- Niche partitioning
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -623,11 +618,9 @@
Ecological Interactions
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Archaeal and Bacterial Corrinoid Supply
- CROSS_FEEDING
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Predicted Soil Corrinoid Supply Capacity
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Thermoproteota, Actinobacteria, and Proteobacteria encode the principal corrinoid-supply capacity in grassland soil, supplying structurally diverse vitamin B12-related cofactors to the surrounding microbial community.
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Metagenome-assembled genomes from Hopland grassland soil suggest that Thermoproteota, Actinobacteria and Proteobacteria contain the principal corrinoid-producing lineages. This is predicted capacity in a subset of genomes, not demonstrated production or exchange by every member of these phyla. HYPOTHESIZED: released corrinoids support dependent organisms directly or through a soil-associated reservoir; release and replenishment were not traced.
Archaeal and bacterial corrinoid supply replenishes the B12-related micronutrient pool that accumulates on the grassland soil matrix.
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+ → Soil Corrinoid Reservoir and Hypothesized Buffering
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HYPOTHESIZED: the source model proposes that corrinoids released by predicted producers can adsorb to the soil matrix and contribute to its reservoir. The mechanism and magnitude of release and pool replenishment remain unknown; the MAG predictions do not trace this flux.
@@ -689,10 +681,10 @@
Evidence
PMID:38832716
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
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"corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria"
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"Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria"
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Evidence
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Corrinoid Structure Shapes Bacterial Community Composition
- NICHE_PARTITIONING
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Corrinoid Amendment and Community Composition
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Enrichment cultures and soil microcosms seeded with different corrinoid structures show distinct community composition shifts, indicating that B12-related cofactor structure is a community-shaping signal.
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Distinct corrinoid amendments altered bacterial composition in soil-derived enrichments and soil microcosms, with context-dependent responses. In soil microcosms, non-cobalamin treatments had stronger early effects than cobalamin, and the treatment effect was largely lost by the final sampling point. These amendment responses do not establish niche partitioning, a direct response by every taxon, or exposure to an equally diverse native reservoir.
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Corrinoid Structure Shapes Bacterial Community Composition
PMID:38832716
- - SUPPORT (IN_VIVO)
+ - SUPPORT (IN_VITRO)
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"soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition"
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"Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities."
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Evidence
PMID:38832716
- - SUPPORT (IN_VIVO)
+ - SUPPORT (IN_VITRO)
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"corrinoid structure can shape communities"
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"Environmental context influenced both community- and taxon-specific responses to specific corrinoids."
Soil Corrinoid Reservoir and Hypothesized Buffering
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Corrinoids accumulate adhered to the soil matrix at levels exceeding cultured-bacterium requirements, acting as a micronutrient reservoir that promotes community stability.
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Soil extraction and bioassays detected an abundant, strongly soil-associated corrinoid pool, expected to be predominantly cobalamin. The assay does not separate intracellular from extracellular corrinoids, and accessibility to resident microbes remains unclear. HYPOTHESIZED: this reservoir buffers community response to additional cobalamin; its role in stability was not isolated experimentally.
- → Corrinoid Structure Shapes Bacterial Community Composition
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The soil-matrix corrinoid reservoir exposes bacteria to structurally diverse B12-related cofactors whose identities shape community composition.
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+ → Corrinoid Amendment and Community Composition
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HYPOTHESIZED: a predominantly cobalamin reservoir may buffer the community response to added cobalamin, helping explain the contrast with other corrinoid amendments and with soil-derived enrichments. This proposed modulation of the amendment response is not demonstrated release of a diverse native pool or proof that the reservoir caused the observed shifts.
@@ -827,10 +816,10 @@
Evidence
PMID:38832716
- - SUPPORT (IN_VIVO)
+ - SUPPORT (IN_VITRO)
-
"Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria"
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"Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria."
@@ -840,10 +829,10 @@
Evidence
PMID:38832716
- - SUPPORT (IN_VIVO)
+ - PARTIAL (OTHER)
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"environmental micronutrient reservoirs promote community stability"
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"These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability."
@@ -856,6 +845,45 @@
Evidence
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Knowledge gaps & discussions (1)
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+ KNOWLEDGE_GAP
+ OPEN
+ How much of the measured corrinoid pool is accessible to resident microbes, and does it mediate the community response to amendment?
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The primary results and discussion distinguish total corrinoid measurement, genome-based producer inference and two proposed cycling routes. Intracellular/extracellular partitioning, producer release and accessibility are unresolved. Both original directions are retained only as explicitly HYPOTHESIZED links in the authors' model. No new donor-recipient mechanism or direction is added. Taxonomic role/evidence overclaims outside the graph remain tracked in issue #1814.
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Attaches to: ecological_interactions#Predicted Soil Corrinoid Supply Capacity, ecological_interactions#Corrinoid Amendment and Community Composition, ecological_interactions#Soil Corrinoid Reservoir and Hypothesized Buffering
These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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The source says suggest: reservoir-mediated stability remains an interpretation.
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@@ -1072,7 +1100,7 @@
Environmental Factors
(function() {
var intId = "interaction:0";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1089,7 +1117,7 @@
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
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- Taxon
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- Mutualism
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- Colonization facilitation
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Network and Exudate Guided SRC1 Assembly
- COLONIZATION_FACILITATION
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SRC1 was assembled from sorghum bacterial isolates selected either for network-predicted community cohesion or for growth on host-specific root-exudate compounds.
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"SRC1 was assembled from bacterial isolates identified either for their potential role in community cohesion through network analysis or for their ability to benefit from host-specific exudate compounds"
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Host-Associated SRC1 Cohesion
- COLONIZATION_FACILITATION
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SRC1 community cohesion was most robust with the sorghum host in laboratory conditions, while some lineages were lost during growth on solid medium or in the native field.
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- regulation of secondary metabolite biosynthetic process
- (GO:1900376)
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Knowledge gaps & discussions (1)
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+ KNOWLEDGE_GAP
+ OPEN
+ Which exact source-backed community does the claimed 16-20-member SRC1 subset represent?
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The record claims a subset but cites parent SRC1 results. The primary paper introduction identifies 57 strains, independently corroborated by the SRC2 primary study; the cached and freshly retrieved SRC1 abstract does not identify a 16-20-member formulation. Four subset-attributed nodes are withheld, not a rejection of the parent study's positive observations. Cohesion does not establish facilitation, host benefit does not establish reciprocal mutualism, and lignin transcription is not proven mediation. Resolve identity, membership and endpoint scope in issue #1813 before restoring a graph. Top-level identity/taxonomy are preserved pending that separately scoped decision; this record remains needs_research.
Here, we engineered a synthetic rhizosphere community (SRC1) with the anticipation that it would exhibit a selective advantage in colonizing the host Sorghum bicolor, thereby potentially fostering its growth
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Identifies the studied SRC1 broadly, but does not identify the record-specific subset.
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"these growth enhancements correlate with the transcriptional dampening of lignin biosynthesis in the host"