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CommunityMech

- Showing 295 of 295 communities + Showing 300 of 300 communities
@@ -931,6 +931,37 @@

Altered Schaedler Flora Gnotobiotic Mouse Community

+ +

Anabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium

+

An anaerobic-digestion microbial consortium studied as part of a bioregenerative life-support concept for Mars: cyanobacterial biomass (Anabaena sp.), which can be grown on Martian resources, is anaerobically digested to mobilize nutrients (ammonium and phosphate) for use as a crop fertilizer, with biogas as a co-product. Ramalho et al. (2025, Bioresource Technology) tested three microbial communities for their ability to digest Anabaena biomass in three matrices — a minimal medium, 200 g/L MGS-1 Mars regolith simulant, and water. In minimal medium the taxonomic (16S) analysis revealed a SYNTROPHIC community: fermentative bacteria degrade the cyanobacterial biomass and cross-feed hydrogenotrophic methanogenic archaea (interspecies H2/CO2 transfer driving methanogenesis). In the MGS-1 regolith matrix, however, the methanogens were outcompeted by sulfate-reducing bacteria, and the regolith also adsorbed organics and lowered phosphate/ammonium recovery. The Anabaena biomass here is the digestion FEEDSTOCK (substrate) rather than a live member of the digesting consortium. All communities produced ammonium and removed organic carbon, supporting the viability of a Mars-relevant bioprocess for fertilizer production. The specific dominant genera resolved by the paper's 16S analysis are reported in the full text, which is paywalled; only the functional guilds (fermentative bacteria, hydrogenotrophic methanogens, sulfate-reducing bacteria) are named in the openly available abstract and are therefore represented here as interactions/roles rather than as NCBITaxon-grounded members. +

+
+
+ + + + + + + 1 + + ENGINEERED +
+ SYNTROPHY +
+ + Bifidobacterium-Ruminococcus Infant HMO Cross-Feeding Coculture + +

BioAsteroid ISS Chondrite Biomining Consortium

+

The BioAsteroid experiment tested microbial biomining of asteroidal (L-chondrite) material under microgravity aboard the International Space Station (ISS). Two heterotrophic microorganisms — the bacterium Sphingomonas desiccabilis CP1D and the fungus Penicillium simplicissimum DSM 1078 — were flown both as single strains and as an artificial two-member consortium on crushed Northwest Africa (NWA) 869 L-chondrite meteorite fragments, in a 50% v/v R2A medium, inside BioMining Reactors housed in KUBIK incubators. The study measured leaching of 44 elements (including the platinum-group elements ruthenium, palladium and platinum, and other elements of industrial interest) from the meteorite and compared microbial versus abiotic (non-biological) leaching under microgravity and terrestrial gravity. Penicillium simplicissimum was the most effective bioleaching organism in microgravity, enhancing release of palladium, platinum and other elements relative to non-biological controls, while Sphingomonas desiccabilis formed a contiguous biofilm on the rock surface but performed similarly or worse than the abiotic control for most platinum-group elements. In the consortium, the fungus alone outperformed the mixture for palladium, suggesting an antagonistic effect of the bacterium. Metabolomic analysis showed distinct, microgravity-dependent changes in microbial metabolism, particularly for P. simplicissimum, with increased production of carboxylic acids and other molecules of potential biomining or pharmaceutical interest. The work demonstrates proof of principle for microbe-driven transformation of asteroidal material for in situ resource utilization in space. +

+
+
+ + + + + + + 2 + + ENGINEERED +
+ BIOMINING +
+ + BioModels MODEL2407300002 Sponge Holobiont Network + +

BioRock ISS Basalt Biomining Consortium

+

A defined three-species bacterial panel flown as the ESA BioRock experiment on board the International Space Station to test microbial bioleaching of economically important elements from basaltic rock under microgravity, simulated Mars gravity, and simulated Earth gravity (with ground 1 x g controls). Sphingomonas desiccabilis CP1D (DSM 16792), Bacillus subtilis NCIB 3610 (DSM 10), and Cupriavidus metallidurans CH34 (DSM 2839) were each cultivated on slides of olivine basalt (collected near Gufunes, Reykjavik, Iceland; chosen as an analogue of Moon/Mars surface material) inside a purposely designed miniature biomining reactor housed in the KUBIK incubator. Sphingomonas desiccabilis enhanced mean leached concentrations of rare earth elements (the lanthanides plus yttrium) relative to non-biological controls in all gravity regimes, while Bacillus subtilis reduced REE bioleaching efficacy and Cupriavidus metallidurans showed no difference, demonstrating the microbial specificity of the process as on Earth. A companion analysis showed that Sphingomonas desiccabilis and Bacillus subtilis both enhanced vanadium leaching by 184.92 to 283.22% relative to sterile controls, and a third study found no significant differences in final bacterial cell concentrations between gravity regimes. Gravity level had no significant effect on mean leaching in any case, establishing the principle of biomining and associated bioindustrial processes on Solar System bodies with non-1 x g gravity. +

+
+
+ + + + + + + 3 + + ENGINEERED +
+ BIOMINING +
+ + Lotus Lj-SC3 Synthetic Community + +

Lunar and Martian Simulant PGPB Lettuce SynCom

+

A defined four-strain plant growth-promoting bacterial (PGPB) consortium designed for space-agriculture (In-Situ Resource Utilization) research, composed of Azotobacter chroococcum 76A, Priestia megaterium EL5, Methylobacterium populi VP2, and Kosakonia pseudosacchari TL13. The strains belong to the microbial collection of the Department of Agricultural Sciences of the University of Naples Federico II and were selected for complementary plant growth-promoting traits (nitrogen fixation, phosphate solubilization, phytohormone biosynthesis) and for mutual non-antagonism in dual-culture assays. In a greenhouse pot experiment, the consortium was combined with green compost derived from plant residues (pH 8.25, low C/N ratio) to improve lettuce (Lactuca sativa cv. Grand Rapids) growth on commercial Lunar (LHS-1) and Martian (MMS-1) regolith simulants with zero external chemical input aside from the compost. Compost amendment increased lettuce biomass and nutrient bioavailability, and PGPB inoculation enhanced leaf biomass and mineral nutritional content while significantly increasing the copy number of functional marker genes for nitrogen fixation (nifH), alkaline phosphatase (phoD), and phytase (BPP) in non-amended substrates. The system is a Bioregenerative Life Support System model relevant to regolith-agriculture and long-term space missions. +

+
+
+ + + + + + + 4 + + ENGINEERED +
+ RHIZOSPHERE +
+ + + +

Lunar Regolith Simulant Phosphorus-Solubilizing Bacteria for Nicotiana benthamiana

+

A defined set of phosphorus-solubilizing bacteria (PSBs) assembled to improve the fertility of lunar regolith simulant for in-situ resource utilization (ISRU) agriculture in bioregenerative life support systems. Five commonly used microbial-fertilizer strains were tested on a CAS-1 lunar soil simulant: Bacillus mucilaginosus (AS1.232), Bacillus megaterium (AS1.217), Bacillus subtilis (CMCC 63501), Bacillus licheniformis (ATCC 11946), and Pseudomonas fluorescens (ATCC 13525). In a 21-day bio-improving experiment followed by a 24-day Nicotiana benthamiana cultivation experiment, three of the strains - Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens - tolerated the lunar regolith simulant conditions and dissociated insoluble inorganic phosphorus from the simulant. The mechanism is chemolithoheterotrophic organic-acid production: the bacteria synthesize organic acids (e.g. oxalic, citric, tartaric acids) from carbon sources in the medium, lowering the pH and chelating metal ions in insoluble phosphates such as Ca3(PO4)2, FePO4, and AlPO4, thereby releasing available phosphate. PSB treatment raised the available phosphorus content of the simulant and promoted Nicotiana benthamiana growth, with the largest improvement when the simulant was pre-cultured with PSBs 18 days before sowing. The work establishes a microbiological route to convert lunar regolith into a plant-cultivation substrate for future lunar bases. +

