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Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics
- Van Goethem, Marc W;
- Osborn, Andrew R;
- Bowen, Benjamin P;
- Andeer, Peter F;
- Swenson, Tami L;
- Clum, Alicia;
- Riley, Robert;
- He, Guifen;
- Koriabine, Maxim;
- Sandor, Laura;
- Yan, Mi;
- Daum, Chris G;
- Yoshinaga, Yuko;
- Makhalanyane, Thulani P;
- Garcia-Pichel, Ferran;
- Visel, Axel;
- Pennacchio, Len A;
- O’Malley, Ronan C;
- Northen, Trent R
- et al.
Published Web Location
https://doi.org/10.1038/s42003-021-02809-4Abstract
Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.
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