Corals are often described as the rainforests of the sea. They build complex reef structures, support extraordinary biodiversity and sustain coastal ecosystems around the world. But a coral is not a single organism working alone. It is a partnership between the animal host and a diverse community of microscopic partners, including photosynthetic algae, bacteria, archaea, fungi and other microorganisms. Together, these partners form what is known as the coral holobiont. For many years, coral microbiome research has helped reveal which microbes live with corals. This has been incredibly valuable, but it also leaves an important question unanswered: what are these organisms actually doing?

This question was the starting point for our study, now published in Microbiome. We wanted to move beyond describing the members of the coral-associated community and instead ask a functional question: within the coral Porites lutea, which members of the holobiont are active, where are they active, and what biological processes are they contributing to? RNA-seq gave us a way to approach this question. DNA-based methods can show which genes are present in a community, but genes that are present are not always being used. RNA captures genes being expressed at the time of sampling, allowing us to examine the active biology of the coral holobiont.

A key feature of this study was that the coral was not treated as a single uniform sample. A coral contains different internal compartments, each with its own physical and biological environment. We focused on three compartments: the coral tissue, the green endolithic algal layer dominated by Ostreobium, and the deeper coral skeleton. These layers are close to one another, but they are not the same habitat. Light, nutrients, oxygen and microbial community structure can all vary across these spaces. This compartment-level view allowed us to ask not only which organisms were active, but also where their activity was taking place. The coral tissue, the Ostreobium layer and the deeper skeleton each contained distinct metabolically active communities, showing that the coral skeleton is not simply a passive structure underneath the living tissue, but an active microbial habitat with its own biological processes.

Working with coral RNA-seq data is challenging because the data are inherently mixed. A sample can contain RNA from the coral animal, photosynthetic symbionts, endolithic algae, bacteria, archaea and other members of the holobiont. This means the analysis cannot stop at quantifying gene expression. It also requires careful assignment of transcripts to their likely biological source and interpretation in the context of the compartment they came from. This complexity also makes the approach especially valuable. Instead of producing only a list of microbes, RNA-seq can help map active functions across the holobiont. In this study, we focused on key processes involved in carbon, nitrogen and sulfur cycling, photosynthesis, sugar transport and the scavenging of reactive oxygen and nitrogen species. These functions are important because they relate directly to how the coral holobiont maintains its internal nutrient economy and responds to changing chemical conditions.

One major theme that emerged was metabolic redundancy. Different members of the holobiont appeared to contribute to similar broad nutrient-cycling functions. This redundancy may be important for stability. In a complex symbiotic system, having multiple organisms capable of contributing to key processes could help maintain function even when environmental conditions shift or when the activity of individual community members changes. Another important finding was the role of the Ostreobium layer. Ostreobium is a green endolithic alga that lives within the coral skeleton, beneath the tissue. It has long been suggested that endolithic algae may contribute to coral nutrition, particularly under stressful conditions. Our study provides transcriptomic evidence supporting the ability of Ostreobium to transfer fixed carbon to other members of the holobiont, including the coral host. This adds molecular-level evidence to a long-standing ecological idea: that life inside the coral skeleton may be actively supporting the coral above it.

The deeper skeleton also stood out. It is easy to imagine the coral skeleton as a mostly inert calcium carbonate framework, but the data showed metabolically active microbial communities in this compartment. These communities were involved in nutrient cycling and stress-related processes, including pathways associated with scavenging reactive oxygen and nitrogen species. Together, these findings support a more spatially organised view of the coral holobiont. The question is not simply “which microbes are present?” but “how are biological roles distributed across the coral?” This shift in perspective is important. In microbiome research, taxonomy is useful, but it does not always explain function. Functional approaches, especially when combined with careful compartment-level sampling, can reveal how different organisms contribute to the biology of the host-associated ecosystem.

This matters because corals are under increasing pressure from warming oceans, pollution and other environmental stressors. Understanding coral resilience will require more than knowing which species are present in healthy or stressed corals. We need to understand the processes that sustain the coral holobiont, how these processes are organised, and which members are actively involved. Our study provides a baseline view of active microbial functions in healthy Porites lutea. It shows that different coral compartments

contain distinct active communities, that nutrient-cycling functions are distributed across multiple holobiont members, and that the coral skeleton contains biologically active microbial habitats.

By looking beneath the coral surface, this study reveals hidden microbial activity within the coral structure itself. These findings add to a growing view of corals as dynamic, multi-partner biological systems, where the health and function of the whole depends on interactions across host tissues, symbiotic algae and microbial communities living both on and within the skeleton. More broadly, it highlights the value of RNA-seq for moving coral microbiome research from “who is there?” toward “who is doing what?”