A soil bacterial community surveyed for secondary-metabolite biosynthetic gene cluster (BGC) content across three sites in a northern California Critical Zone Observatory with varying vegetation and bedrock. 1,334 metagenome-assembled genomes were reconstructed and screened for BGCs, including genomes for prolific producers among Actinobacteria, Chloroflexi, and candidate phylum Candidatus Dormibacteraeota. One Candidate Phyla Radiation (CPR) bacterial genome encoded a ribosomally synthesized linear azole/azoline-containing peptide, a capacity also found in other publicly available CPR genomes. Bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with BGC-type patterns varying by taxonomy.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
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| Actinobacteria (prolific BGC producers) — ontology label: Actinomycetota | NCBITaxon:201174 · TaxonMech · TraitMech | N/A | |
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| Chloroflexi (prolific BGC producers) — ontology label: Chloroflexota | NCBITaxon:200795 · TaxonMech · TraitMech | N/A | |
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| Candidatus Dormibacteraeota (prolific BGC producers) — ontology label: Candidatus Dormiibacterota | NCBITaxon:2052312 · TaxonMech · TraitMech | N/A | |
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| BGC-encoding CPR bacterium — ontology label: Patescibacteria group | NCBITaxon:1783273 · TaxonMech · TraitMech | N/A | |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Phylum-Scale Biosynthetic-Potential Heterogeneity
Predicted BGC content varied among recovered genomes and within soil bacterial lineages. Some genomes assigned to Actinobacteria, Chloroflexi and Candidatus Dormibacteraeota had high biosynthetic potential. This does not establish metabolite production by every member of those clades or reduced competition through niche partitioning.
Participating Taxa: Actinobacteria (prolific BGC producers), Chloroflexi (prolific BGC producers), Candidatus Dormibacteraeota (prolific BGC producers)
Evidence
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PMID:32546614 - SUPPORT (COMPUTATIONAL)"We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum "Candidatus Dormibacteraeota." "
CPR Linear Azole/Azoline-Containing Peptide BGC Prediction
A soil CPR genome carried a predicted linear azole/azoline-containing peptide (LAP) biosynthetic gene cluster, with related predictions in additional public CPR genomes. LAP is the reported class, not linaridin. The finding is genomic potential, not measured peptide production, antibiotic action or an ecological partner effect in the sampled community.
Participating Taxa: BGC-encoding CPR bacterium
Evidence
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PMID:32546614 - SUPPORT (COMPUTATIONAL)"one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide "
Depth and Vegetation Associations of Biosynthetic Potential
Genomes enriched in shallow samples encoded more predicted BGCs and ketosynthase domains on average; genomes enriched in grasslands encoded more ketosynthase domains than those enriched at tree-covered sites. These field-sample associations do not show that biosynthetic products caused the abundance patterns or reduced interspecies competition. BGC-type distributions were not broadly different between the environmental groups.
Evidence
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PMID:32546614 - SUPPORT (IN_VIVO)"bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy"
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PMID:32546614 - SUPPORT (IN_VIVO)"genomes that were enriched in grasslands encoded more KS domains than genomes that were enriched at tree-covered sites"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which predicted soil BGCs yield active products and demonstrable ecological effects in the surveyed communities?
The primary main text and relevant cached passages were checked. Genome predictions and depth/vegetation associations do not establish expression, product identity or partner effects. The comparison to an experimentally active Rhizobium product is not a demonstration for the CPR prediction. Fragmented assemblies also limit genomic completeness. Product and ecological-function evidence for the actual surveyed taxa would resolve these claims; no additional causal edges are inferred.
Attaches to: ecological_interactions#Phylum-Scale Biosynthetic-Potential Heterogeneity, ecological_interactions#CPR Linear Azole/Azoline-Containing Peptide BGC Prediction, ecological_interactions#Depth and Vegetation Associations of Biosynthetic Potential
1 evidence item(s)
While we can only predict the function of these clusters with the present data
Explicitly distinguishes the CPR cluster prediction from a measured function.
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the soil BGC community
PubMed record for the Sharrar et al. 2020 mBio paper. |
OTHER | PMID:32546614 |
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DOI landing page
DOI link to the mBio paper. |
OTHER | doi:10.1128/mBio.00416-20 |
Environmental Factors
| Factor | Value | Unit |
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| Site number | three Critical Zone Observatory sites | N/A |
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| Genome count | 1,334 metagenome-assembled genomes | N/A |
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Cross-Mech Suite Links
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