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GENIA Nine-Member Multi-Pollutant Bioremediation SynCom

Community ID CommunityMech:000352
Ecological State ENGINEERED
Environment aerobic M9 minimal-medium pollutant-degradation flask culture — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗
Modeled Environment soil
ENVO:00001998 · HabitatMech ↗

A nine-member bacterial synthetic community selected by the GENIA genome-informed machine-learning framework for simultaneous degradation of lignin, atrazine, and perfluoroalkyl substances. The SynCom combines Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis isolates from xenobiotic-enriched cotton detritusphere material. In controlled M9 minimal-medium flask assays, the assembled consortium removed more PFOS, atrazine, and lignin than any single member and retained all nine strains during full-length 16S rRNA tracking.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Atlantibacter hermannii NCBITaxon:565 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "
Bacillus cabrialesii NCBITaxon:2487276 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "
Bacillus licheniformis NCBITaxon:1402 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "
Bacillus pseudomycoides NCBITaxon:64104 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "
Micrococcus luteus NCBITaxon:1270 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "
Paenibacillus polymyxa NCBITaxon:1406 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "
Pantoea dispersa NCBITaxon:59814 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "
Pseudomonas fulva NCBITaxon:47880 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "
Pseudomonas pergaminensis NCBITaxon:2853159 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The resulting nine-member community, comprising Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis, demonstrated broad catabolic capacity. "

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 GENIA Nine-Member Multi-Pollutant Bioremediation SynCom Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Other

Predicted GENIA Metabolic Complementarity

HYPOTHESIZED: Genome annotations and computational network models predict complementary degradation potential across nine selected members, including five predicted generalists and four specialists. Agreement between GENIA and iNAP is computational cross-validation, not measured interspecies metabolite transfer, active expression or catalytic necessity. Growth-screen fluorescence does not independently establish pollutant degradation. The assembly workflow is not itself a biological cause of the measured removal phenotype; no design-to-removal arrow is retained.

Participating Taxa: Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, Pseudomonas pergaminensis

Metabolites: lignin (CHEBI:6457 · MediaIngredientMech · CMMMech), atrazine (CHEBI:15930 · MediaIngredientMech · CMMMech), perfluorooctane-1-sulfonic acid (CHEBI:39421 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:42036878 - PARTIAL (COMPUTATIONAL)
    "Functional classification based on genomic capacity identified two ecological roles: 5 generalist strains (55.6% of consortium) possessing enzymatic capacity across all three pollutant classes "

Reported GENIA Liquid Pollutant Removal

The source reports consortium removal above the best assayed monoculture: PFOS 93.1%, atrazine 91.4% and lignin 91.6% in the separate treatment comparisons. A distinct seven-day mixed-pollutant experiment reports PFOS 87.1%, atrazine 84.7% and lignin 88.9%; do not substitute the higher figures for this mixture. LC-MS/MS loss and lignin UV-visible changes are community-level endpoints, not proof of reciprocal member benefit, assigned cross-feeding or complete carbon mineralization. The paper reports fluoride and intermediates, but its PFOS fluorine denominator and atrazine nitrogen/method descriptions conflict; removal is retained as source-reported, not independent certification of defluorination efficiency or complete mineralization. Supplements and raw data were not audited.

Participating Taxa: Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, Pseudomonas pergaminensis

Metabolites: lignin (CHEBI:6457 · MediaIngredientMech · CMMMech), atrazine (CHEBI:15930 · MediaIngredientMech · CMMMech), perfluorooctane-1-sulfonic acid (CHEBI:39421 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:42036878 - SUPPORT (IN_VITRO)
    "The 9-member consortium achieved 93.1% PFOS removal (2.23-fold improvement over best individual), 91.4% atrazine removal (1.47-fold), and 91.6% lignin removal (1.46-fold). "
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "yielded 84.7 ± 2.3% atrazine, 87.1 ± 3.6% PFOS, and 88.9 ± 2.9% lignin removal after 7 days"

GENIA DNA Composition and Ratio-Management Comparison

Full-length 16S rRNA gene profiles track relative DNA composition during removal; predicted hub taxa increased in relative abundance and other inoculated taxa remained detectable. These measurements do not establish absolute viable persistence, member-resolved flux or hub necessity. The source also compares self-organizing communities with daily dilution/remixing to equal ratios, reporting lower PFOS and atrazine removal in the remixed condition; the lignin comparison had p=0.092. PARTIAL: this treatment comparison supports a composition-management association with performance, but does not isolate a particular taxon, metabolite or persistence-mediated pathway from the handling intervention.

Participating Taxa: Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, Pseudomonas pergaminensis

Downstream Effects:
→ Reported GENIA Liquid Pollutant Removal

PARTIAL: Allowing composition to reorganize was associated with greater PFOS and atrazine removal than daily equal-ratio dilution/remixing. This reported intervention supports a bounded community-management effect, not selective proof that persistence or a particular cross-feeding network causes removal. Dilution/remixing changes handling as well as ratios; the reported lignin difference was not significant at p<0.05.

