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Apple Fire Blight A+N+P SynCom

Community ID CommunityMech:000377
Ecological State ENGINEERED
Environment apple flower and apple-plant host tissue — ontology label: plant-associated environment
ENVO:01001001 · HabitatMech ↗
Modeled Environment plant-associated environment
ENVO:01001001 · HabitatMech ↗

A nine-member bacterial synthetic community assembled from three apple fire-blight biocontrol design groups: Streptomyces recifensis SN1E1 and Paenibacillus polymyxa AF2927 as direct anti-Erwinia amylovora strains, Labrys miyagiensis NBRC101365, Labrys okinawensis DSM18385, Novosphingobium mathurense SM117, Novosphingobium endophyticum EGI60015, and Terriglobus aquaticus 03SUJ4 as healthy apple network taxa, and Kitasatospora papulosa AF6313 plus Pseudomonas lundensis AB23 as pathway-associated strains. The full A+N+P mixture eliminated visible disease in Fuji apple fruit wounds, matched oxytetracycline at 1.67% disease severity in rose flowers, and reduced Erwinia amylovora TS3128 density in apple flower exudate during follow-up co-cultivation assays.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Streptomyces recifensis SN1E1 — ontology label: Streptomyces recifensis NCBITaxon:67355 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Streptomyces recifensis Soil 98.62 SN1E1"
Paenibacillus polymyxa AF2927 — ontology label: Paenibacillus polymyxa NCBITaxon:1406 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Paenibacillus polymyxa Apple flower bud 99.66 AF2927"
Labrys miyagiensis NBRC101365 — ontology label: Labrys miyagiensis NCBITaxon:346912 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Labrys miyagiensis Grassland soil of an experimental farm 99.92 NBRC101365"
Labrys okinawensis DSM18385 — ontology label: Labrys okinawensis NCBITaxon:346911 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Labrys okinawensis Root-nodule of Entada phaseoloides 97.40 DSM18385"
Novosphingobium mathurense SM117 — ontology label: Novosphingobium mathurense NCBITaxon:428990 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Novosphingobium mathurense Sea sand soil 100 SM117"
Novosphingobium endophyticum EGI60015 — ontology label: Novosphingobium endophyticum NCBITaxon:1955250 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Novosphingobium endophyticum Roots of Glycyrrhiza uralensis 99.92 EGI60015"
Terriglobus aquaticus 03SUJ4 — ontology label: Terriglobus aquaticus NCBITaxon:940139 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Terriglobus aquaticus Freshwater 99.88 03SUJ4"
Kitasatospora papulosa AF6313 — ontology label: Kitasatospora papulosa NCBITaxon:1464011 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Kitasatospora papulosa Apple flower 100 AF6313"
Pseudomonas lundensis AB23 — ontology label: Pseudomonas lundensis NCBITaxon:86185 · TaxonMech · TraitMech
PATHOGEN_ANTAGONIST
DOMINANT
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Pseudomonas lundensis Bee gut 99.93 AB23"

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 Apple Fire Blight A+N+P 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

A+N+P Fire-Blight Severity Reduction in Rosaceae Tissue

The nine-member A+N+P treatment reduced measured fire-blight severity to 0% in Fuji apple-fruit wounds and 1.67% in rose-flower ovaries. These are tissue-disease endpoints, not measurements of pathogen density or proof of a particular antagonistic mechanism.

Participating Taxa: Streptomyces recifensis SN1E1, Paenibacillus polymyxa AF2927, Labrys miyagiensis NBRC101365, Labrys okinawensis DSM18385, Novosphingobium mathurense SM117, Novosphingobium endophyticum EGI60015, Terriglobus aquaticus 03SUJ4, Kitasatospora papulosa AF6313, Pseudomonas lundensis AB23, Erwinia amylovora TS3128

Biological Processes:

Evidence

  • PMID:40223277 - SUPPORT (IN_VIVO)
    "EA+A+P at 9.33%, EA+N+P at 2.67%, EA+A+N+P at 0% severity, and control at 0%, in descending order."
  • PMID:40223277 - SUPPORT (IN_VIVO)
    "EA+P at 6.67%, EA+A+P at 6.67%, EA+N at 3.33%, EA+A+N+P at 1.67%, EA+oxytetracycline at 1.67%, and control at 0%, in descending order."

A+N+P Erwinia Density Suppression in Flower Exudate

PARTIAL - the A+N+P treatment reduced E. amylovora TS3128 density over 72 hours in apple-flower exudate. Substrate-use overlap supports nutrient competition as a candidate explanation, but does not distinguish it from antibiosis or establish reciprocal harm to the SynCom.

Participating Taxa: Streptomyces recifensis SN1E1, Paenibacillus polymyxa AF2927, Labrys miyagiensis NBRC101365, Labrys okinawensis DSM18385, Novosphingobium mathurense SM117, Novosphingobium endophyticum EGI60015, Terriglobus aquaticus 03SUJ4, Kitasatospora papulosa AF6313, Pseudomonas lundensis AB23, Erwinia amylovora TS3128

Biological Processes:

Evidence

  • PMID:40468884 - SUPPORT (IN_VITRO)
    "A linear regression analysis indicated that the concentration of E. amylovora decreased over time in groups treated with antibacterial agents: antibacterial (A), pathway (P), antibacterial+pathway (AP), and antibacterial+network+pathway (ANP). For the control, the slope change over time was not statistically significant, with an R2 of 0.0227 (P > 0.05). The R2 values of the linear regression equations over time for each treatment are as follows: A was 0.7639 (P < 0.001), N was 0.52 (P < 0.001), ANP was 0.506 (P < 0.001), P was 0.354 (P < 0.01), AP was 0.2563 (P < 0.05), NP was 0.0141 (P > 0.05), A+N was 0.0326 (P > 0.05)."
  • PMID:40468884 - SUPPORT (IN_VITRO)
    "When SynCom was co-cultivated with E. amylovora in extracts of apple flowers, a decrease in E. amylovora density was observed compared to its monoculture."

Associated Datasets

Dataset Type Repository Accession
Apple fire blight SynCom BioProject
NCBI BioProject accession cited by the primary SynCom paper for the apple fire blight SynCom project. 		OTHER NCBI_BIOPROJECT PRJNA1144217

Knowledge gaps & discussions (3)

KNOWLEDGE_GAP OPEN Does Terriglobus aquaticus TAH1 in the follow-up genome paper represent the same strain as Terriglobus aquaticus 03SUJ4 in the SynCom construction paper?

The construction paper's membership table names Terriglobus aquaticus strain 03SUJ4, but the genome table in the follow-up paper names the analyzed Terriglobus aquaticus strain TAH1.

Attaches to: taxonomy#Terriglobus aquaticus 03SUJ4

KNOWLEDGE_GAP OPEN Which predicted secondary-metabolite clusters are experimentally responsible for Erwinia amylovora suppression by the non-A network and pathway SynCom members?

The follow-up paper predicted secondary-metabolite clusters from the network and pathway strain genomes, but Supplementary Table 1 was available only as a PDF/image supplement during curation and the publication does not chemically validate member-level effectors for the full A+N+P community.

Attaches to: ecological_interactions#A+N+P Fire-Blight Severity Reduction in Rosaceae Tissue, ecological_interactions#A+N+P Erwinia Density Suppression in Flower Exudate

KNOWLEDGE_GAP OPEN How much of exudate pathogen suppression is caused by resource competition rather than antibiosis?

PMIDs:40223277 and 40468884 distinguish tissue disease scores from exudate pathogen counts. Biolog overlap and co-culture responses do not identify the active mechanism; predicted biosynthetic clusters are not chemically validated effectors. Preserve the separate strain-alias and effector gaps.

Attaches to: ecological_interactions#A+N+P Fire-Blight Severity Reduction in Rosaceae Tissue, ecological_interactions#A+N+P Erwinia Density Suppression in Flower Exudate

External Resources

Name Repository Resource ID
Primary publication - Apple fire blight ANP SynCom
Journal of Microbiology and Biotechnology 2025 open-access article, doi:10.4014/jmb.2501.01047, describing construction of the nine-member A+N+P apple fire-blight biocontrol SynCom. 		OTHER PMID:40223277
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "Design and Evaluation of Synthetic Microbial Communities for Effective Fire Blight Disease Control in Apples"
Follow-up publication - Apple fire blight SynCom mechanisms
Plant Pathology Journal 2025 open-access article, doi:10.5423/PPJ.OA.03.2025.0040, describing genome analysis and apple-flower-exudate nutrient competition for the SynCom. 		OTHER PMID:40468884
  • PMID:40468884 - SUPPORT (IN_VITRO)
    "Genetic and Nutritional Dynamics of SynCom in Suppressing Apple Fire Blight"
NCBI BioProject PRJNA1144217
NCBI BioProject accession cited by the primary SynCom paper for the apple fire blight SynCom project. 		OTHER PRJNA1144217
  • PMID:40223277 - SUPPORT (IN_VITRO)
    "The project has been deposited at NCBI under the BioProject (PRJNA1144217)."

Environmental Factors

Factor Value Unit
Fuji apple flower exudate nutrient limitation N/A
  • PMID:40468884 - SUPPORT (IN_VITRO)
    "Apple flowers (cv. Fuji) were disinfected with 0.5 g in 70% ethanol for 30 s and then washed twice with ddH2O. The washed flowers were dried and then sonicated in 5 mL of ddH2O for 30 min. After sonication, the solution was filtered through a 0.45 μm filter, and to remove any residual debris, the supernatant was separated by centrifugation at 1,077 ×g for 5 min."

Growth Media

R2A agar or broth with 0.5% mannitol

Temperature 28 °C

Preparation notes: The follow-up genome analysis cultured SynCom strains on R2A agar or in broth supplemented with 0.5% mannitol before genome sequencing and nutrient utilization assays.

Evidence

PMID:40468884

"All strains were cultured at 28°C for 2–4 days on R2A agar (0.5 g casamino acid hydrolysate, 0.5 g yeast extract, 0.5 g proteose peptone, 0.5 g dextrose, 0.5 g soluble starch, 0.3 g dipotassium phosphate, 0.05 g magnesium sulfate, 0.3 g sodium pyruvate and 15 g agar per L, pH 7.0–7.4) or broth media supplemented with 0.5% mannitol."

Fuji apple flower exudate co-culture

Temperature 28 °C

Preparation notes: SynCom groups were mixed at OD600 0.5, combined 1:1:1 with OD600 0.1 Erwinia amylovora TS3128 and Fuji apple flower exudate, incubated shaking at 28 °C, and enumerated on 1/5 TSA with 50 micrograms/mL rifampicin at 0, 24, 48, and 72 h.

Evidence

PMID:40468884

"The E. amylovora suspension was adjusted to OD600 0.1, and the flower extract and SynCom mixture, containing the pathogen in a 1:1:1 ratio, were cultured at 28°C in a shaking incubator."

PMID:40468884

"SynCom strains were adjusted to an OD600 0.5 and mixed according to their respective groups. These mixtures were combined with OD600 0.1 E. amylovora and flower extracts in proportion."

PMID:40468884

"Subsequently, the cell density of E. amylovora was determined at 0, 24, 48, and 72 h on 1/5 TSA (6 g tryptic soy broth, 20 g agar per L) with 50 μg/mL rifampicin."

Cross-Mech Suite Links

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

HabitatMech: apple flower and apple-plant host tissue ↗ TaxonMech: Streptomyces recifensis SN1E1 ↗ TraitMech: Streptomyces recifensis SN1E1 ↗ TaxonMech: Paenibacillus polymyxa AF2927 ↗ TraitMech: Paenibacillus polymyxa AF2927 ↗ TaxonMech: Labrys miyagiensis NBRC101365 ↗ TraitMech: Labrys miyagiensis NBRC101365 ↗ TaxonMech: Labrys okinawensis DSM18385 ↗ TraitMech: Labrys okinawensis DSM18385 ↗ TaxonMech: Novosphingobium mathurense SM117 ↗ TraitMech: Novosphingobium mathurense SM117 ↗ TaxonMech: Novosphingobium endophyticum EGI60015 ↗ TraitMech: Novosphingobium endophyticum EGI60015 ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