Exploration of the biosynthetic potential of the Populus microbiome
Patricia M. Blair, Miriam L. Land, Marek J. Piatek, Daniel A. Jacobson, Tse-Yuan Lu, Mitchel J. Doktycz, and Dale A. Pelletier
2 October 2018 mSystems 3(5): e00045-18; doi: 10.1128/mSystems00045-18
Natural products (NPs) isolated from bacteria have dramatically advanced human society, especially in medicine and agriculture. The rapidity and ease of genome sequencing have enabled bioinformatics-guided NP discovery and characterization. As a result, NP potential and diversity within a complex community, such as the microbiome of a plant, are rapidly expanding areas of scientific exploration. Here, we assess biosynthetic diversity in the Populus microbiome by analyzing both bacterial isolate genomes and metagenome samples. We utilize the fully sequenced genomes of isolates from the Populus root microbiome to characterize a subset of organisms for NP potential. The more than 3,400 individual gene clusters identified in 339 bacterial isolates, including 173 newly sequenced organisms, were diverse across NP types and distinct from known NP clusters. The ribosomally synthesized and posttranslationally modified peptides were both widespread and divergent from previously characterized molecules. Lactones and siderophores were prevalent in the genomes, suggesting a high level of communication and pressure to compete for resources. We then consider the overall bacterial diversity and NP variety of metagenome samples compared to the sequenced isolate collection and other plant microbiomes. The sequenced collection, curated to reflect the phylogenetic diversity of the Populus microbiome, also reflects the overall NP diversity trends seen in the metagenomic samples. In our study, only about 1% of all clusters from sequenced isolates were positively matched to a previously characterized gene cluster, suggesting a great opportunity for the discovery of novel NPs involved in communication and control in the Populus root microbiome.
Blair, P. M., M. L. Land, M. J. Piatek, T.-Y. S. Lu, D. Jacobson, M. J. Doktycz and D. A. Pelletier (2018). “Exploration of the biosynthetic potential of the Populus microbiome.” mSystems 3(5): 300045-18.