Abstract
Polyketides (PK) and nonribosomal peptides (NRP) are two microbial secondary metabolite (SM) families largely known for their variety of functions, including antimicrobials, siderophores and others. Despite their involvement in bacteria-bacteria and bacteria-plant interactions, root-associated SM are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity, composition and expression of SM-encoding biosynthetic gene clusters (BGC) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) relative to the adjacent bulk soil, and specific BGCs were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with BGCs encoding antimicrobials, the low similarity to characterized genes suggests their potential novelty. A subset of these genes were screened against a large set of soil-derived cosmid libraries, from which five whole NRPS/PKS BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria, while the remaining two were associated with hosts of unknown phylogeny. One Streptomyces-derived BGC was predicted to encode for a polyene with potential antifungal activity, while the others were too novel to predict. Screening against a suite of metagenomic datasets revealed that all clusters were profuse in soil and roots, and almost completely absent in aquatic and gut environments, supporting the notion that they play a specific role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of yet undiscovered SM.
Importance We identified distinct secondary metabolite (polyketide and nonribosomal peptide) encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems, yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding for antimicrobials and siderophores, although the high sequence variability suggests that they encode for novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary metabolite encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes are undoubtedly required for bacterial colonization and persistence in the root environment and are most likely associated with inter-bacterial and bacterial-plant interactions.
Competing Interest Statement
The authors have declared no competing interest.