+
+
+ + + + + + + 5 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + + + + + + Anabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium - CommunityMech + + + +
+
+ ← Back to Communities +

Anabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000307 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + anaerobic-digestion laboratory culture (Mars regolith-simulant context) +
+ + ENVO:01001405 + + +
+ +
+
+ + + +
+

An anaerobic-digestion microbial consortium studied as part of a bioregenerative life-support concept for Mars: cyanobacterial biomass (Anabaena sp.), which can be grown on Martian resources, is anaerobically digested to mobilize nutrients (ammonium and phosphate) for use as a crop fertilizer, with biogas as a co-product. Ramalho et al. (2025, Bioresource Technology) tested three microbial communities for their ability to digest Anabaena biomass in three matrices — a minimal medium, 200 g/L MGS-1 Mars regolith simulant, and water. In minimal medium the taxonomic (16S) analysis revealed a SYNTROPHIC community: fermentative bacteria degrade the cyanobacterial biomass and cross-feed hydrogenotrophic methanogenic archaea (interspecies H2/CO2 transfer driving methanogenesis). In the MGS-1 regolith matrix, however, the methanogens were outcompeted by sulfate-reducing bacteria, and the regolith also adsorbed organics and lowered phosphate/ammonium recovery. The Anabaena biomass here is the digestion FEEDSTOCK (substrate) rather than a live member of the digesting consortium. All communities produced ammonium and removed organic carbon, supporting the viability of a Mars-relevant bioprocess for fertilizer production. The specific dominant genera resolved by the paper's 16S analysis are reported in the full text, which is paywalled; only the functional guilds (fermentative bacteria, hydrogenotrophic methanogens, sulfate-reducing bacteria) are named in the openly available abstract and are therefore represented here as interactions/roles rather than as NCBITaxon-grounded members. +

+
+ + + + +
+

Taxonomy

+ + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Anabaena sp. (cyanobacterial digestion feedstock) + + + NCBITaxon:1163 + + + +
+ + PRIMARY_PRODUCER + +
+ + 		N/A
+
    + +
  • + + PMID:40089033 + + - SUPPORT (IN_VITRO) + +
    "digest the biomass of Anabaena sp. in minimal medium,"
    + +
    • + +
+
+
+ + + +
+

Ecological Interactions

+ + + +
+
+ + Ecological interaction network for Anabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium + Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism). + +
+
+ Taxon +
+
+ Cross-feeding +
+
+ Mutualism +
+
+ Syntrophy +
+
+ Competition +
+
+ Commensalism +
+
+ Niche partitioning +
+
+ Colonization facilitation +
+
+ Strain competition +
+
+ Predation +
+
+
+ + +
+
+

Fermenter-to-methanogen syntrophy (interspecies H2/CO2 transfer)

+ SYNTROPHY +
+ + + + + + +

Metabolites: + + dihydrogen + (CHEBI:18276), + + carbon dioxide + (CHEBI:16526), + + acetate + (CHEBI:30089), + + methane + (CHEBI:16183) + +

+ + + +

Biological Processes:

+
    + +
  • + methanogenesis + (GO:0015948) +
    • + +
  • + biological process involved in interspecies interaction between organisms + (GO:0044419) +
    • + +
+ + + + + +

Evidence

+
    + +
  • +
    + + PMID:40089033 + + - SUPPORT (IN_VITRO) +
    + +
    "taxonomic analysis revealed a syntrophic fermentative community and"
    + +
    • + +
  • +
    + + PMID:40089033 + + - SUPPORT (IN_VITRO) +
    + +
    "hydrogenotrophic methanogens in minimal medium, but methanogens were outcompeted"
    + +
    • + +
+ +
+ +
+
+

Sulfate-reducer outcompetition of methanogens in MGS-1 regolith

+ COMPETITION +
+ + + + + + +

Metabolites: + + dihydrogen + (CHEBI:18276), + + sulfate + (CHEBI:16189) + +

+ + + +

Biological Processes:

+
    + +
  • + dissimilatory sulfate reduction + (GO:0019420) +
    • + +
+ + + + + +

Evidence

+
    + +
  • +
    + + PMID:40089033 + + - SUPPORT (IN_VITRO) +
    + +
    "in MGS-1 by sulfate-reducing bacteria."
    + +
    • + +
  • +
    + + PMID:40089033 + + - SUPPORT (IN_VITRO) +
    + +
    "hydrogenotrophic methanogens in minimal medium, but methanogens were outcompeted"
    + +
    • + +
+ +
+ + +
+ + + + + + +
+

External Resources

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameRepositoryResource ID
+ Primary publication - anaerobic digestion of cyanobacterial biomass for Mars fertilizer + +
Ramalho et al. 2025, Bioresource Technology — tests three microbial communities for anaerobic digestion of Anabaena sp. biomass in minimal medium, 200 g/L MGS-1 Mars regolith simulant, and water, for Mars crop-fertilizer production. + + + 		OTHER + + doi:10.1016/j.biortech.2025.132383 + +
+
    + +
  • + + PMID:40089033 + + - SUPPORT (IN_VITRO) + +
    "this study suggests the viability of a bioprocess which could"
    + +
    • + +
+
+ NCBI Taxonomy - Anabaena + +
NCBI Taxonomy record for the genus Anabaena (cyanobacterial digestion feedstock). + + 		OTHER + + NCBITaxon:1163 + +
+
+ + + +
+

Environmental Factors

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
MGS-1 Mars regolith simulant matrix200 g/L MGS-1 Mars global simulantN/A
+
    + +
  • + + PMID:40089033 + + - SUPPORT (IN_VITRO) + +
    "simulant (MGS-1), and water."
    + +
    • + +
  • + + PMID:40089033 + + - SUPPORT (IN_VITRO) + +
    "adsorbed organics and reduced the phosphate and ammonium recovery efficiency. A"
    + +
    • + +
+
Anaerobic-digestion nutrient outputsammonium production and organic-carbon removalN/A
+
    + +
  • + + PMID:40089033 + + - SUPPORT (IN_VITRO) + +
    "All communities produced ammonium and removed organic carbon in all"
    + +
    • + +
+
+
+ + + + +
+

Growth Media

+ +
+

+ Anabaena anaerobic-digestion assay (minimal medium / MGS-1 / water) + +

+ + + +
+ + + + + +
+ Atmosphere + ANAEROBIC +
+ +
+ + + + +

+ Preparation notes: Three matrices were tested for anaerobic digestion of Anabaena sp. biomass: a minimal medium, 200 g/L MGS-1 Mars regolith simulant, and water. Detailed medium composition, temperature, pH, and incubation parameters are in the paper's Methods, which is paywalled and therefore not asserted here. + +

+ + + +
+

Evidence

+ +
+ + + PMID:40089033 + + + + +

"digest the biomass of Anabaena sp. in minimal medium,"

+ +
+ +
+ + + PMID:40089033 + + + + +

"simulant (MGS-1), and water."

