TY - JOUR
T1 - Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics
AU - Van Goethem, Marc W.
AU - Osborn, Andrew R.
AU - Bowen, Benjamin P.
AU - Andeer, Peter F.
AU - Swenson, Tami L.
AU - Clum, Alicia
AU - Riley, Robert
AU - He, Guifen
AU - Koriabine, Maxim
AU - Sandor, Laura
AU - Yan, Mi
AU - Daum, Chris G.
AU - Yoshinaga, Yuko
AU - Makhalanyane, Thulani P.
AU - Garcia-Pichel, Ferran
AU - Visel, Axel
AU - Pennacchio, Len A.
AU - O’Malley, Ronan C.
AU - Northen, Trent R.
N1 - Funding Information:
This work was partially supported by funds provided by the Office of Science Early Career Research Program Office of Biological and Environmental Research, of the U.S. Department of Energy and by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 to Lawrence Berkeley National Laboratory. We also wish to acknowledge Simon Roux, Emiley Eloe-Fadrosh and Eoin Brodie for their constructive feedback.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - 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.
AB - 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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U2 - 10.1038/s42003-021-02809-4
DO - 10.1038/s42003-021-02809-4
M3 - Article
C2 - 34795375
AN - SCOPUS:85119399122
VL - 4
JO - Communications Biology
JF - Communications Biology
SN - 2399-3642
IS - 1
M1 - 1302
ER -