Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0–30%). Fish gut microbiomes were significantly more variable at degraded reefs, a pattern driven by changes in the relative abundance of the most common taxa potentially associated with stress. We also demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which may suggest a less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions may be vulnerable to severe coral degradation.

Environmental degradation has the potential to alter key mutualisms that underline the structure and function of ecological communities. While it is well recognized that the global loss of coral reefs alters fish communities, the effects of habitat degradation on microbial communities associated with fishes remain largely unknown despite their fundamental roles in host nutrition and immunity. Using a gradient of reef degradation, we show that the gut microbiome of a facultative, coral-feeding butterflyfish (Chaetodon capistratus) is significantly more variable among individuals at degraded reefs with very low live coral cover (~0%) than reefs with higher coral cover (~30%), mirroring a known pattern of microbial imbalance observed in immunodeficient humans and other stressed or diseased animals. We demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which suggests a broader and less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions are vulnerable to severe coral degradation.

Temperature is a primary factor affecting the survival, development, and physiology of aquatic ectothermic animals and global warming of water bodies may therefore impact several biological levels of aquatic life. Understanding the effects of near-future predicted temperature changes on the behaviour and the underlying molecular mechanisms of aquatic animals is of particular importance, since behaviour mediates key interactions and, in turn, population dynamics. In this study, we investigate the effects of elevated developmental temperature on locomotor behaviour and olfactory learning in the zebrafish, Danio rerio. We exposed zebrafish from cleavage embryonic stage to either current day control (28°C) or predicted future elevated temperature (30°C) for seven days. Overall, warming reduced the total routine swimming distance and caused the upregulation of a small number of genes involved in metabolism and neuron development, suggesting accelerated development at elevated temperature. When fish were exposed to two different olfactory cues, namely catfish cue, a non-alarming but novel odour, and injured conspecifics alarm cue expected to cause a fear reaction, warming differently affected larvae response to the two cues. In particular, a large transcriptional reprogramming was observed at elevated temperature in response to novel odour exposure, with upregulation of cell signalling, neuron development and neuron functioning genes. As this response was coupled with downregulation of genes involved in protein translation and ATP metabolism, it indicates that novel odour recognition in future-predicted thermal conditions will require energetic trade-offs between expensive baseline processes and responsive functions. To also evaluate their learning abilities at both temperatures, 7 days post fertilization (dpf) zebrafish were conditioned with a mixture of injured conspecifics alarm cue and non-alarming catfish cue. Regardless of temperature, no behavioural (freezing) nor gene expression changes were detected, reinforcing our previous findings that warming mainly affects zebrafish molecular response to novel odours. Overall, our results show that future thermal conditions will likely impact developing stages, causing energy trade-offs following olfactory detection of novel substances in the environment.