Home ← Back to Communities Text Map Taxonomic UMAP Sequence Map Network Schema All Mech projects

PMSX Carbon-Substrate Biofilm SynCom

Community ID CommunityMech:000400
Ecological State ENGINEERED
Environment M9 carbon-substrate biofilm laboratory assay — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗

A defined four-member bacterial SynCom, abbreviated PMSX, containing Paenibacillus amylolyticus, Microbacterium oxydans, Stenotrophomonas rhizophila, and a strain reclassified as Stenotrophomonas maltophilia. Zhu et al. grew the soil isolates in M9 media and chemically defined 3D-printed hydrogels with diffusible sugars or polymeric cellulose/xylan carbon sources, measured crystal-violet biofilm biomass and FISH spatial patterning, and found that the complete SynCom robustly formed more biofilm than subsets while polymer-rich carbon sources drove self-organization around the Paenibacillus member.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Paenibacillus amylolyticus NCBITaxon:1451 · TaxonMech · TraitMech
PRIMARY_DEGRADER
N/A
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "Strain Abbreviation Gram Reference genome from European Nucleotide Archive (ENA) Stenotrophomonas rhizophila S Negative PRJEB15263 Stenotrophomonas maltophilia* X Negative PRJEB18431 Microbacterium oxydans M Positive PRJEB15265 Paenibacillus amylolyticus P Positive PRJEB15262"
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "the red curve is the mean g(r) of the putative primary degrader P against the other three members"
Microbacterium oxydans NCBITaxon:82380 · TaxonMech · TraitMech
CROSS_FEEDER
N/A
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "Strain Abbreviation Gram Reference genome from European Nucleotide Archive (ENA) Stenotrophomonas rhizophila S Negative PRJEB15263 Stenotrophomonas maltophilia* X Negative PRJEB18431 Microbacterium oxydans M Positive PRJEB15265 Paenibacillus amylolyticus P Positive PRJEB15262"
Stenotrophomonas rhizophila NCBITaxon:216778 · TaxonMech · TraitMech
CROSS_FEEDER
N/A
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "Strain Abbreviation Gram Reference genome from European Nucleotide Archive (ENA) Stenotrophomonas rhizophila S Negative PRJEB15263 Stenotrophomonas maltophilia* X Negative PRJEB18431 Microbacterium oxydans M Positive PRJEB15265 Paenibacillus amylolyticus P Positive PRJEB15262"
Stenotrophomonas maltophilia NCBITaxon:40324 · TaxonMech · TraitMech
CROSS_FEEDER
N/A
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "Strain Abbreviation Gram Reference genome from European Nucleotide Archive (ENA) Stenotrophomonas rhizophila S Negative PRJEB15263 Stenotrophomonas maltophilia* X Negative PRJEB18431 Microbacterium oxydans M Positive PRJEB15265 Paenibacillus amylolyticus P Positive PRJEB15262"
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "* Genome-wide taxonomy analysis by Genome BLAST Distance Phylogeny (GBDP) shows this genome should refer to Stenotrophomonas maltophilia instead of Xanthomonas retroflexus in ENA."

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.

Ecological interaction network for PMSX Carbon-Substrate Biofilm SynCom Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Cross-feeding
Other

Polymeric carbon-driven spatial self-organization

Cellobiose-grown communities were relatively intermixed; CMC/xylan conditions produced non-degrader clusters with putative primary degrader P. amylolyticus at their periphery. This single-time-point architecture is not demonstrated competition reduction, a time-resolved assembly mechanism or proof of crystalline-cellulose degradation.

Source Taxon: Paenibacillus amylolyticus

Metabolites: cellobiose (CHEBI:17057 · MediaIngredientMech · CMMMech), carboxymethylcellulose (CHEBI:85146 · MediaIngredientMech · CMMMech), xylan (CHEBI:37166 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:42658845 - SUPPORT (IN_VITRO)
    "On the simple substrates (e.g. cellobiose) both curves stay near 1, indicating a well-mixed, unstructured community; while on the polymeric substrates (e.g. CMC, xylan) the non-degrader members show strong short-range co-clustering"
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "P. amylolyticus is enriched at the periphery of those clusters which is consistent with substrate complexity driving spatial self-organization around P. amylolyticus."

Predicted Exchange and Conditioned-Supernatant Biofilm Support

CROSS_FEEDING

PARTIAL - CAZyme/genome-scale predictions suggest exchange, and community-conditioned supernatants generally support more crystal-violet biomass than P-only supernatants. These results do not identify each transferred nutrient, isolate nutrient transfer from other soluble effects, or establish reciprocal fitness. Spatial mediation remains unproven.