+ +
+ +
+ +
+ +
+ +
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/BioAsteroid_ISS_Chondrite_Biomining_Consortium.html b/docs/communities/BioAsteroid_ISS_Chondrite_Biomining_Consortium.html new file mode 100644 index 00000000..5816b006 --- /dev/null +++ b/docs/communities/BioAsteroid_ISS_Chondrite_Biomining_Consortium.html @@ -0,0 +1,1593 @@ + + + + + + BioAsteroid ISS Chondrite Biomining Consortium - CommunityMech + + + +
+
+ ← Back to Communities +

BioAsteroid ISS Chondrite Biomining Consortium

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000305 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + BioAsteroid ISS microgravity biomining hardware +
+ + ENVO:01001405 + + +
+ +
+
+ + + +
+

The BioAsteroid experiment tested microbial biomining of asteroidal (L-chondrite) material under microgravity aboard the International Space Station (ISS). Two heterotrophic microorganisms — the bacterium Sphingomonas desiccabilis CP1D and the fungus Penicillium simplicissimum DSM 1078 — were flown both as single strains and as an artificial two-member consortium on crushed Northwest Africa (NWA) 869 L-chondrite meteorite fragments, in a 50% v/v R2A medium, inside BioMining Reactors housed in KUBIK incubators. The study measured leaching of 44 elements (including the platinum-group elements ruthenium, palladium and platinum, and other elements of industrial interest) from the meteorite and compared microbial versus abiotic (non-biological) leaching under microgravity and terrestrial gravity. Penicillium simplicissimum was the most effective bioleaching organism in microgravity, enhancing release of palladium, platinum and other elements relative to non-biological controls, while Sphingomonas desiccabilis formed a contiguous biofilm on the rock surface but performed similarly or worse than the abiotic control for most platinum-group elements. In the consortium, the fungus alone outperformed the mixture for palladium, suggesting an antagonistic effect of the bacterium. Metabolomic analysis showed distinct, microgravity-dependent changes in microbial metabolism, particularly for P. simplicissimum, with increased production of carboxylic acids and other molecules of potential biomining or pharmaceutical interest. The work demonstrates proof of principle for microbe-driven transformation of asteroidal material for in situ resource utilization in space. +

+
+ + + + +
+

Taxonomy

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Sphingomonas desiccabilis CP1D + + + NCBITaxon:429134 + + + +
+ + PRIMARY_DEGRADER + +
+ + 		N/A
+
    + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "a Gram-negative, non-motile and non-spore-forming bacterium, first isolated from soil crusts in the Colorado plateau"
    + +
    • + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "extract rare earth elements and vanadium from basalt rock under microgravity"
    + +
    • + +
+
+ Penicillium simplicissimum DSM 1078 + + + NCBITaxon:69488 + + + +
+ + PRIMARY_DEGRADER + +
+ + 		N/A
+
    + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "DSM 1078 (DSMZ), an Ascomycota known for its capacity to perform bioleaching"
    + +
    • + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "Penicillium simplicissimum enhanced the release of palladium, platinum and other elements in microgravity"
    + +
    • + +
+
+
+ + + +
+

Ecological Interactions

+ + + +
+
+ + Ecological interaction network for BioAsteroid ISS Chondrite Biomining Consortium + Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism). + +
+
+ Taxon +
+
+ Cross-feeding +
+
+ Mutualism +
+
+ Syntrophy +
+
+ Competition +
+
+ Commensalism +
+
+ Niche partitioning +
+
+ Colonization facilitation +
+
+ Strain competition +
+
+ Predation +
+
+
+ + +
+
+

Fungal bioleaching of platinum-group and critical elements from L-chondrite

+ CROSS_FEEDING +
+ + +

Source Taxon: Penicillium simplicissimum DSM 1078

+ + + + + +

Metabolites: + + palladium + (CHEBI:33363), + + vanadium + (CHEBI:27698), + + copper(2+) + (CHEBI:29036), + + carboxylic acid + (CHEBI:33575) + +

+ + + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41617698 + + - SUPPORT (IN_VITRO) +
    + +
    "Penicillium simplicissimum enhanced the release of palladium, platinum and other elements in microgravity"
    + +
    • + +
  • +
    + + PMID:41617698 + + - SUPPORT (IN_VITRO) +
    + +
    "enhanced bioleaching of phosphorus, vanadium and copper compared to the bacterium"
    + +
    • + +
  • +
    + + PMID:41617698 + + - SUPPORT (IN_VITRO) +
    + +
    "increased production of carboxylic acids"
    + +
    • + +
+ +
+ +
+
+

Bacterial and fungal biofilm colonization of the meteorite surface

+ COLONIZATION_FACILITATION +
+ + +

Source Taxon: Sphingomonas desiccabilis CP1D

+ + + +

Target Taxon: Penicillium simplicissimum DSM 1078

+ + + + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41617698 + + - SUPPORT (IN_VITRO) +
    + +
    "formed a contiguous biofilm across many areas of the rock"
    + +
    • + +
  • +
    + + PMID:41617698 + + - SUPPORT (IN_VITRO) +
    + +
    "the bacterium and the fungus interacting in a similar fashion in both gravity conditions"
    + +
    • + +
+ +
+ +
+
+

Bacterial antagonism of fungal palladium leaching in the consortium

+ COMPETITION +
+ + +

Source Taxon: Sphingomonas desiccabilis CP1D

+ + + +

Target Taxon: Penicillium simplicissimum DSM 1078

+ + + +

Metabolites: + + palladium + (CHEBI:33363) + +

+ + + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41617698 + + - SUPPORT (IN_VITRO) +
    + +
    "the fungus alone outperformed the consortium, possibly due to the antagonistic effects of the bacterium"
    + +
    • + +
+ +
+ + +
+ + + + + + +
+

External Resources

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameRepositoryResource ID
+ Primary publication - BioAsteroid ISS microbial biomining (npj Microgravity 2026) + +
Version-of-record publication reporting the BioAsteroid experiment: microbial biomining of 44 elements from L-chondrite asteroidal material aboard the ISS under microgravity (PMID:41617698). + + + 		OTHER + + doi:10.1038/s41526-026-00567-3 + +
+
    + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "tested the use of microorganisms (bacteria and fungi) to extract 44 elements from L-chondrite asteroidal material"
    + +
    • + +
+
+ bioRxiv preprint - BioAsteroid experiment + +
bioRxiv preprint of the same BioAsteroid experiment; the npj Microgravity version of record (doi:10.1038/s41526-026-00567-3) is preferred for evidence. + + + 		OTHER + + doi:10.1101/2024.01.13.575412 + +
+ NCBI Taxonomy - Sphingomonas desiccabilis + +
NCBI Taxonomy record for Sphingomonas desiccabilis. + + 		OTHER + + NCBITaxon:429134 + +
+ NCBI Taxonomy - Penicillium simplicissimum + +
NCBI Taxonomy record for Penicillium simplicissimum. + + 		OTHER + + NCBITaxon:69488 + +
+
+ + + +
+

Environmental Factors

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Microgravity (ISS spaceflight)microgravityN/A
+
    + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "installation into the microgravity (non-centrifuged) slots within the two KUBIK (ESA) incubators"
    + +
    • + +
+
Meteorite substrate (L-chondrite, NWA 869)Northwest Africa (NWA) 869 L3-6 chondrite regolith brecciaN/A
+
    + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "was the Northwest Africa (NWA) 869 meteorite, a L3-6 chondrite regolith breccia"
    + +
    • + +
+
Incubation temperature and duration~19.5-20 °C for 19 daysN/A
+
    + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "Samples grew for 19 days at 19.5"
    + +
    • + +
+
Medium pH7.2pH
+
    + +
  • + + PMID:41617698 + + - SUPPORT (IN_VITRO) + +
    "The medium used for this experiment was a solution of 50% v/v R2A medium"
    + +
    • + +
+
+
+ + + + +
+

Growth Media

+ +
+

+ BioAsteroid 50% v/v R2A biomining medium + +

+ + + +
+ +
+ pH + 7.2 +
+ + + +
+ Temperature + 20 °C +
+ + + +
+ Atmosphere + AEROBIC +
+ +
+ + +

Composition

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ComponentConcentrationUnitCHEBI
glucose0.25g/L + + + CHEBI:17234 + + +
soluble starch0.25g/L + + + CHEBI:28017 + + +
sodium pyruvate0.15g/L + + + CHEBI:15361 + + +
yeast extract0.25g/L + + N/A + +
peptone0.25g/L + + N/A + +
casamino acids0.25g/L + + N/A + +
+ + + +

+ Preparation notes: 50% v/v R2A medium, 5 mL per sample. Reported composition (g/L): yeast extract 0.25; peptone 0.25; casamino acids 0.25; glucose 0.25; soluble starch 0.25; Na-pyruvate 0.15; K2HPO4 0.15; MgSO4.7H2O 0.025; pH 7.2. + +

+ + + +
+

Evidence

+ +
+ + + PMID:41617698 + + + + +

"The medium used for this experiment was a solution of 50% v/v R2A medium"

+ +
+ +
+ + + PMID:41617698 + + + + +

"yeast extract 0.25; peptone 0.25; casamino acids 0.25; glucose 0.25, soluble starch 0.25, Na-pyruvate 0.15"

+ +
+ +
+ +
+ +
+ +
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/BioRock_ISS_Basalt_Biomining_Consortium.html b/docs/communities/BioRock_ISS_Basalt_Biomining_Consortium.html new file mode 100644 index 00000000..7b474d2b --- /dev/null +++ b/docs/communities/BioRock_ISS_Basalt_Biomining_Consortium.html @@ -0,0 +1,1606 @@ + + + + + + BioRock ISS Basalt Biomining Consortium - CommunityMech + + + +
+
+ ← Back to Communities +

BioRock ISS Basalt Biomining Consortium

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000303 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + BioRock ISS basalt biomining reactor (laboratory/spaceflight culture) +
+ + ENVO:01001405 + + +
+ +
+
+ + + +
+

A defined three-species bacterial panel flown as the ESA BioRock experiment on board the International Space Station to test microbial bioleaching of economically important elements from basaltic rock under microgravity, simulated Mars gravity, and simulated Earth gravity (with ground 1 x g controls). Sphingomonas desiccabilis CP1D (DSM 16792), Bacillus subtilis NCIB 3610 (DSM 10), and Cupriavidus metallidurans CH34 (DSM 2839) were each cultivated on slides of olivine basalt (collected near Gufunes, Reykjavik, Iceland; chosen as an analogue of Moon/Mars surface material) inside a purposely designed miniature biomining reactor housed in the KUBIK incubator. Sphingomonas desiccabilis enhanced mean leached concentrations of rare earth elements (the lanthanides plus yttrium) relative to non-biological controls in all gravity regimes, while Bacillus subtilis reduced REE bioleaching efficacy and Cupriavidus metallidurans showed no difference, demonstrating the microbial specificity of the process as on Earth. A companion analysis showed that Sphingomonas desiccabilis and Bacillus subtilis both enhanced vanadium leaching by 184.92 to 283.22% relative to sterile controls, and a third study found no significant differences in final bacterial cell concentrations between gravity regimes. Gravity level had no significant effect on mean leaching in any case, establishing the principle of biomining and associated bioindustrial processes on Solar System bodies with non-1 x g gravity. +

+
+ + + + +
+

Taxonomy

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Sphingomonas desiccabilis CP1D + + + NCBITaxon:429134 + + + +
+ + PRIMARY_DEGRADER + +
+ + 		N/A
+
    + +
  • + + PMID:33173035 + + - SUPPORT (IN_VITRO) + +
    "Sphingomonas desiccabilis CP1D (DSM 16792; Type strain)"
    + +
    • + +
  • + + PMID:33173035 + + - SUPPORT (IN_VITRO) + +
    "Sphingomonas desiccabilis enhanced mean leached concentrations of REEs compared to non-biological controls in all gravity conditions"
    + +
    • + +
+
+ Bacillus subtilis NCIB 3610 + + + NCBITaxon:1423 + + + +
+ + PRIMARY_DEGRADER + +
+ + 		N/A
+
    + +
  • + + PMID:33173035 + + - SUPPORT (IN_VITRO) + +
    "Bacillus subtilis NCIB 3610 (DSM 10; Type strain)"
    + +
    • + +
  • + + PMID:33868198 + + - SUPPORT (IN_VITRO) + +
    "Sphingomonas desiccabilis and Bacillus subtilis enhanced the leaching of vanadium under the three gravity conditions compared to sterile controls by 184.92 to 283.22%"
    + +
    • + +
+
+ Cupriavidus metallidurans CH34 + + + NCBITaxon:119219 + + + + N/A
+
    + +
  • + + PMID:33173035 + + - SUPPORT (IN_VITRO) + +
    "Cupriavidus metallidurans CH34 (DSM 2839; Type strain)"
    + +
    • + +
  • + + PMID:33154740 + + - SUPPORT (IN_VITRO) + +
    "Cupriavidus metallidurans CH34"
    + +
    • + +
+
+
+ + + +
+

Ecological Interactions

+ + + +
+
+ + Ecological interaction network for BioRock ISS Basalt Biomining Consortium + Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism). + +
+
+ Taxon +
+
+ Cross-feeding +
+
+ Mutualism +
+
+ Syntrophy +
+
+ Competition +
+
+ Commensalism +
+
+ Niche partitioning +
+
+ Colonization facilitation +
+
+ Strain competition +
+
+ Predation +
+
+
+ + +
+
+

Sphingomonas desiccabilis rare-earth-element bioleaching from basalt

+ CROSS_FEEDING +
+ + +

Source Taxon: Sphingomonas desiccabilis CP1D

+ + + + + +

Metabolites: + + lanthanum(3+) + (CHEBI:49701), + + cerium(3+) + (CHEBI:48782), + + neodymium(3+) + (CHEBI:229785), + + yttrium(3+) + (CHEBI:49962) + +

+ + + +

Biological Processes:

+
    + +
  • + response to metal ion + (GO:0010038) +
    • + +
+ + + + + +

Evidence

+
    + +
  • +
    + + PMID:33173035 + + - SUPPORT (IN_VITRO) +
    + +
    "Sphingomonas desiccabilis enhanced mean leached concentrations of REEs compared to non-biological controls in all gravity conditions"
    + +
    • + +
  • +
    + + PMID:33173035 + + - SUPPORT (IN_VITRO) +
    + +
    "Content of rare earth elements (REEs; reported as μg/g"
    + +
    • + +
+ +
+ +
+
+

Vanadium bioleaching by Sphingomonas desiccabilis and Bacillus subtilis

+ CROSS_FEEDING +
+ + +

Source Taxon: Bacillus subtilis NCIB 3610

+ + + + + + + +

Biological Processes:

