A host-filtered bacterial endosphere community from the edible aquatic plant Wolffia globosa Mankai, sampled from industrial rotating raceway cultivation. Amplicon and shotgun metagenomic analyses showed that Mankai medium, phyllosphere, and surface-sterilized internal-tissue fractions formed distinct communities; downstream MAG analysis of the endosphere found a low-diversity Proteobacteria/Pseudomonadota-dominated consortium in which Alphaproteobacterial members encoded near-complete cobamide biosynthesis pathways, while many Gammaproteobacteria and Bacteroidota lineages carried incomplete pathways enriched for cobamide salvage and remodeling. A MAG-derived functional-complementarity network placed Hyphomicrobium zavarzinii, Methylobacterium, Devosia, Labrys, and Ferrovibrionaceae among the inferred producer-side taxa, supporting a producer-salvager model for cobamide metabolism in the plant-associated niche.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Hyphomicrobium zavarzinii | NCBITaxon:48292 · TaxonMech · TraitMech | N/A | |
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| Methylobacterium sp. Mankai endosphere — ontology label: Methylobacterium | NCBITaxon:407 · TaxonMech · TraitMech | N/A | |
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| Devosia sp. Mankai endosphere — ontology label: Devosia | NCBITaxon:46913 · TaxonMech · TraitMech | N/A | |
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| Labrys sp. Mankai endosphere — ontology label: Labrys <a-proteobacteria> | NCBITaxon:204476 · TaxonMech · TraitMech | N/A | |
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| Ferrovibrionaceae Mankai endosphere — ontology label: Ferrovibrionaceae | NCBITaxon:3120696 · TaxonMech · TraitMech | N/A | |
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| Gammaproteobacteria cobamide salvagers — ontology label: Gammaproteobacteria | NCBITaxon:1236 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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| Bacteroidota cobamide salvagers — ontology label: Bacteroidota | NCBITaxon:976 · TaxonMech · TraitMech |
CROSS_FEEDER
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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.
Mankai Compartment-Associated Community Differentiation
Bacterial DNA profiles from cultivation medium, washed fronds and surface-sterilized tissue differed in composition and diversity. Environmental and host filtering is an interpretation of these compartment associations, not a selectively perturbed host mechanism or demonstrated microbial niche partitioning. Endosphere denotes the operational sterilized-tissue fraction; washed whole fronds are not a strictly epiphytic sample.
Evidence
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PMID:42304541 - PARTIAL (IN_VIVO)"The pronounced differences in richness and composition between the medium, phyllosphere and endosphere (Fig. 2 ) indicate strong environmental and host filtering along the plant-water interface"
MAG-Inferred Cobamide Producer-Salvager Guild
Genome-resolved endosphere analysis predicted an uneven cobamide pathway architecture: Hyphomicrobium zavarzinii, Methylobacterium, Devosia, Labrys, Ferrovibrionaceae, and other Alphaproteobacteria encoded most biosynthetic steps, while many Gammaproteobacteria and Bacteroidota lineages had incomplete pathways and were inferred to salvage or remodel exogenous intermediates. The network edges represent MAG-derived metabolic compatibility, not direct metabolite-flux or abundance-correlation evidence. HYPOTHESIZED cross-feeding is not established by gene presence or pathway gaps. Missing genes in individual MAGs can reflect reconstruction limitations. Cultured species-level comparators were not strain-matched endophytes, so their cobalamin production does not validate exchange in this guild or adaptive gene loss. The host is not established as a B12-dependent recipient.
Participating Taxa: Hyphomicrobium zavarzinii, Methylobacterium sp. Mankai endosphere, Devosia sp. Mankai endosphere, Labrys sp. Mankai endosphere, Ferrovibrionaceae Mankai endosphere, Gammaproteobacteria cobamide salvagers, Bacteroidota cobamide salvagers
Metabolites: cobamide (CHEBI:33913 · MediaIngredientMech · CMMMech), vitamin B12 (CHEBI:176843 · MediaIngredientMech · CMMMech)
Biological Processes:
- cobalamin biosynthetic process (GO:0009236 · PathwayMech)
- cobalamin metabolic process (GO:0009235 · PathwayMech)
Evidence
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PMID:42304541 - SUPPORT (COMPUTATIONAL)"The functional complementarity network identified a small set of taxa with near-complete cobamide biosynthetic capacity as highly connected hub nodes"
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PMID:42304541 - PARTIAL (COMPUTATIONAL)"many Gammaproteobacteria and Bacteroidota lineages harbored incomplete pathways, implying reliance on exogenous cobamide intermediates"
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PMID:42304541 - SUPPORT (COMPUTATIONAL)"edges represent the number of cobamide pathway intermediates that could be supplied by one taxon and utilized by another based on complementary gene content, thereby capturing putative exchange relationships inferred from pathway annotation rather than abundance correlations"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
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Wolffia globosa Mankai endosphere amplicon and metagenomic reads
NCBI BioProject carrying the raw amplicon and metagenomic reads used to profile medium, phyllosphere, and endosphere communities and to reconstruct endosphere MAGs. |
METAGENOMICS | NCBI_BIOPROJECT | PRJNA1356720 |
Knowledge gaps & discussions (2)
KNOWLEDGE_GAP OPEN The cobamide producer-salvager structure is inferred from MAG annotations and network complementarity; direct exchange of cobamide intermediates among endosphere members remains unmeasured.
Resolving this would distinguish true metabolite handoff from shared niche preference or correlated cobamide pathway potential.
Attaches to: ecological_interactions#MAG-Inferred Cobamide Producer-Salvager Guild
1 proposed experiment(s)
Approach: stable-isotope tracing with metatranscriptomics
Decision: Labeled intermediates move from predicted producers into predicted salvagers in a producer-dependent manner.
1 evidence item(s)
Future work integrating transcriptomics, metabolite flux measurements, and controlled manipulation of key producer and salvager taxa will be essential to move from genomic potential and inferred interactions to directly measured cobamide exchange
The primary source explicitly frames direct cobamide exchange as a future measurement need.
KNOWLEDGE_GAP OPEN Do compartment profiles and comparator genomes establish host-selected cobamide dependence?
Operational fractions and possible carryover limit localization claims. Only endosphere MAGs were reconstructed, so pathway architecture was not compared across all compartments. Non-strain-matched culture-collection representatives cannot establish endophyte-specific gene loss or validate metabolite exchange. The existing direct-flux knowledge gap remains open.
Attaches to: ecological_interactions#Mankai Compartment-Associated Community Differentiation, ecological_interactions#MAG-Inferred Cobamide Producer-Salvager Guild
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication - Mankai endosphere cobamide guild
Open-access Environmental Microbiome study that combined 16S amplicon sequencing, endosphere metagenomics, MAG annotation, cobamide functional-complementarity networks, and comparator isolate genomics. |
OTHER | PMID:42304541 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| industrial rotating greenhouse raceway | Mankai from Hinoman rotating raceway basins | N/A |
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| operational endosphere fraction | surface-sterilized W. globosa Mankai tissue-associated fraction | N/A |
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