A rare-biosphere community of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea recovered from grassland soil by concentrating particles smaller than 0.2 micrometers prior to metagenomic sequencing. CPR and DPANN sequences were enriched 100- to 1,000-fold compared to bulk soil (estimated at roughly 1 to 100 cells per gram of soil for each lineage) and include Doudnabacteria (SM2F11) and Pacearchaeota - organisms rarely reported in soil - alongside Saccharibacteria, Parcubacteria, and Microgenomates as well as Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota. Most members likely live symbiotic anaerobic lifestyles, but some Saccharibacteria, Parcubacteria, and Doudnabacteria encode components of aerobic metabolism that may be particularly relevant in oxic soil habitats.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| soil Candidate Phyla Radiation (CPR) bacteria — ontology label: Patescibacteria group | NCBITaxon:1783273 · TaxonMech · TraitMech | N/A | |
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| soil DPANN archaea — ontology label: Nanobdellati | NCBITaxon:1783276 · 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.
Rare Soil CPR and DPANN Sequence Detection
CPR and DPANN sequences were recovered from small-particle concentrates, while paired bulk samples gave low or undetectable coverage and no recovered CPR/DPANN draft genomes. The reported 100- to 1,000-fold enrichment is a sample-processing comparison, not natural population growth. Abundances of roughly 1 to 100 cells per gram are coverage-based estimates, not direct counts; nondetection does not establish ecological absence.
Evidence
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PMID:34402646 - SUPPORT (IN_VIVO)"enriched 100- to 1,000-fold compared to that in bulk soil"
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PMID:34402646 - SUPPORT (IN_VIVO)"we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil"
Reduced Genomic Inventories and Hypothesized Resource Dependence
HYPOTHESIZED: reduced metabolic inventories in most recovered CPR and DPANN draft genomes suggest dependence on resources from other organisms. Incomplete genomes and uncharacterized functions limit absence-based inference. No partner, transfer route or neutral effect on a host was demonstrated, so this is not assigned a commensal fitness relationship.
Evidence
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PMID:34402646 - PARTIAL (COMPUTATIONAL)"suggesting they live anaerobic lifestyles and depend on resources from other organisms "
Predicted Respiratory Components in Soil CPR
Specific soil CPR lineages carried predicted respiratory components; the claim is not extended to DPANN or every CPR lineage. HYPOTHESIZED: these components may support some aerobic respiratory activity. Missing quinone-biosynthesis genes and incomplete assemblies limit that inference. Phylogenetic analysis suggests lateral acquisition, but neither realized respiration nor an adaptive benefit in soil was measured.
Participating Taxa: soil Candidate Phyla Radiation (CPR) bacteria
Evidence
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PMID:34402646 - PARTIAL (COMPUTATIONAL)"suggests the possibility of some aerobic respiratory capacity"
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PMID:34402646 - PARTIAL (COMPUTATIONAL)"This analysis suggests that this gene cluster has been laterally transferred from other bacteria"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which ecological partners and realized functions correspond to the reduced soil CPR/DPANN genomic inventories?
The complete primary main text was read. It presents metabolic and phylogenetic inferences, while explicitly leaving ecological roles unclear. Co-occurrence does not establish a CPR-DPANN partnership, and detection of respiratory components does not demonstrate activity or adaptive benefit. Evidence resolving actual partners, resource use and function in the sampled lineages remains necessary. Supplementary methods and raw data were not inspected.
Attaches to: ecological_interactions#Rare Soil CPR and DPANN Sequence Detection, ecological_interactions#Reduced Genomic Inventories and Hypothesized Resource Dependence, ecological_interactions#Predicted Respiratory Components in Soil CPR
1 evidence item(s)
While the precise ecological roles of these organisms remain unclear
The primary discussion explicitly leaves ecological roles unresolved.
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the soil CPR/DPANN rare-biosphere community
PubMed record for the Nicolas et al. 2021 mSystems paper. |
OTHER | PMID:34402646 |
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DOI landing page
DOI link to the mSystems paper. |
OTHER | doi:10.1128/mSystems.01205-20 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Particle size filtration | < 0.2 micrometer fraction | N/A |
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