Northern pike (Esox lucius) young-of-year gut microbiota and associations with wetland nursery water microbial communities in the St. Lawrence River

The core-microbiome hypothesis postulates that key fish gut microbiota develop independently from the environment they exist in. Fish nursery habitats serve as critical environments early in ontogeny that support fish growth and development, but their relationship to the development of gut microbiota is poorly understood. We compared gut microbiota of first growing season northern pike (Esox lucius) and source water from two spatially distinct nursery wetlands to examine their potential association and as a field test of the core-microbiome hypothesis. Microbial communities within the pike hindguts and associated water column samples were characterized through metabarcoding and sequencing of the 16S rRNA gene. As expected, community level non-metric multidimensional scaling analysis revealed significant separation in microbial community composition between fish and water samples. Unifrac distances indicated no significant dissimilarity among fish gut and source water combinations compared to fish gut samples pairwise tested with non-source water samples, suggesting similar patterns of in vivo selection of the gut microbiome. This was consistent among habitats for three of four dominant hindgut bacterial genera (Aeromonas spp., Clostridium sensu stricto, and Plesiomonas spp.). Cetobacterium spp. was an exception, where they dominated fish guts in one wetland system. Because these four-core gut microbiota were only minor components of the source water environment, it is possible that environmental exposure is a selective process in the developing fish gut. Further experimental and field research with examination of the influence of diet is needed to isolate mechanisms involved in gut microbiome development in freshwater fishes.