Metabolites: cellobiose (CHEBI:17057 · MediaIngredientMech · CMMMech), xylan (CHEBI:37166 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:42658845 - PARTIAL (COMPUTATIONAL)
    "Bioinformatic analyses of carbohydrate-active enzyme (CAZyme) repertoires and genome-scale metabolic modeling suggested bidirectional metabolite exchange among the SynCom members"
  • PMID:42658845 - PARTIAL (IN_VITRO)
    "For each SynCom member, biofilm formation in PMSX-conditioned supernatants exceeded that in P-conditioned supernatants in the majority of conditions."

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which measured nutrient transfers and time-resolved perturbations connect polymer use to spatial organization?

PMID:42658845 abstract, cached supplement excerpts and selected primary indexed passages support bounded spatial and supernatant observations, not exchange-to-pattern causality. Complete main methods and images remain unread. Preserve zero arrows, putative degrader attribution, removed mutualism and separate hydrogel/M9 contexts; CMC is chemically distinct from its cellulose parent.

Attaches to: ecological_interactions#Polymeric carbon-driven spatial self-organization, ecological_interactions#Predicted Exchange and Conditioned-Supernatant Biofilm Support

Environmental Factors

Factor Value Unit
diffusible versus polymeric carbon substrates glucose, xylose, cellobiose, CMC, microcrystalline cellulose, sodium alginate, and corncob xylan N/A
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "Carbon source name Abbrev. Final Conc. Carbon source type D-(+)-Glucose Glu 10 mM Monosaccharide D-(+)-Xylose Xylose 12 mM Monosaccharide D-(+)-Cellobiose Clbs 5 mM Disaccharide"
  • PMID:42658845 - SUPPORT (IN_VITRO)
    "Carboxymethyl cellulose CMC 1.0 wt% Polysaccharide (cellulose) Microcrystalline cellulose Cellulose 1.0 wt% Polysaccharide (cellulose) Sodium alginate Alginate 1.0 wt% Polysaccharide (alginate) Xylan (from corncob) Xylan 1.0 wt% Polysaccharide (hemicellulose)"

Growth Media

M9 carbon-source biofilm media

Temperature 24 °C
Atmosphere AEROBIC

Composition

Component Concentration Unit CHEBI
D-(+)-Glucose · MediaIngredientMech 10 mM CHEBI:17234
D-(+)-Xylose · MediaIngredientMech 12 mM N/A
D-(+)-Cellobiose · MediaIngredientMech 5 mM CHEBI:17057
Carboxymethyl cellulose · MediaIngredientMech 1.0 wt% N/A
Microcrystalline cellulose · MediaIngredientMech 1.0 wt% CHEBI:18246
Sodium alginate · MediaIngredientMech 1.0 wt% N/A
Xylan (from corncob) · MediaIngredientMech 1.0 wt% CHEBI:37166

Preparation notes: M9 media were amended with one carbon source for utilization screens or with cellobiose, cellobiose plus xylan, or cellobiose plus CMC for supernatant assays.

Evidence

PMID:42658845

"Growth curves of the mono- and quadruple-cultures in M9 supplemented with different carbon sources (Table S2) were measured using a plate reader"

PMID:42658845

"The supernatants of P. amylolyticus (P) and the SynCom were prepared from cultures on different carbon sources in M9 media with cellobiose, cellobiose+xylan, and cellobiose+CMC, respectively."

cellulose-nanofiber 3D-printed hydrogel substrates

Temperature 24 °C
Atmosphere AEROBIC

Composition

Component Concentration Unit CHEBI
cellulose nanofiber · MediaIngredientMech 1 % N/A
Carboxymethyl cellulose or xylan · MediaIngredientMech 1 % N/A

Preparation notes: Cellulose-nanofiber hydrogels were printed with CMC or xylan, with or without glucose or cellobiose, to compare spatial biofilm assembly on polymer-rich structured surfaces.

Evidence

PMID:42658845

"CNF+CMC 1 % cellulose nanofiber mixed with 1 % CMC CNF+Xylan 1 % cellulose nanofiber mixed with 1 % Xylan"

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

HabitatMech: M9 carbon-substrate biofilm laboratory assay ↗ TaxonMech: Paenibacillus amylolyticus ↗ TraitMech: Paenibacillus amylolyticus ↗ TaxonMech: Microbacterium oxydans ↗ TraitMech: Microbacterium oxydans ↗ TaxonMech: Stenotrophomonas rhizophila ↗ TraitMech: Stenotrophomonas rhizophila ↗ TaxonMech: Stenotrophomonas maltophilia ↗ TraitMech: Stenotrophomonas maltophilia ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