the impact of abiotic factors on the microbiome, most notably due to the volcanic nature of the environment. This study contributes to a better understanding of the factors that modulate the microbiome signatures of migratory and sedentary fish populations. It will also help better monitor climate change's impacts on the colonization process in the sub-Antarctic region.

A niche-adapted brain microbiome in salmonids at homeostasis

“…Chitinobacteriaceae, however, only represented 1% and 1.8% of the total blood and spleen bacterial communities, respectively, but was detected in all brain samples at similar abundances to the gut. Burkholderiaceae and Propionibacteriaceae, frequently reported in salmonids gut and blood (24)(25)(26)(27)(28), were only detected in the blood and, at lower abundance, in the brain (Fig. 2B).…”