A rhizosphere community of Avena fatua traced with stable isotope probing (SIP) by growing the plant in a 13CO2 atmosphere. Paired rhizosphere and nonrhizosphere soils sampled at 6 and 9 weeks were density-fractionated and sequenced to recover 55 bacterial genomes (>=70 percent complete), complete 18S rRNA sequences of 13C-enriched microeukaryotic bacterivores and fungi, and 10 circularized bacteriophage genomes. Some phages were the most labeled entities in the rhizosphere, suggesting phage are important agents of turnover of plant-derived carbon in soil. CRISPR spacer targeting linked one phage to a Burkholderiales host predicted to be a plant pathogen and another to a Catenulispora sp. predicted to be a plant growth-promoting bacterium. Heavily 13C-labeled bacterial genes include those involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| 13C-labeled rhizosphere bacteria — ontology label: Bacteria | NCBITaxon:2 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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N/A |
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| 13C-labeled rhizosphere microeukaryotic bacterivores and fungi — ontology label: Eukaryota | NCBITaxon:2759 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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N/A |
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| 13C-labeled rhizosphere bacteriophages — ontology label: Viruses | NCBITaxon:10239 · TaxonMech · TraitMech | N/A | |
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| Burkholderiales (predicted plant pathogen) — ontology label: Burkholderiales | NCBITaxon:80840 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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N/A |
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| Catenulispora sp. (predicted PGPR) — ontology label: Catenulispora | NCBITaxon:414878 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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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.
Plant-Derived Carbon Incorporation into Phage DNA
Stable-isotope probing detected plant-derived carbon in reconstructed circular phage genomes, some among the most highly labeled entities. This directly supports tracer incorporation into phage DNA. Active infection and lysis-driven nutrient recycling are interpretations; nutrient-release flux and bacterial mortality were not measured by isotope enrichment alone.
Participating Taxa: 13C-labeled rhizosphere bacteria, 13C-labeled rhizosphere bacteriophages
Evidence
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PMID:34468166 - SUPPORT (IN_VIVO)"Many of the phage we identified appear to be highly labeled."
Candidate Burkholderiales Phage-Host Link
PARTIAL - a CRISPR spacer match identifies Burkholderiales_62_29 as a possible host for a highly labeled phage. Plant pathogenicity is predicted from genomic content, not demonstrated infection or disease in this experiment.
Source Taxon: 13C-labeled rhizosphere bacteriophages
Target Taxon: Burkholderiales (predicted plant pathogen)
Biological Processes:
- symbiont-mediated perturbation of host process (GO:0044003 · PathwayMech)
HYPOTHESIZED - replication in this candidate plant-carbon-assimilating host could transfer labeled nucleotide carbon into the observed phage DNA. Host identity and infection dynamics remain inferred, and this arrow does not measure lysis-mediated nutrient release.
Evidence
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PMID:34468166 - PARTIAL (COMPUTATIONAL)"CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen"
Candidate Catenulispora Phage-Host Link
PARTIAL - shared GH25 sequence and phylogeny support a candidate Catenulisporales/Catenulispora host for another labeled phage; this is not a CRISPR assignment. Plant-growth promotion is a genomic prediction, not a measured host-benefit phenotype.
Source Taxon: 13C-labeled rhizosphere bacteriophages
Target Taxon: Catenulispora sp. (predicted PGPR)
Biological Processes:
- symbiont-mediated perturbation of host process (GO:0044003 · PathwayMech)
HYPOTHESIZED - replication in this candidate plant-carbon-assimilating host could transfer labeled nucleotide carbon into the observed phage DNA. Host identity and infection dynamics remain inferred, and this arrow does not measure lysis-mediated nutrient release.
Evidence
-
PMID:34468166 - PARTIAL (COMPUTATIONAL)"Another highly labeled phage is predicted to replicate in a Catenulispora sp."
13C-Labeled Plant-Signaling and Defense Functions
COMPUTATIONAL POTENTIAL - labeled bacterial genomes encode homologs proposed to affect plant hormones, pathogenicity and defense against grazing. Annotation supports candidate functions, not expression or activity in this experiment; homologs may have alternative substrates. Related-study expression results are not measurements from this isotope experiment.
Participating Taxa: 13C-labeled rhizosphere bacteria, 13C-labeled rhizosphere microeukaryotic bacterivores and fungi
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:34468166 - PARTIAL (COMPUTATIONAL)"bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which hosts are infected, and how much plant carbon is released by phage-mediated lysis?
PMID:34468166 measures isotope incorporation and infers host/function links. Circular genomes can represent particles or replicating phage, and lysogenic genes are also present. There are no biological replicates; the enrichment threshold is model-derived, and growth estimates are not mortality measurements. Host validation, functional assays and release flux remain unresolved.
Attaches to: ecological_interactions#Plant-Derived Carbon Incorporation into Phage DNA, ecological_interactions#Candidate Burkholderiales Phage-Host Link, ecological_interactions#Candidate Catenulispora Phage-Host Link, ecological_interactions#13C-Labeled Plant-Signaling and Defense Functions
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the Avena rhizosphere cross-kingdom SIP community
PubMed record for the Starr et al. 2021 mSphere paper on stable-isotope-informed genome-resolved metagenomics of the Avena fatua rhizosphere. |
OTHER | PMID:34468166 |
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DOI landing page
DOI link to the mSphere paper. |
OTHER | doi:10.1128/mSphere.00085-21 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Plant growth atmosphere | 13CO2 labeling | N/A |
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| Sampling time | 6 and 9 weeks of growth | N/A |
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Growth Media
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