Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown. This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB’s abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP. We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.

Coral reef ecosystems support over a quarter of the world’s marine life and play important ecological and economic roles. However, the increasingly severe weather events associated with ocean warming and climate change are believed to be rapidly altering the functions of coral reefs and their ecosystems. Corals and their associated microbiota form a “holobiont,” which includes symbiotic algae and other associated microbiota dominated by bacteria. These microbiota have a direct relationship with the health of the coral host. Their composition is influenced by various environmental factors, such as increasing sea water temperatures. Previous studies of the effects of temperature changes on coral physiology and associated bacterial communities have been conducted based on stable water temperatures set by mean temperatures, or by slowly increasing/decreasing temperatures. However, the daily temperature fluctuations that corals experience in nature are not stable. Rather, there may be significant differences of up to 6°C in a single day. The current understanding of the effects of large daily temperature fluctuations on coral and associated bacterial community dynamics is limited. Hence, in this study, we conducted a four-week tank experiment using different large daily temperature fluctuations accompanied by continuous warming conditions to investigate the effects on two common reef-building corals, Stylophora pistillata and Pocillopora acuta , in Taiwan. During the experiment, the activity of coral host catalase was measured, the photosynthetic ability of symbiotic algae was recorded, and the variation in bacterial communities was analyzed using the V6-V8 region of 16S rDNA. According to the results, different parts of the holobionts of different coral species exhibited varying response rates to the continuous warming conditions and diurnal temperature fluctuations. Additionally, it was found that diurnal temperature fluctuations may mitigate the heat stress on the host and reduce the changes in bacterial response to warming. Furthermore, the holobionts of different coral species may adopt different adaptation and survival strategies in response to diurnal temperature fluctuations and warming. Finally, based on the response of these two coral species under the conditions of diurnal temperature fluctuations and continuous warming, Acinetobacter and Rhodobacteraceae were identified as potential indicator coral-associated bacteria. This is the first study to investigate the tripartite dynamic response of coral, symbiotic algae and bacteria to daily temperature fluctuations.

Octocorals are keystone reef species and sources of valuable bioactive compounds, yet the microbial dynamics underlying their acclimation to cultivation remain poorly characterized. We examined whether transplanted corals would show differential recovery trajectories between bacterial community and metabolome, and explored the potential role of microbial functional redundancy in shaping holobiont resilience. To address this, we analyzed a 19‑week multi‑omics time series dataset (16S rRNA sequencing, amino‑acid and lipid profiling) from transplanted octocorals, Lobophytum sp. and Sclerophytum sp., benchmarked against wild reef baselines. Bacterial communities diverged initially, converged by week 12, and re‑diverged by week 19, whereas metabolomes consistently converged toward wild norms despite species-specific variations. Integration of microbial and metabolomic data further revealed that microbe–metabolite associations were restructured across environments, consistent with environment-driven reorganization of holobiont interactions. These findings characterize the temporal dynamics of octocoral bacterial communities during acclimation and identify metabolomic stability as a complementary indicator of holobiont resilience, with implications for monitoring and optimizing octocoral cultivation.