Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type
Abstract
Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum “Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy.
- Authors:
-
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, USA, Innovative Genomics Institute, Berkeley, California, USA
- Publication Date:
- Research Org.:
- Univ. of California, Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1633383
- Alternate Identifier(s):
- OSTI ID: 1816397
- Grant/Contract Number:
- DOE-SC10010566; SC0010566; CZP EAR-1331940
- Resource Type:
- Published Article
- Journal Name:
- mBio
- Additional Journal Information:
- Journal Name: mBio Journal Volume: 11 Journal Issue: 3; Journal ID: ISSN 2161-2129
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; metagenomics; secondary metabolism; soil microbiology
Citation Formats
Sharrar, Allison M., Crits-Christoph, Alexander, Méheust, Raphaël, Diamond, Spencer, Starr, Evan P., Banfield, Jillian F., and Davies, ed., Julian E. Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type. United States: N. p., 2020.
Web. doi:10.1128/mBio.00416-20.
Sharrar, Allison M., Crits-Christoph, Alexander, Méheust, Raphaël, Diamond, Spencer, Starr, Evan P., Banfield, Jillian F., & Davies, ed., Julian E. Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type. United States. https://doi.org/10.1128/mBio.00416-20
Sharrar, Allison M., Crits-Christoph, Alexander, Méheust, Raphaël, Diamond, Spencer, Starr, Evan P., Banfield, Jillian F., and Davies, ed., Julian E. Tue .
"Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type". United States. https://doi.org/10.1128/mBio.00416-20.
@article{osti_1633383,
title = {Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type},
author = {Sharrar, Allison M. and Crits-Christoph, Alexander and Méheust, Raphaël and Diamond, Spencer and Starr, Evan P. and Banfield, Jillian F. and Davies, ed., Julian E.},
abstractNote = {Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum “Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy.},
doi = {10.1128/mBio.00416-20},
journal = {mBio},
number = 3,
volume = 11,
place = {United States},
year = {Tue Jun 30 00:00:00 EDT 2020},
month = {Tue Jun 30 00:00:00 EDT 2020}
}
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