The coral skeleton contains a colorful and animated world of endolithic life forms, ranging from macro- and microorganisms, including sponge, algae, protists, bacteria, archaea, and viruses. Until recently, little attention was paid to the role of microbes in the ecological functions for corals, with the exception of the dominant endolithic algae Ostreobium. Our team (Yang et al., 2016; 2019) and other researchers uncovered glut of endolithic microbes that range in diversity, composition, and functions using contemporary methods such as metacording methods, whole-genome shotgun metagenomics, FISH-Nano SIMs, and stable isotope labelling. I highly recommend two comprehensive review articles recently published in Microbiome and ISME J (Ricci et al., 2019; Pernice et al., 2020) that introduce and update the most recent discoveries on coral endolithic microbes, and emphasize evidence that endolithic microbes are important for coral health, resilience to stress and disease, and nutrient supply. Furthermore, environmental factors in the coral skeleton are critical drivers that make endolithic microbes dynamic and changeable. For example, diurnal changes in oxygen concentration may cause dynamic shifts in aerobic and anaerobic communities; moreover, light availability also affects phototrophic microbes delicately in finding their new micro-niches in the skeleton.

After publishing our findings on endolithic microbes in 2019, Dr. Shan-Hua Yang, accepted a tenure-track faculty position at National Taiwan University, the best university in Taiwan. She continues to study coral-associated bacteria, including coral skeleton microbiology. We are now using metabolomics and stable isotope-labelling approaches to investigate the mechanism and chemicals involves in the interaction between endolithic bacteria and their coral hosts. Moreover, we continue to explore the green layer, which constitutes specific green sulfur bacteria called coral-associated Prosthecochloris (CAP), in the coral Isopora palifera, and have uncovered more specific micro-niches in the tiny layer that are actually occupied by different CAP groups (Fig 1), suggesting that a) the coral skeleton houses more diverse, heterogeneous micro-niches than previously thought and b) the environmental properties of these micro-niches can vary. It also suggests that the ecological functions of coral skeleton microbes are dynamic, complex, and far reaching.

Although studying coral skeleton bacteria often involves technical challenges—such as difficulties with cultivation, scarce genetic materials for microbes of interest, changes in microbial assembly, diverse micro-niches, etc.—determining the ecological roles of microbes in corals is indispensable for understanding the coral skeleton. More research is definitely needed, particularly direct evidence of how endolithic microbes function with their coral hosts—this is the most interesting and challenging research question in my laboratory.     

Reference

1. Pernice, M., Raina, JB., Rädecker, N. et al.Down to the bone: the role of overlooked endolithic microbiomes in reef coral health. ISME J 14, 325–334 (2020).
2. Ricci, F., Rossetto Marcelino, V., Blackall, L.L. et al.Beneath the surface: community assembly and functions of the coral skeleton microbiome. Microbiome 7, 159 (2019).
3. Yang, S.-H., Lee, S. T. M., Huang, C.-R., et al. Prevalence of potential nitrogen-fixing, green sulphur bacteria in the skeleton of reef-building coral Isopora palifera, Limnology and Oceanography 61, 1078–1086 (2016)
4. Yang, SH., Tandon, K., Lu, CY. et al.Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera. Microbiome 7, 3 (2019)