Evidence

  • PMID:42036878 - SUPPORT (IN_VITRO)
    "Hub strains showed predicted expansion: P. polymyxa increased from 11.1% (day 0) to 14.2% (day 3) to 15.6% (day 7), representing a 40.5% relative increase "
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "Critically, no invasive taxa (noninoculated strains) exceeded 1% relative abundance at any time point "
  • PMID:42036878 - PARTIAL (IN_VITRO)
    "Comparison of self-organizing community dynamics vs artificially maintained equal ratios"

Associated Datasets

Dataset Type Repository Accession
GENIA biodegradation strain genomes and 16S data
NCBI BioProject for the 45 whole-genome assemblies and SRA reads generated from GENIA candidate isolates, plus the full-length 16S rRNA data used for community-composition tracking. 		GENOMICS NCBI_BIOPROJECT PRJNA1370521

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which mechanisms and quantitative balances can be established independently of the GENIA predictions?

Retain reported removal and relative DNA profiles, not mutualism, measured handoffs or necessary hubs. The daily equal-ratio intervention supports only PARTIAL management-level causality because handling and composition change together; lignin p=0.092. A PFOS-only inventory at the stated 37.1 micromolar gives approximately 12.0 mg/L fluorine, not the alternatively stated 64.08 mg/L. Methods also mention a PFOA/PFOS mixture, so the true denominator needs treatment-specific reconciliation rather than a blanket impossibility claim. Atrazine concentrations, nitrogen yield and Nessler versus indophenol methods also conflict. Source-reported fluoride/intermediates are not ignored, but no efficiency or complete-mineralization certification follows. Raw data and supplements were not inspected; follow-up #1468 remains open. Existing graph corrections address #1466 without new structure or provider spend.

Attaches to: ecological_interactions#Predicted GENIA Metabolic Complementarity, ecological_interactions#Reported GENIA Liquid Pollutant Removal, ecological_interactions#GENIA DNA Composition and Ratio-Management Comparison

Environmental Factors

Factor Value Unit
Liquid-culture PFOS removal 93.1% removal within 7 days N/A
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "PFOS degradation follows sigmoid kinetics with a distinct lag phase (days 0-1, < 5% removal), exponential degradation (days 2-5), and an asymptotic approach (93.1% final). "
Liquid-culture atrazine removal 91.4% removal by day 3 N/A
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "Atrazine degradation exhibits the fastest kinetics among pollutants: 91.4% removal by day 3 "
Liquid-culture lignin removal 91.6% removal by day 5 N/A
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "Lignin degradation ( Figure b) proceeded from an initial concentration of 490.7 +/- 12.1 mg/L to a final concentration of 41.6 +/- 1.0 mg/L, representing 91.6% removal after 5 days. "
Soil-microcosm PFOS, PFOA, and atrazine removal 68.7% PFOS removal, 64.3% PFOA removal, and 73.2% atrazine removal N/A
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "Atrazine removal achieved 73.2 +/- 5.1% by day 7 compared to 18.4 +/- 3.2% in noninoculated controls "
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "PFOS degradation reached 68.7 +/- 6.8% vs 12.1 +/- 2.9% in controls "
  • PMID:42036878 - SUPPORT (IN_VITRO)
    "PFOA showed a similar pattern (64.3 +/- 7.2% removal; data not shown in the main text but included in the Supporting Information). "

Growth Media

M9 minimal medium with lignin, atrazine, or PFAS pollutants

Temperature 27 degrees Celsius

Composition

Component Concentration Unit CHEBI
disodium hydrogen phosphate · MediaIngredientMech 6.78 g/L N/A
monopotassium phosphate · MediaIngredientMech 3.0 g/L N/A
ammonium chloride · MediaIngredientMech 1.0 g/L N/A
sodium chloride · MediaIngredientMech 0.5 g/L N/A
magnesium sulfate · MediaIngredientMech 1 mM N/A
calcium chloride · MediaIngredientMech 0.1 mM N/A
kraft lignin · MediaIngredientMech 500 mg/L CHEBI:6457
atrazine · MediaIngredientMech 30 mg/L CHEBI:15930
perfluorooctane-1-sulfonic acid · MediaIngredientMech 20 mg/L CHEBI:39421
perfluorooctanoic acid · MediaIngredientMech 20 mg/L CHEBI:35549

Preparation notes: Individual-pollutant assays used kraft lignin, atrazine, or a PFAS mixture of PFOA and PFOS in the M9 formulation; the nine normalized member suspensions were mixed in equal volumes before inoculation.

Evidence

PMID:42036878

"The assembled synthetic communities were inoculated into fresh M9 minimal medium (Na2HPO4, 6.78 g L-1; KH2PO4, 3.0 g L-1; NH4Cl, 1.0 g L-1; NaCl, 0.5 g L-1; MgSO4, 1 mM; CaCl2, 0.1 mM) containing one of the three target pollutants as the sole carbon source. "

PMID:42036878

"Treatment conditions included kraft lignin (500 mg L-1), atrazine (30 mg L-1), or PFAS mixture (20 mg L-1 each of PFOA and PFOS). "

Cross-Mech Suite Links

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

HabitatMech: aerobic M9 minimal-medium pollutant-degradation flask culture ↗ TaxonMech: Atlantibacter hermannii ↗ TraitMech: Atlantibacter hermannii ↗ TaxonMech: Bacillus cabrialesii ↗ TraitMech: Bacillus cabrialesii ↗ TaxonMech: Bacillus licheniformis ↗ TraitMech: Bacillus licheniformis ↗ TaxonMech: Bacillus pseudomycoides ↗ TraitMech: Bacillus pseudomycoides ↗ TaxonMech: Micrococcus luteus ↗ TraitMech: Micrococcus luteus ↗ TaxonMech: Paenibacillus polymyxa ↗ TraitMech: Paenibacillus polymyxa ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