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Bacillus A1-A3 Naphthalene Biofilm Consortium

Community ID CommunityMech:000358
Ecological State ENGINEERED
Environment laboratory PAH-degradation biofilm assay — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗
Modeled Environment petroleum-contaminated soil — ontology label: soil
ENVO:00001998 · HabitatMech ↗

A defined two-isolate Bacillus consortium, Consortium 3, assembled from Bacillus paranthracis isolate A1 and Bacillus licheniformis isolate A3 after enrichment of petroleum-contaminated soil from Ras Gharib, Egypt on polycyclic aromatic hydrocarbons. The A1/A3 pair was one of four consortia built from the three strongest phenanthrene- and naphthalene-degrading isolates. Consortium 3 was induced to grow as a glass-attached biofilm, showed the highest reported synergistic interaction during planktonic naphthalene degradation, reached 94.69% naphthalene degradation as a biofilm culture, and its preformed biofilm degraded 81.47% of naphthalene in artificially contaminated soil. Phenanthrene behaved differently: individual isolates outperformed the consortia, and the authors attributed the lower consortium rates to antagonistic interactions under the more complex PAH substrate.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Bacillus paranthracis A1 — ontology label: Bacillus paranthracis NCBITaxon:2026186 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "A1(Bacillus paranthracis), and A3(Bacillus licheniformis)"
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "Consortium 3 (A1 and A3)"
Bacillus licheniformis A3 — ontology label: Bacillus licheniformis NCBITaxon:1402 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "A1(Bacillus paranthracis), and A3(Bacillus licheniformis)"
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "Consortium 3 (A1 and A3)"

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 Bacillus A1-A3 Naphthalene Biofilm Consortium 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

Consortium 3 naphthalene synergy

The A1/A3 Consortium 3 improved naphthalene degradation relative to the A1 and A3 monocultures in both planktonic and biofilm growth modes, including 92.43% planktonic and 94.69% biofilm naphthalene biodegradation in the seven-day HPLC assay. These are HPLC parent-substrate-disappearance endpoints, not complete mineralization or reciprocal member fitness; comparisons here concern A1/A3, not every isolate in the study.

Participating Taxa: Bacillus paranthracis A1, Bacillus licheniformis A3

Metabolites: naphthalene (CHEBI:16482 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:42587276 - SUPPORT (IN_VITRO)
    "The result demonstrated that the naphthalene biodegradation rates of 41.01, 38.92, 75.54, 44.71, 92.43, and 64.47% for the planktonic cultures"
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "whereas were 87.72, 64.57, 77.45, 86.88, 94.69, and 79.74% for the biofilm cultures of isolates A1, A3, consortium 1, consortium 2, consortium 3, and consortium 4, respectively."
  • PMID:42587276 - PARTIAL (IN_VITRO)
    "This finding demonstrated the synergistic interaction between the consortia`s members, with the highest synergistic interaction between the planktonic isolates (A1 and A3) in the consortium 3"

Lower Consortium Phenanthrene Removal

Individual isolates removed more phenanthrene than the tested consortia in planktonic and biofilm assays. PARTIAL - the authors propose antagonism and nutrient competition as explanations; aggregate HPLC removal does not measure harm to both consortium members.

Participating Taxa: Bacillus paranthracis A1, Bacillus licheniformis A3

Metabolites: phenanthrene (CHEBI:28851 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:42587276 - SUPPORT (IN_VITRO)
    "Surprisingly, the biodegradation rates by the individual isolates were higher than those of the consortium. This observation may relate to an antagonistic effect of the consortium isolates"
  • PMID:42587276 - PARTIAL (IN_VITRO)
    "In the case of phenanthrene, a complex substrate, it promotes antagonistic interactions and negative growth"

Consortium 3 soil naphthalene removal

A preformed Consortium 3 biofilm degraded 81.47% of naphthalene from artificially contaminated soil after seven days in sealed flasks. This controlled microcosm HPLC result measures parent-compound disappearance, not field efficacy, complete mineralization or mutualism.

Participating Taxa: Bacillus paranthracis A1, Bacillus licheniformis A3

Metabolites: naphthalene (CHEBI:16482 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:42587276 - SUPPORT (IN_VITRO)
    "The HPLC results exhibited that the biofilm of isolate A1 degraded 60.98% of phenanthrene, and the biofilm of the consortium 3 degraded 81.47% of naphthalene in soil samples"

Knowledge gaps & discussions (3)

KNOWLEDGE_GAP OPEN Which GenBank 16S rRNA accession corresponds to Bacillus paranthracis A1 and which corresponds to Bacillus licheniformis A3?

The article reports the three accessions PV848451, PV848453, and PV848454 for the selected isolates, but the flattened OA text does not map those accessions to the A1 and A3 isolate records without relying on figure interpretation.

Attaches to: taxonomy#Bacillus paranthracis A1, taxonomy#Bacillus licheniformis A3

1 evidence item(s)
full_text SUPPORT PMID:42587276

The 16SrRNA gene sequences of the three most efficient isolates have been submitted to NCBI GenBank under the accession numbers PV848451 , PV848453 , and PV848454 , respectively.

Shows that three accessions exist but does not map each accession onto Consortium 3's A1 and A3 isolates in the flattened OA text.

KNOWLEDGE_GAP OPEN Which metabolite or enzymatic step mediates the observed naphthalene synergy between A1 and A3?