+
    + +
  • + response to metal ion + (GO:0010038) +
    • + +
+ + + + + +

Evidence

+
    + +
  • +
    + + PMID:33868198 + + - SUPPORT (IN_VITRO) +
    + +
    "Sphingomonas desiccabilis and Bacillus subtilis enhanced the leaching of vanadium under the three gravity conditions compared to sterile controls by 184.92 to 283.22%"
    + +
    • + +
  • +
    + + PMID:33868198 + + - SUPPORT (IN_VITRO) +
    + +
    "One element of interest in mining is vanadium (V)"
    + +
    • + +
+ +
+ +
+
+

Microbial specificity of basalt bioleaching among panel members

+ NICHE_PARTITIONING +
+ + +

Source Taxon: Sphingomonas desiccabilis CP1D

+ + + +

Target Taxon: Cupriavidus metallidurans CH34

+ + + + + + + + + +

Evidence

+
    + +
  • +
    + + PMID:33173035 + + - SUPPORT (IN_VITRO) +
    + +
    "Bacillus subtilis exhibited a reduction in bioleaching efficacy and Cupriavidus metallidurans showed no difference compared to non-biological controls"
    + +
    • + +
  • +
    + + PMID:33173035 + + - SUPPORT (IN_VITRO) +
    + +
    "showing the microbial specificity of the process, as on Earth"
    + +
    • + +
+ +
+ + +
+ + + + + + +
+

External Resources

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameRepositoryResource ID
+ Primary publication - REE extraction in microgravity and Mars gravity + +
Nature Communications 2020 primary publication reporting rare earth element bioleaching from basalt by the BioRock panel on the ISS. + + + 		OTHER + + doi:10.1038/s41467-020-19276-w + +
+
    + +
  • + + PMID:33173035 + + - SUPPORT (IN_VITRO) + +
    "bioleaching of REEs from basaltic rock"
    + +
    • + +
+
+ Companion publication - vanadium mining and bioremediation + +
Frontiers in Microbiology 2021 companion publication reporting microbially-enhanced vanadium leaching by the BioRock panel under micro- and Mars gravity. + + + 		OTHER + + doi:10.3389/fmicb.2021.641387 + +
+
    + +
  • + + PMID:33868198 + + - SUPPORT (IN_VITRO) + +
    "One element of interest in mining is vanadium (V)"
    + +
    • + +
+
+ Companion publication - final bacterial cell concentrations + +
Frontiers in Microbiology 2020 companion publication reporting no significant effect of microgravity or simulated Mars gravity on final bacterial cell concentrations, with detailed cultivation methods for the three-species panel. + + + 		OTHER + + doi:10.3389/fmicb.2020.579156 + +
+
    + +
  • + + PMID:33154740 + + - SUPPORT (IN_VITRO) + +
    "no significant differences in final cell counts and optical densities between the three gravity regimens on the ISS"
    + +
    • + +
+
+ NCBI Taxonomy - Sphingomonas desiccabilis + +
NCBI Taxonomy record for Sphingomonas desiccabilis. + + 		OTHER + + NCBITaxon:429134 + +
+ NCBI Taxonomy - Bacillus subtilis + +
NCBI Taxonomy record for Bacillus subtilis. + + 		OTHER + + NCBITaxon:1423 + +
+ NCBI Taxonomy - Cupriavidus metallidurans + +
NCBI Taxonomy record for Cupriavidus metallidurans. + + 		OTHER + + NCBITaxon:119219 + +
+
+ + + +
+

Environmental Factors

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Gravity regimemicrogravity, simulated Mars gravity, and simulated Earth gravity (plus ground 1 x g controls)N/A
+
    + +
  • + + PMID:33154740 + + - SUPPORT (IN_VITRO) + +
    "microbe-mineral interactions in microgravity, simulated Mars gravity and simulated Earth gravity"
    + +
    • + +
+
Basalt substrateolivine basalt slides (Gufunes, Reykjavik, Iceland)N/A
+
    + +
  • + + PMID:33173035 + + - SUPPORT (IN_VITRO) + +
    "olivine basalt rock collected near Gufunes, Reykjavik in Iceland"
    + +
    • + +
+
Incubation temperature and duration21 days at ~20 CN/A
+
    + +
  • + + PMID:33154740 + + - SUPPORT (IN_VITRO) + +
    "Samples grew for 21 days at 20.16°C"
    + +
    • + +
+
+
+ + + + +
+

Growth Media

+ +
+

+ 50% R2A medium (BioRock spaceflight cultivation) + +

+ + + +
+ + + +
+ Temperature + 20.16 °C +
+ + + +
+ Atmosphere + AEROBIC +
+ +
+ + + + +

+ Preparation notes: The medium used for the BioRock experiment was R2A at 50% v/v of the published component concentrations, approved for spaceflight and supporting growth of all three panel members. Overnight cultures were pre-grown in 100% v/v R2A at 20-22 C to stationary phase; five millilitres of 50% R2A were used per sample chamber. + +

+ + + +
+

Evidence

+ +
+ + + PMID:33868198 + + + + +

"The medium used for the BioRock experiment was R2A"

+ +
+ +
+ + + PMID:33868198 + + + + +

"at 50% v/v of the published component concentrations"

+ +
+ +
+ + + PMID:33154740 + + + + +

"Five milliliters of a 50% v/v solution of R2A growth medium"

+ +
+ +
+ +
+ +
+ +
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Lunar_Martian_Simulant_PGPB_Lettuce_SynCom.html b/docs/communities/Lunar_Martian_Simulant_PGPB_Lettuce_SynCom.html new file mode 100644 index 00000000..275dcd4d --- /dev/null +++ b/docs/communities/Lunar_Martian_Simulant_PGPB_Lettuce_SynCom.html @@ -0,0 +1,1607 @@ + + + + + + Lunar and Martian Simulant PGPB Lettuce SynCom - CommunityMech + + + +
+
+ ← Back to Communities +

Lunar and Martian Simulant PGPB Lettuce SynCom

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000304 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + greenhouse regolith-simulant pot cultivation +
+ + ENVO:01001405 + + +
+ +
+
+ + + +
+

A defined four-strain plant growth-promoting bacterial (PGPB) consortium designed for space-agriculture (In-Situ Resource Utilization) research, composed of Azotobacter chroococcum 76A, Priestia megaterium EL5, Methylobacterium populi VP2, and Kosakonia pseudosacchari TL13. The strains belong to the microbial collection of the Department of Agricultural Sciences of the University of Naples Federico II and were selected for complementary plant growth-promoting traits (nitrogen fixation, phosphate solubilization, phytohormone biosynthesis) and for mutual non-antagonism in dual-culture assays. In a greenhouse pot experiment, the consortium was combined with green compost derived from plant residues (pH 8.25, low C/N ratio) to improve lettuce (Lactuca sativa cv. Grand Rapids) growth on commercial Lunar (LHS-1) and Martian (MMS-1) regolith simulants with zero external chemical input aside from the compost. Compost amendment increased lettuce biomass and nutrient bioavailability, and PGPB inoculation enhanced leaf biomass and mineral nutritional content while significantly increasing the copy number of functional marker genes for nitrogen fixation (nifH), alkaline phosphatase (phoD), and phytase (BPP) in non-amended substrates. The system is a Bioregenerative Life Support System model relevant to regolith-agriculture and long-term space missions. +

