Diversity and predicted function of non-ribosomal peptides and polyketides in root microbial communities

The rhizosphere microbiome is known to positively affect plant health, for instance by inhibiting various plant pathogens. Non-ribosomal peptides and polyketides are secondary metabolites produced by complex enzymes encoded by large biosynthetic gene clusters (BGC) coined non-ribosomal peptide and polyketide synthases (NRPS/PKS). NRPS and PKS produced by soil bacteria are responsible for the synthesis of many siderophores and antimicrobials- but despite their ecological importance, little is known about their diversity and dynamics within microbe-plant interactions.

We aim to elucidate the scope, dynamics and potential function of bacterial secondary metabolites in the rhizosphere, specifically focusing on NRPS and PKS BGCs. We used culture-independent methods, namely amplicon sequencing, metagenome and meta-transcriptome, coupled with custom bioinformatic pipeline and manually-made and public secondary metabolites-related databases.

We found the diversity and abundance of NRPS and PKS BGCs on tomato and lettuce root surfaces was significantly different from that of the surrounding bulk soil. Large portion of these NRPS and PKS were unique to the root environment, and many of these were associated with genes encoding for antimicrobials and siderophores. Interestingly, the vast majority of identified NRPS and PKS amplicons shared only 70%-85% sequence identity to publicly known clusters. We also found a distinct expression profile of mined NRPS/PKS between root microbiomes of tomato and lettuce roots, highlighting phylogeny-related dependency of secondary metabolites synthesis.

To conclude, the rhizosphere microbiome harbors a profuse array of BGCs encoding potentially novel antibacterial and antifungal compounds that play a crucial role in bacterial-bacterial and bacterial-plant interactions and thereby shape this highly dynamic ecosystem.