The study measured enhanced naphthalene disappearance by the A1/A3 consortium, but it did not sequence the isolates' naphthalene pathways or experimentally identify a transferred intermediate. The current record therefore treats synergy as a community-level observation and does not assert a directional cross-feeding edge.

Attaches to: ecological_interactions#Consortium 3 naphthalene synergy

1 evidence item(s)
full_text SUPPORT PMID:42587276

One possible reason that makes the bacterial consortia have a superior naphthalene biodegradation efficiency is that, during the process of biotransformation, the product of one bacterium can be employed as the foundation for the catabolism and growth of another.

Records the paper's proposed but untested metabolite exchange explanation for Consortium 3's naphthalene synergy.

KNOWLEDGE_GAP OPEN What member-specific fitness and carbon balance explain the substrate-dependent consortium outcomes?

PMID:42587276 supports enhanced naphthalene removal and lower consortium phenanthrene removal. These performance endpoints do not establish reciprocal benefit/harm or a complete carbon balance. Preserve the existing exchange and accession gaps; no workflow arrow is restored.

Attaches to: ecological_interactions#Consortium 3 naphthalene synergy, ecological_interactions#Lower Consortium Phenanthrene Removal, ecological_interactions#Consortium 3 soil naphthalene removal

External Resources

Name Repository Resource ID
Primary publication - Bacillus A1-A3 naphthalene biofilm consortium
BMC Microbiology 2026 open-access article describing Bacillus paranthracis A1 plus Bacillus licheniformis A3 Consortium 3 and its PAH-degrading biofilms. 		OTHER PMID:42587276
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "Enhancing biodegradation of polycyclic aromatic hydrocarbons using bacterial consortia and biofilm"

Environmental Factors

Factor Value Unit
Neutral MSM enrichment pH 7.0 +/- 0.2 N/A
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "The broth media was prepared, and the pH value was adjusted to 7.0 ± 0.2 using 1 N HCl or 1 N NaOH before sterilization."
Naphthalene in artificially contaminated soil 200 mg/g
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "A 5 g sample of the soil was artificially contaminated with 200 mg/g of phenanthrene or naphthalene."
Optimized PAH degradation temperature and pH 37 deg C and pH 7 N/A
  • PMID:42587276 - SUPPORT (IN_VITRO)
    "The results showed that the highest growth and degradation rate of phenanthrene and naphthalene were achieved at 37 °C and pH 7."

Growth Media

Mineral salt medium PAH degradation assay

pH 7.0
Temperature 37 °C

Preparation notes: Overnight individual isolates and consortia were inoculated into 7 mL MSM with 200 mg/L phenanthrene or naphthalene for planktonic assays. For biofilm-mediated assays, each isolate or consortium was first grown as a static biofilm in TSB on the walls of glass tubes, washed, overlaid with 7 mL MSM plus 200 mg/L PAH, sealed, and incubated for seven days.

Evidence

PMID:42587276

"Degradation of the PAHs, phenanthrene or naphthalene, was analysed using High Performance Liquid Chromatography"

PMID:42587276

"The analysis was conducted to determine the degradation efficiency at an initial concentration of 200 mg L⁻¹."

PMID:42587276

"For planktonic–mediated biodegradation, individual isolates and consortia were grown overnight and inoculated in tubes containing 7 mL MSM medium supplemented with 200 mg L⁻¹phenanthrene."

PMID:42587276

"After 48 h, free planktonic cells were carefully removed from the glass tube, and the biofilm formed inside the walls was rinsed once with sterile water. Afterwards, 7 mL of MSM medium containing 200 mg L⁻¹ phenanthrene was added to each tube."

Trypticase soy broth static biofilm induction medium

Temperature 37 °C

Preparation notes: Fresh-grown cell cultures were diluted in TSB, transferred to glass tubes, and incubated statically for 48 h to form crystal-violet-stained biofilms on the tube walls.

Evidence

PMID:42587276

"fresh-grown cell cultures were diluted to OD550 = 0.2 in Trypticase soy broth (TSB) medium. One mL of this suspension was transferred to a glass tube containing 1 mL of TSB medium. Then the tubes were incubated at 37 °C under static conditions for 48 h."

Artificial naphthalene-contaminated soil biofilm assay

Temperature 37 °C

Composition

Component Concentration Unit CHEBI
naphthalene · MediaIngredientMech 200 mg/g soil CHEBI:16482

Preparation notes: Consortium 3 biofilms were preformed for 48 h in static 100 mL conical flasks with 50 mL TSB. The planktonic culture was removed, 5 g of uncontaminated soil was added and artificially contaminated with naphthalene, and the closed flasks were incubated for seven days before HPLC analysis.

Evidence

PMID:42587276

"The selected isolate-developed biofilm was developed in advance at 37 °C for 48 h under static conditions in 100 mL conical flasks containing 50 mL of TSB medium."

PMID:42587276

"A 5 g sample of the soil was artificially contaminated with 200 mg/g of phenanthrene or naphthalene. Then the flasks were tightly closed and incubated at 37 °C for 7 days."

Cross-Mech Suite Links

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

HabitatMech: laboratory PAH-degradation biofilm assay ↗ TaxonMech: Bacillus paranthracis A1 ↗ TraitMech: Bacillus paranthracis A1 ↗ TaxonMech: Bacillus licheniformis A3 ↗ TraitMech: Bacillus licheniformis A3 ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