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Avena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds

Community ID CommunityMech:000245
Ecological State STABLE
Environment Avena fatua rhizosphere and detritusphere
ENVO:00002233

A rhizosphere and detritusphere microbial community of Avena fatua characterized by time-resolved metatranscriptomics across rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable-isotope-probing metagenomes. Soil habitat significantly affected both community composition and overall gene expression, but the succession of microbial functions occurred faster than compositional change. Hierarchical clustering of upregulated decomposition genes resolved four microbial guilds whose functional succession patterns suggest specialization for fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Avena rhizosphere and detritusphere decomposer community NCBITaxon:2
PRIMARY_DEGRADER CROSS_FEEDER
N/A
  • PMID:31953507 - SUPPORT (IN_VIVO)
    "Transcripts were binned using a unique reference database generated from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable isotope probing metagenomes"

Ecological Interactions

Ecological interaction network for Avena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds 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

Functional Succession Outpaces Compositional Change

NICHE_PARTITIONING

Evidence

  • PMID:31953507 - SUPPORT (IN_VIVO)
    "the succession of microbial functions occurred at a faster time scale than compositional changes"

Four Guilds with Substrate-Specific Specialization

NICHE_PARTITIONING

Evidence

  • PMID:31953507 - SUPPORT (IN_VIVO)
    "identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization"

Rhizosphere Upregulates Carbohydrate Depolymerization

CROSS_FEEDING

Biological Processes:

Evidence

  • PMID:31953507 - SUPPORT (IN_VIVO)
    "Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere"

External Resources

Name Repository Resource ID
Primary publication for the Avena rhizosphere/detritusphere community
PubMed record for the Nuccio et al. 2020 ISME J paper. 		OTHER PMID:31953507
  • PMID:31953507 - SUPPORT (IN_VIVO)
    "Niche differentiation is spatially and temporally regulated in the rhizosphere"
DOI landing page
DOI link to the ISME J paper. 		OTHER doi:10.1038/s41396-019-0582-x

Environmental Factors

Factor Value Unit
Habitat type rhizosphere vs detritusphere vs combined N/A
  • PMID:31953507 - SUPPORT (IN_VIVO)
    "time-resolved metatranscriptomes to compare microbial functions in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats"
Plant host Avena fatua N/A
  • PMID:31953507 - SUPPORT (IN_VIVO)
    "Using Avena fatua, a common annual grass"