Global-scale analysis reveals distinct patterns of non-ribosomal peptide and polyketide synthase encoding genes in root and soil bacterial communities

Abstract

● The overall abundance of secondary metabolites-encoding genes in soil and root microbiomes is similar.

● Certain biosynthetic gene clusters (BGCs) are ubiquitous and more abundant in roots compared with soil.

● The majority of identified BGCs are potentially novel.

Secondary metabolites (SMs) produced by soil bacteria, for instance antimicrobials and siderophores, play a vital role in bacterial adaptation to soil and root ecosystems and can contribute to plant health. Many SMs are non-ribosomal peptides and polyketides, assembled by non-ribosomal peptides synthetase (NRPS) and polyketide synthase (PKS) and encoded by biosynthetic gene clusters (BGCs). Despite their ecological importance, little is known about the occurrence and diversity of NRPs and PKs in soil. We extracted NRPS- and PKS-encoding BGCs from 20 publicly available soil and root-associated metagenomes and annotated them using antiSMASH-DB. We found that the overall abundance of NRPSs and PKSs is similar in both environments, however NRPSs and PKSs were significantly clustered between soil and root samples. Moreover, the majority of identified sequences were unique to either soil- or root-associated datasets and had low identity to known BGCs, suggesting their novelty. Overall, this study illuminates the huge untapped diversity of predicted SMs in soil and root microbiomes, and indicates presence of specific SMs, which may play a role in inter- and intra-bacterial interactions in root ecosystems.

Graphical abstract

Keywords

Secondary metabolites / Plant-microbe interactions / Non-ribosomal peptides / Polyketides / Rhizosphere microbiome / Soil microbiome

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