Avena Rhizosphere Cross-Kingdom 13C-SIP Community

Community ID CommunityMech:000236

Ecological State STABLE

Environment Avena fatua root rhizosphere
ENVO:00002233

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	NCBITaxon:2	PRIMARY_DEGRADER	N/A
PMID:34468166 - SUPPORT (IN_VIVO) "55 unique bacterial genomes"
13C-labeled rhizosphere microeukaryotic bacterivores and fungi	NCBITaxon:2759	PRIMARY_DEGRADER	N/A
PMID:34468166 - SUPPORT (IN_VIVO) "complete 18S rRNA sequences of several 13C-enriched microeukaryotic bacterivores and fungi"
13C-labeled rhizosphere bacteriophages	NCBITaxon:10239		N/A
PMID:34468166 - SUPPORT (IN_VIVO) "10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere"
Burkholderiales (predicted plant pathogen)	NCBITaxon:80840	PRIMARY_DEGRADER	N/A
PMID:34468166 - SUPPORT (IN_VIVO) "a Burkholderiales host predicted to be a plant pathogen"
Catenulispora sp. (predicted PGPR)	NCBITaxon:223957	PRIMARY_DEGRADER	N/A
PMID:34468166 - SUPPORT (IN_VIVO) "a Catenulispora sp., a possible plant growth-promoting bacterium"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Phage Lysis Turns Over Plant-Derived Carbon

PREDATION

Metabolites: carbon dioxide (CHEBI:16526)

Evidence

PMID:34468166 - SUPPORT (IN_VIVO)

"phage may be important agents of turnover of plant-derived C in soil"

Phage Targets Burkholderiales Plant Pathogen

PREDATION

Source Taxon: 13C-labeled rhizosphere bacteriophages

Target Taxon: Burkholderiales (predicted plant pathogen)

Evidence

PMID:34468166 - SUPPORT (IN_VIVO)

"CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen"

Phage Replicates in Catenulispora PGPR

PREDATION

Source Taxon: 13C-labeled rhizosphere bacteriophages

Target Taxon: Catenulispora sp. (predicted PGPR)

Evidence

PMID:34468166 - SUPPORT (IN_VIVO)

"Another highly labeled phage is predicted to replicate in a Catenulispora sp."

13C-Labeled Plant-Signaling and Defense Functions

COMMENSALISM

Evidence

PMID:34468166 - SUPPORT (IN_VIVO)

"bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing"

External Resources

Name	Repository	Resource ID
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
PMID:34468166 - SUPPORT (IN_VIVO) "Cross-Kingdom Interactions in Rhizosphere Soil"
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
PMID:34468166 - SUPPORT (IN_VIVO) "Avena fatua grown in a 13CO2 atmosphere"
Sampling time	6 and 9 weeks of growth	N/A
PMID:34468166 - SUPPORT (IN_VIVO) "paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth"