rRNA depletion for holobiont metatranscriptome profiling across demosponges

Abstract

Despite the extensive knowledge of sponge microbiome diversity, a critical knowledge gap persists concerning the molecular mechanisms that govern host-symbiont interactions. Deciphering these mechanisms is crucial for understanding how sponge holobionts respond to environmental changes and identifying potential disruptions in sponge-microbe associations. A hindrance to progress in characterizing these molecular crosstalk mechanisms is the scarcity of broadly applicable molecular methods for efficiently sequencing meta-transcriptomes across a diverse array of sponge species. To tackle this challenge, we have introduced a hybrid-capture strategy capable of selectively depleting sponge and bacterial rRNA from total RNA extracts obtained from highly divergent demosponges with varying microbiome complexities. Our innovative pan-demosponge rRNA depletion approach streamlines the efficient characterization of metatranscriptomes within diverse demosponge holobionts, concurrently facilitating the quantification of gene expression in both the host and its microbiome. This methodological advancement represents a significant stride in unraveling the molecular intricacies of sponge-microbe interactions, providing a robust platform for future investigations across a broad spectrum of sponge species.