Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics

While
thousands of environmental metagenomes have been mined for
the presence of novel biosynthetic gene clusters, such computational
predictions do not provide evidence of their in vivo biosynthetic functionality. Using fluorescent in situ enzyme assay targeting carrier proteins common to polyketide (PKS)
and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated
cell sorting to tunicate microbiome to enrich for microbes with active
secondary metabolic capabilities. Single-cell genomics uncovered the
genetic basis for a wide biosynthetic diversity in the enzyme-active
cells and revealed a member of marine Oceanospirillales harboring a novel NRPS gene cluster with high similarity to phylogenetically
distant marine and terrestrial bacteria. Interestingly, this synthase
belongs to a larger class of siderophore biosynthetic gene clusters
commonly associated with pestilence and disease. This demonstrates
activity-guided single-cell genomics as a tool to guide novel biosynthetic
discovery.