# Marine Heatwaves, Ocean Warming and Acidification Reshape Reef Fish Gut Microbiomes

## TL;DR

Marine heatwaves, warming, and acidification are changing the gut microbes of reef fish, with different effects on tropical and subtropical species.

## Contribution

This study reveals how climate stressors reshape gut microbiomes in reef fish species with distinct ecological responses.

## Key findings

- A. vaigiensis showed reduced gut microbiome diversity and increased Vibrio bacteria at warmer and more acidic reefs.
- M. strigatus had increased microbiome diversity at warm reefs, but this was lost at extreme reefs.
- Microbiome changes in both species were not linked to physiological performance metrics.

## Abstract

Extreme climatic events and gradual climate change are increasingly anticipated to interact and reshape ecological communities. However, the combined effects of ocean warming, acidification and marine heatwaves on host‐associated microbial communities and their potential role in host adaptation remain poorly understood. Here, we assessed shifts in gut microbiome communities and their associations with physiological performance in one tropical (
Abudefduf vaigiensis
) and one subtropical (
Microcanthus strigatus
) reef fish species, across three temperate reefs representing natural analogues of climate change: a present‐day baseline (‘cool reef’), a chronically warmed reef (‘warm reef’) and a reef experiencing combined warming and extreme acidification (‘extreme reef’). We also examined gut microbiome changes in
A. vaigiensis
before and during a severe marine heatwave.
A. vaigiensis
had lower gut microbiome evenness and diversity at the warm (43% and 44% decrease, respectively) and extreme (38% and 31% decrease) reefs compared to the cool reef, and its gut microbiome community shifted at the extreme reef with a 122% increase in abundance of opportunistic bacteria Vibrio.
A. vaigiensis
also had lower gut microbiome richness at the warm (42% decrease) and extreme (52% decrease) reefs during the heatwave compared to pre‐heatwave individuals. In contrast,
M. strigatus
showed higher microbiome evenness (99% increase) and diversity (98% increase) at the warm reef compared to the cool reef; however, these gains were lost at the extreme reef, with microbiome diversity and evenness returning to cool reef levels. Microbiome changes in both species were generally not associated with their physiological performance (protein content, oxidative stress, antioxidant capacity or body condition). Our findings suggest that marine heatwaves, ocean warming and acidification can reshape reef fish gut microbiomes, driving simplification in
Abudefduf vaigiensis
but distinct restructuring in
Microcanthus strigatus
. We conclude that climate‐driven microbiome reshuffling may alter host–microbiome relationships and functions in fishes in a future ocean.