RNA-seq sheds light on “who is doing what” in the coral Porites lutea

BACKGROUND: The coral holobiont functions as a complex biogeochemical system, sustained by intricate metabolic exchanges between the host and its associated microbiome. While the taxonomic diversity of these communities is well documented, the specific metabolic roles and biogeochemical contributions of microorganisms across distinct coral compartments, particularly within the endolithic habitats, remain poorly understood. Using RNA-seq, we investigated the active microbiome of healthy stony coral Porites lutea, focusing on the coral tissue, the green endolithic algal layer (Ostreobium layer), and the deeper coral skeleton. RESULTS: We identified distinct, metabolically active communities within these compartments and highlight substantial metabolic redundancy across carbon, nitrogen, and sulfur pathways. Our study provides the first transcriptomic evidence of Ostreobium's ability to transfer fixed carbon to other holobiont members and the coral host. We highlight the critical roles of diverse coral holobiont members in nutrient cycling and maintaining homeostasis through scavenging of reactive oxygen and nitrogen species. CONCLUSIONS: This study provides a novel molecular-level understanding of the functional roles played by diverse coral holobiont members in their respective compartments and underscores that corals harbor distinct microbiomes with wide-ranging functions. Video Abstract.