+
+ + + + +
+

Taxonomy

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Azotobacter chroococcum 76A + + + NCBITaxon:353 + + + + N/A
+ +
+ Priestia megaterium EL5 + + + NCBITaxon:1404 + + + + N/A
+ +
+ Methylobacterium populi VP2 + + + NCBITaxon:223967 + + + + N/A
+ +
+ Kosakonia pseudosacchari TL13 + + + NCBITaxon:1646340 + + + + N/A
+ +
+
+ + + +
+

Ecological Interactions

+ + + +
+
+ + Ecological interaction network for Lunar and Martian Simulant PGPB Lettuce SynCom + Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism). + +
+
+ Taxon +
+
+ Cross-feeding +
+
+ Mutualism +
+
+ Syntrophy +
+
+ Competition +
+
+ Commensalism +
+
+ Niche partitioning +
+
+ Colonization facilitation +
+
+ Strain competition +
+
+ Predation +
+
+
+ + +
+
+

Non-antagonistic PGPB consortium assembly

+ COMMENSALISM +
+ + + + + + + + + + + + +

Evidence

+ + +
+ +
+
+

PGPB rhizosphere colonization and functional-gene enrichment

+ COLONIZATION_FACILITATION +
+ + + + +

Target Taxon: Lactuca sativa (lettuce host)

+ + + + + +

Biological Processes:

+ + + + + + +

Evidence

+ + +
+ +
+
+

PGPB-enhanced lettuce growth and mineral nutrition

+ MUTUALISM +
+ + + + +

Target Taxon: Lactuca sativa (lettuce host)

+ + + + + +

Biological Processes:

+
    + +
  • + indoleacetic acid biosynthetic process + (GO:0009684) +
    • + +
+ + + + + +

Evidence

+
    + +
  • +
    + + doi:10.1007/s00374-025-01923-3 + + - SUPPORT (IN_VITRO) +
    + +
    "PGPB treatment enhanced leaf biomass by 35%"
    + +
    • + +
  • +
    + + doi:10.1007/s00374-025-01923-3 + + - SUPPORT (IN_VITRO) +
    + +
    "microbial consortium could exert positive impact on plants grown in nutrient-limited substrates"
    + +
    • + +
+ +
+ + +
+ + + + + + +
+

External Resources

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameRepositoryResource ID
+ Primary publication - PGPB consortia and green compost on regolith simulants + +
Duri et al. 2025, Biology and Fertility of Soils - primary source describing the four-strain PGPB consortium and green compost improving lettuce growth on Lunar and Martian regolith simulants. + + + 		OTHER + + doi:10.1007/s00374-025-01923-3 + +
+
    + +
  • + + doi:10.1007/s00374-025-01923-3 + + - SUPPORT (IN_VITRO) + +
    "application of microbial consortium along with green compost is a promising strategy"
    + +
    • + +
+
+ NCBI Taxonomy - Azotobacter chroococcum + +
NCBI Taxonomy record for Azotobacter chroococcum. + + 		OTHER + + NCBITaxon:353 + +
+ NCBI Taxonomy - Priestia megaterium + +
NCBI Taxonomy record for Priestia megaterium. + + 		OTHER + + NCBITaxon:1404 + +
+ NCBI Taxonomy - Methylorubrum populi + +
NCBI Taxonomy record for Methylorubrum populi (formerly Methylobacterium populi). + + 		OTHER + + NCBITaxon:223967 + +
+ NCBI Taxonomy - Kosakonia pseudosacchari + +
NCBI Taxonomy record for Kosakonia pseudosacchari. + + 		OTHER + + NCBITaxon:1646340 + +
+
+ + + +
+

Environmental Factors

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Regolith simulant substrateLunar Highlands Simulant (LHS-1) and Mojave Mars Simulant (MMS-1)N/A
+ +
Regolith alkalinity and nutrient limitationalkaline pH (9 to 10), organic-matter-poorN/A
+ +
Green compost amendmentgreen compost, pH 8.25, low C/N ratio, 20% v/vN/A
+ +
Greenhouse climatemean air temperature 13 C; 10/14 photoperiodN/A
+ +
+
+ + + + +
+

Growth Media

+ +
+

+ PGPB inoculum production media (per-strain fermentor cultivation) + +

+ + + +
+ +
+ pH + 7.00 +
+ + + + + +
+ Atmosphere + AEROBIC +
+ +
+ + + + +

+ Preparation notes: Each strain was cultivated separately in a strain-specific complex medium: Brain Heart Infusion (BHI) for K. pseudosacchari TL13, Yeast Mannitol Broth (YMB) for A. chroococcum 76A, Plate Count Broth (PCB) for P. megaterium EL5, and Nutrient Broth (NB) for M. populi VP2. Fermentations were run at 30 C (K. pseudosacchari, P. megaterium), 28 C (A. chroococcum), and for M. populi, at pH 7.00, 130 rpm agitation, air sparging 0.5 vvm, with antifoam added. Biomass was centrifuged and freeze-dried; inocula were resuspended to 1e6 CFU/mL per strain and applied to lettuce by a root-dip method plus repeated collar application after transplanting. + +

+ + + +
+

Evidence

+ +
+ + + doi:10.1007/s00374-025-01923-3 + + + + +

"pH 7.00, agitation at 130 rpm, air sparging at 0.5"

+ +
+ +
+ + + doi:10.1007/s00374-025-01923-3 + + + + +

"freeze-dried for long term"

+ +
+ +
+ + + doi:10.1007/s00374-025-01923-3 + + + + +

"root dip method"

+ +
+ +
+ +
+ +
+ +
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.html b/docs/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.html new file mode 100644 index 00000000..a0b7af96 --- /dev/null +++ b/docs/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.html @@ -0,0 +1,1536 @@ + + + + + + Lunar Regolith Simulant Phosphorus-Solubilizing Bacteria for Nicotiana benthamiana - CommunityMech + + + +
+
+ ← Back to Communities +

Lunar Regolith Simulant Phosphorus-Solubilizing Bacteria for Nicotiana benthamiana

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000306 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + lunar regolith simulant plant-cultivation laboratory experiment +
+ + ENVO:01001405 + + +
+ +
+
+ + + +
+

A defined set of phosphorus-solubilizing bacteria (PSBs) assembled to improve the fertility of lunar regolith simulant for in-situ resource utilization (ISRU) agriculture in bioregenerative life support systems. Five commonly used microbial-fertilizer strains were tested on a CAS-1 lunar soil simulant: Bacillus mucilaginosus (AS1.232), Bacillus megaterium (AS1.217), Bacillus subtilis (CMCC 63501), Bacillus licheniformis (ATCC 11946), and Pseudomonas fluorescens (ATCC 13525). In a 21-day bio-improving experiment followed by a 24-day Nicotiana benthamiana cultivation experiment, three of the strains - Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens - tolerated the lunar regolith simulant conditions and dissociated insoluble inorganic phosphorus from the simulant. The mechanism is chemolithoheterotrophic organic-acid production: the bacteria synthesize organic acids (e.g. oxalic, citric, tartaric acids) from carbon sources in the medium, lowering the pH and chelating metal ions in insoluble phosphates such as Ca3(PO4)2, FePO4, and AlPO4, thereby releasing available phosphate. PSB treatment raised the available phosphorus content of the simulant and promoted Nicotiana benthamiana growth, with the largest improvement when the simulant was pre-cultured with PSBs 18 days before sowing. The work establishes a microbiological route to convert lunar regolith into a plant-cultivation substrate for future lunar bases. +

