Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon

Abstract

Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.

Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii)

“…Deep investigations of host-associated microbiota through high-throughput sequencing technologies can illuminate microbiota dynamics and their influential factors, and aid the engineering of microbiota-based solutions to disease prevention in an unprecedented manner ( Borges et al, 2021 ). Even though deep sequencing data based on 16S rDNA amplicons of teleost microbiota are now accumulating, the data on the whole microbiota of the early life stages are limited ( Duval et al, 2022 ; Lokesh et al, 2024 ). Further, the transition during the ontogeny of fish and the establishment of their microbial communities are relatively less explored.…”