Effect of early rearing conditions on the behaviour and microbiome of fish with low genetic diversity

Fish performance is influenced by their genotype and environment. For populations with low genetic diversity, adaptation to environmental change can be compromised, but it has been suggested that the microbiome can act as an additional source of variability. Early rearing conditions can be particularly important for fish development and behaviour, due to their dependence on the environmental conditions. This thesis explored the interactions between fish genotype and rearing environment (diet and enrichment) on behaviour, metabolic rate and microbiome (gut, skin) using captive and wild populations of naturally inbred mangrove killifishes (Kryptolebias sp.), where the exploratory behaviour and closed respirometry were used to test the captive killifish and microbiome diversity analyses were performed in both captive and wild killifishes. Behavioural trials in self-fertilizing killifish (Kryptolebias marmoratus) indicated a significant effect of both genetic strain and rearing environment (environmental enrichment and diet) on fish activity measurements. Incubation time also had a substantial role on both fish behaviour and microbiome diversity. Gut-microbiome alpha diversity was shaped by strain, diet, and hatching time in K. marmoratus with interactions between diet and physical enrichment. An intergenerational influence of rearing environment on fish behaviour was detected in K.armoratus, where parental activity was found to influence offspring activity. Gut-microbial comparisons between parents and offspring identified Vibrionaceae as the dominant colonizers in laboratory reared K. marmoratus. A dominant effect of the rearing environment over strain on both microbiome composition and distribution was observed. The influence of the interaction between parental and own environments on microbiome alpha diversity in K. marmoratus offspring suggests long-term effects of the rearing environment on the fish (gut) microbiome. In the wild, results from the outcrossing K. ocelatus and the self-fertilising K. hermaphroditus identified that the diversity and community composition of the skin microbiome were strongly shaped by their environment but also by the species and host genetic diversity at different levels. This study also found first-time evidence of a relationship between microbiome and epigenetic diversity in these wild populations, suggesting that both mechanisms could be potential sources of additional variability for fish species with low genetic diversity. The global findings of this thesis on mangrove killifishes from different origins (laboratory and natural conditions) highlighted the importance of the interactions between genotype and environment in shaping fish microbiome composition and diversity.