+
+ + + + +
+

Taxonomy

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Bacillus mucilaginosus (AS1.232) + + + NCBITaxon:61624 + + + + N/A
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "the phosphorus-solublizing bacteria Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens can tolerate the lunar regolith simulant conditions and dissociate the insoluble phosphorus from the regolith simulant"
    + +
    • + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232)"
    + +
    • + +
+
+ Bacillus megaterium (AS1.217) + + + NCBITaxon:1404 + + + + N/A
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "the phosphorus-solublizing bacteria Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens can tolerate the lunar regolith simulant conditions and dissociate the insoluble phosphorus from the regolith simulant"
    + +
    • + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232)"
    + +
    • + +
+
+ Pseudomonas fluorescens (ATCC 13525) + + + NCBITaxon:294 + + + + N/A
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "the phosphorus-solublizing bacteria Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens can tolerate the lunar regolith simulant conditions and dissociate the insoluble phosphorus from the regolith simulant"
    + +
    • + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232)"
    + +
    • + +
+
+ Bacillus subtilis (CMCC 63501) + + + NCBITaxon:1423 + + + + N/A
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232)"
    + +
    • + +
+
+ Bacillus licheniformis (ATCC 11946) + + + NCBITaxon:1402 + + + + N/A
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232)"
    + +
    • + +
+
+
+ + + +
+

Ecological Interactions

+ + + +
+
+ + Ecological interaction network for Lunar Regolith Simulant Phosphorus-Solubilizing Bacteria for Nicotiana benthamiana + Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism). + +
+
+ Taxon +
+
+ Cross-feeding +
+
+ Mutualism +
+
+ Syntrophy +
+
+ Competition +
+
+ Commensalism +
+
+ Niche partitioning +
+
+ Colonization facilitation +
+
+ Strain competition +
+
+ Predation +
+
+
+ + +
+
+

Phosphorus solubilization from lunar regolith simulant via organic-acid secretion

+ CROSS_FEEDING +
+ + + + + + +

Metabolites: + + phosphate + (CHEBI:18367), + + oxalic acid + (CHEBI:16995), + + citrate + (CHEBI:16947) + +

+ + + +

Biological Processes:

+
    + +
  • + organic acid biosynthetic process + (GO:0016053) +
    • + +
+ + + + + +

Evidence

+
    + +
  • +
    + + PMID:37945659 + + - SUPPORT (IN_VITRO) +
    + +
    "PSBs to synthesize organic acids by using carbon sources in the medium to reduce regolith pH, thus activating insoluble inorganic phosphorus in lunar regolith simulant"
    + +
    • + +
  • +
    + + PMID:37945659 + + - SUPPORT (IN_VITRO) +
    + +
    "organic acid ions also facilitate the dissolution of phosphate minerals through chelating with the metal ions in Ca 3 (PO 4 ) 2 , FePO 4 , AlPO 4"
    + +
    • + +
+ +
+ +
+
+

Phosphorus-enabled promotion of Nicotiana benthamiana growth

+ COLONIZATION_FACILITATION +
+ + + + +

Target Taxon: Nicotiana benthamiana

+ + + +

Metabolites: + + phosphate + (CHEBI:18367) + +

+ + + + + + + +

Evidence

+
    + +
  • +
    + + PMID:37945659 + + - SUPPORT (IN_VITRO) +
    + +
    "The phosphorus-solubilizing bacteria treatment improves the available phosphorus content of the regolith simulant, promoting the growth of Nicotiana benthamiana"
    + +
    • + +
  • +
    + + PMID:37945659 + + - SUPPORT (IN_VITRO) +
    + +
    "the growth of Nicotiana benthamiana could be most improved by treating the regolith simulant with PSBs 18 days before sowing"
    + +
    • + +
+ +
+ + +
+ + + + + + +
+

External Resources

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameRepositoryResource ID
+ Primary publication - phosphorus-solubilizing bacteria improve Nicotiana benthamiana on lunar regolith simulant + +
Xia et al., Communications Biology (2023). Primary source describing the five tested PSB strains, phosphorus solubilization from CAS-1 lunar regolith simulant, and improved Nicotiana benthamiana growth. + + + 		OTHER + + doi:10.1038/s42003-023-05391-z + +
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "five species of phosphorus-solubilizing bacteria are used as test strains"
    + +
    • + +
+
+ NCBI Taxonomy - Paenibacillus mucilaginosus + +
NCBI Taxonomy record for Paenibacillus mucilaginosus (reported as Bacillus mucilaginosus). + + 		OTHER + + NCBITaxon:61624 + +
+ NCBI Taxonomy - Priestia megaterium + +
NCBI Taxonomy record for Priestia megaterium (reported as Bacillus megaterium). + + 		OTHER + + NCBITaxon:1404 + +
+ NCBI Taxonomy - Pseudomonas fluorescens + +
NCBI Taxonomy record for Pseudomonas fluorescens. + + 		OTHER + + NCBITaxon:294 + +
+
+ + + +
+

Environmental Factors

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Lunar regolith simulant substrateCAS-1 lunar soil simulantN/A
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "The simulant used in our study is a copy of the CAS-1 lunar soil simulant"
    + +
    • + +
+
Available phosphorus increase in liquid mediumsoluble inorganic phosphorus increased by 212 percentN/A
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "soluble inorganic phosphorus in the liquid medium was significantly increased by 212"
    + +
    • + +
+
Acidification as the phosphorus-dissolving factorbacterial acidic substances lower pHN/A
+
    + +
  • + + PMID:37945659 + + - SUPPORT (IN_VITRO) + +
    "the acidic substances were the key factor in dissolving inorganic phosphorus from the simulant"
    + +
    • + +
+
+
+ + + + +
+

Growth Media

+ +
+

+ PSB phosphorus-solubilization liquid medium (shaking-flask assay) + +

+ + + +
+ +
+ pH + 7.0 +
+ + + +
+ Temperature + 30 °C +
+ + + +
+ Atmosphere + AEROBIC +
+ +
+ + +

Composition

+ + + + + + + + + + + + + + + + + + + + + + + + + + +
ComponentConcentrationUnitCHEBI
glucose10g/L + + N/A + +
Ca3(PO4)2 (insoluble inorganic phosphorus source)5g/L + + + CHEBI:18367 + + +
+ + + +

+ Preparation notes: Strains were cultured overnight in a shaking flask at 180 rpm and 30 C. The phosphorus-solubilization assay used a liquid medium containing glucose 10 g/L, (NH4)2SO4 0.5 g/L, Ca3(PO4)2 5 g/L (insoluble inorganic phosphorus source), NaCl 0.3 g/L, FeSO4 0.03 g/L, KCl 0.3 g/L, MgSO4 0.3 g/L, MnSO4 0.03 g/L, at pH 7.0. + +

+ + + +
+

Evidence

+ +
+ + + PMID:37945659 + + + + +

"cultured overnight in a shaking flask at 180 rpm and 30 °C"

+ +
+ +
+ + + PMID:37945659 + + + + +

"glucose 10 g/L"

+ +
+ +
+ +
+ +
+ +
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/index.html b/docs/index.html index 20f4cf2e..79b42482 100644 --- a/docs/index.html +++ b/docs/index.html @@ -75,7 +75,7 @@

CommunityMech

Microbial community knowledge base — curated, evidence-backed interaction networks.

