Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs’ gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods

• Published in: Evolutionary Applications
• Main Authors: Lavoie, Camille, Courcelle, Maxime, Redivo, Baptise, Derome, Nicolas
• Other Authors: Institut de Biologie Intégrative et des Systèmes Québec (IBIS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2018
• Subjects: 16S SSU rRNA gene; aquaculture; Atlantic salmon; host–microbiota interactions; metabarcoding sequencing; microbial ecology; stocking; [SDV]Life Sciences [q-bio]; [SDV.BBM]Life Sciences [q-bio]/Biochemistry; Molecular Biology; [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology; Salmo salar
• Online Access: https://hal.science/hal-03125533; https://hal.science/hal-03125533/document; https://hal.science/hal-03125533/file/eva.12658.pdf; https://doi.org/10.1111/eva.12658

International audience Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery‐raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild‐born parrs’ gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, because the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs’ gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs’ microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery‐reared parrs.