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Brachypodium Young Root Rhizosphere EcoFAB Community

Community ID CommunityMech:000225
Ecological State STABLE
Environment young Brachypodium primary-root rhizosphere
ENVO:00002233

A young Brachypodium distachyon primary-root rhizosphere community analyzed at two spatially distinct zones (root tip and root base) using EcoFABs fabricated ecosystems and conventional pot and tube containers with natural soil. 16S rRNA gene analysis shows a strong rhizosphere effect with significant enrichment of OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, while community composition did not differ between root tips and root base or across growth containers. Bulk metagenomic functional analysis revealed enrichment of metabolic-pathway and root-colonization genes in root tips, whereas nutrient-limitation and environmental-stress genes were enriched in bulk soil, indicating root-driven gradients in labile carbon and nutrient availability.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
rhizosphere Actinobacteria NCBITaxon:201174
PRIMARY_DEGRADER
N/A
  • PMID:37280433 - SUPPORT (IN_VIVO)
    "significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria"
rhizosphere Bacteroidetes NCBITaxon:976
PRIMARY_DEGRADER
N/A
  • PMID:37280433 - SUPPORT (IN_VIVO)
    "Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria"
rhizosphere Firmicutes NCBITaxon:1239
PRIMARY_DEGRADER
N/A
  • PMID:37280433 - SUPPORT (IN_VIVO)
    "Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria"
rhizosphere Proteobacteria NCBITaxon:1224
PRIMARY_DEGRADER
N/A
  • PMID:37280433 - SUPPORT (IN_VIVO)
    "Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria"

Ecological Interactions

Ecological interaction network for Brachypodium Young Root Rhizosphere EcoFAB Community Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).
Taxon
Cross-feeding
Mutualism
Syntrophy
Competition
Commensalism
Niche partitioning
Colonization facilitation
Strain competition
Predation

Root-Driven Rhizosphere Effect

COLONIZATION_FACILITATION

Evidence

  • PMID:37280433 - SUPPORT (IN_VIVO)
    "a strong rhizosphere effect resulting in significant enrichment of several OTUs"

Tip-Versus-Bulk Functional Gradient

NICHE_PARTITIONING

Evidence

  • PMID:37280433 - SUPPORT (IN_VIVO)
    "genes associated with different metabolic pathways and root colonization were enriched in root tips"
  • PMID:37280433 - SUPPORT (IN_VIVO)
    "genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips"

Compositional Invariance Across Containers and Root Zones

COLONIZATION_FACILITATION

Evidence

  • PMID:37280433 - SUPPORT (IN_VIVO)
    "microbial community composition did not differ between root tips and root base or across different growth containers"

External Resources

Name Repository Resource ID
Primary publication for the Brachypodium young-root rhizosphere community
PubMed record for the 2023 ISME Communications paper on early differentiation of the Brachypodium rhizosphere microbiome. 		OTHER PMID:37280433
  • PMID:37280433 - SUPPORT (IN_VIVO)
    "rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers"
DOI landing page
DOI link to the ISME Communications paper. 		OTHER doi:10.1038/s43705-023-00265-1

Environmental Factors

Factor Value Unit
Growth container EcoFABs versus conventional pots and tubes N/A
  • PMID:37280433 - SUPPORT (IN_VIVO)
    "standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes"
Root spatial zone root tip versus root base N/A
  • PMID:37280433 - SUPPORT (IN_VIVO)
    "two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon"