Genome Scale Metabolic Modeling Reveals New Insights into Biomass Production in the Marine Sponge Amphimedon Queenslandica

Marine sponges are among the simplest multicellular animals, but under this simple façade exists complex metabolic crosstalk between the host sponge and its symbiotic bacteria. Sponge bacterial symbionts perform diverse functions for their host, including anoxic respiration, denitrification of waste products and production of secondary metabolites that often attract pharmacological interest. Indeed sponges and their associated bacteria are the most prolific producers of bioactive compounds in the marine environment, with over 5000 compounds identified to date. Yet despite this enormous potential, only one compound has been approved for therapeutic use. The lack of commercial development of sponge-derived compounds is attributed to a biomass supply problem: no reliable method to culture sponges exists, either at the scale of the whole organism or as a cell culture. In addition, the current lack of understanding of the sponge microbiome interaction limits the applicability of metabolic engineering approaches to microbial isolates or sponge cells for over-production of secondary metabolites.

To better understand the metabolic processes underlying sponge growth, we want to apply genome scale modeling and flux analysis to the marine demosponge, Amphimedon queenslandica. As a first step, we have characterized the biochemical composition of A. queenslandica and the associated bacteria, essential information for metabolic modeling. We have complemented these methods with comprehensive, high resolution transcriptional profiling of developmental changes in gene expression throughout the sponge life cycle. This integrative approach will give the first detailed insights into sponge biomass production and will lay the basis for the metabolic reconstruction of a sponge / microbiome metamodel. This work will quantify carbon fluxes within a sponge holobiont for the first time.