-
295communities
+
300communities
16categories
512-Dv3 embeddings
diff --git a/kb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml b/kb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml new file mode 100644 index 00000000..3e931761 --- /dev/null +++ b/kb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml @@ -0,0 +1,269 @@ +id: CommunityMech:000307 +name: Anabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium +description: > + An anaerobic-digestion microbial consortium studied as part of a bioregenerative + life-support concept for Mars: cyanobacterial biomass (Anabaena sp.), which can be + grown on Martian resources, is anaerobically digested to mobilize nutrients + (ammonium and phosphate) for use as a crop fertilizer, with biogas as a co-product. + Ramalho et al. (2025, Bioresource Technology) tested three microbial communities + for their ability to digest Anabaena biomass in three matrices — a minimal medium, + 200 g/L MGS-1 Mars regolith simulant, and water. In minimal medium the taxonomic + (16S) analysis revealed a SYNTROPHIC community: fermentative bacteria degrade the + cyanobacterial biomass and cross-feed hydrogenotrophic methanogenic archaea + (interspecies H2/CO2 transfer driving methanogenesis). In the MGS-1 regolith + matrix, however, the methanogens were outcompeted by sulfate-reducing bacteria, and + the regolith also adsorbed organics and lowered phosphate/ammonium recovery. The + Anabaena biomass here is the digestion FEEDSTOCK (substrate) rather than a live + member of the digesting consortium. All communities produced ammonium and removed + organic carbon, supporting the viability of a Mars-relevant bioprocess for + fertilizer production. The specific dominant genera resolved by the paper's 16S + analysis are reported in the full text, which is paywalled; only the functional + guilds (fermentative bacteria, hydrogenotrophic methanogens, sulfate-reducing + bacteria) are named in the openly available abstract and are therefore represented + here as interactions/roles rather than as NCBITaxon-grounded members. +ecological_state: ENGINEERED +community_origin: ENGINEERED +community_category: SYNTROPHY +engineering_design: + objective: > + Determine whether the nutrients mobilized by Mars-grown cyanobacteria can be + extracted through anaerobic digestion of the cyanobacterial biomass and used as a + crop fertilizer, including under a Mars regolith-simulant matrix. + assembly_strategy: > + Inoculate three microbial communities into three matrices — a minimal medium, + 200 g/L MGS-1 Mars regolith simulant, and water — each supplied with Anabaena sp. + cyanobacterial biomass as the digestion feedstock, and follow ammonium production, + organic-carbon removal, and community composition (16S taxonomic analysis). + measurement_endpoints: + - Ammonium production + - Organic carbon removal + - Phosphate and ammonium recovery efficiency + - Microbial community composition (16S taxonomic analysis) + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We therefore tested the abilities of three microbial communities to + explanation: States the study design of testing three microbial communities for anaerobic digestion. + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: nutrients they mobilize could be extracted through anaerobic digestion and used + explanation: States the fertilizer-production objective driving the community design. +environment_term: + preferred_term: anaerobic-digestion laboratory culture (Mars regolith-simulant context) + term: + id: ENVO:01001405 + label: laboratory environment + notes: > + Controlled laboratory anaerobic-digestion experiment rather than a sampled natural + community. The applied context is a Mars bioregenerative life-support system in + which cyanobacterial biomass is digested in a 200 g/L MGS-1 Mars regolith-simulant + matrix; the Mars/simulant context is captured in the description and environmental + factors rather than as an ENVO term. +taxonomy: +- taxon_term: + preferred_term: Anabaena sp. (cyanobacterial digestion feedstock) + term: + id: NCBITaxon:1163 + label: Anabaena + notes: > + FEEDSTOCK / SUBSTRATE, not a live member of the digesting consortium: Anabaena + sp. biomass is the cyanobacterial material that the anaerobic-digestion + communities break down. Grounded at genus level because the source reports only + "Anabaena sp." (no species/strain in the openly available abstract). Listed under + taxonomy so the feedstock organism is captured with its NCBITaxon grounding. + functional_role: + - PRIMARY_PRODUCER + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: digest the biomass of Anabaena sp. in minimal medium, + explanation: Names Anabaena sp. biomass as the feedstock digested by the communities. +ecological_interactions: +- name: Fermenter-to-methanogen syntrophy (interspecies H2/CO2 transfer) + description: > + In minimal medium, fermentative bacteria degrade the Anabaena biomass and their + fermentation products (notably H2 and CO2, and acetate) are consumed by + hydrogenotrophic methanogenic archaea, forming a syntrophic cross-feeding loop that + drives methanogenesis. Both partners are named only as functional guilds in the + openly available abstract, so this is captured as a community-level interaction + without NCBITaxon-grounded source/target taxa. + interaction_type: SYNTROPHY + scope: COMMUNITY_LEVEL + metabolites: + - preferred_term: dihydrogen + term: + id: CHEBI:18276 + label: dihydrogen + - preferred_term: carbon dioxide + term: + id: CHEBI:16526 + label: carbon dioxide + - preferred_term: acetate + term: + id: CHEBI:30089 + label: acetate + - preferred_term: methane + term: + id: CHEBI:16183 + label: methane + biological_processes: + - preferred_term: methanogenesis + term: + id: GO:0015948 + label: methanogenesis + - preferred_term: biological process involved in interspecies interaction between organisms + term: + id: GO:0044419 + label: biological process involved in interspecies interaction between organisms + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: taxonomic analysis revealed a syntrophic fermentative community and + explanation: Identifies a syntrophic fermentative community in the minimal-medium digestion. + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: hydrogenotrophic methanogens in minimal medium, but methanogens were outcompeted + explanation: Identifies hydrogenotrophic methanogens as the syntrophic partners, consistent with interspecies H2 transfer and methanogenesis. +- name: Sulfate-reducer outcompetition of methanogens in MGS-1 regolith + description: > + In the 200 g/L MGS-1 Mars regolith-simulant matrix, sulfate-reducing bacteria + outcompeted the hydrogenotrophic methanogens — a competition for shared electron + donors (H2/acetate) in which dissimilatory sulfate reduction displaces + methanogenesis. Represented as a community-level interaction because the competing + guilds are not resolved to NCBITaxon-grounded taxa in the available abstract. + interaction_type: COMPETITION + scope: COMMUNITY_LEVEL + metabolites: + - preferred_term: dihydrogen + term: + id: CHEBI:18276 + label: dihydrogen + - preferred_term: sulfate + term: + id: CHEBI:16189 + label: sulfate + biological_processes: + - preferred_term: dissimilatory sulfate reduction + term: + id: GO:0019420 + label: dissimilatory sulfate reduction + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: in MGS-1 by sulfate-reducing bacteria. + explanation: States that sulfate-reducing bacteria outcompeted the methanogens in the MGS-1 regolith matrix. + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: hydrogenotrophic methanogens in minimal medium, but methanogens were outcompeted + explanation: States that methanogens were outcompeted in MGS-1, the basis for the competition interaction. +environmental_factors: +- name: MGS-1 Mars regolith simulant matrix + value: 200 g/L MGS-1 Mars global simulant + description: > + Anaerobic digestion was tested in a 200 g/L MGS-1 Mars regolith-simulant matrix + (alongside minimal medium and water). The regolith adsorbed organics and reduced + phosphate and ammonium recovery efficiency, and shifted the community toward + sulfate-reducing bacteria over methanogens. + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: simulant (MGS-1), and water. + explanation: Names the MGS-1 Mars regolith simulant as one of the tested digestion matrices. + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: adsorbed organics and reduced the phosphate and ammonium recovery efficiency. A + explanation: Describes the effect of the MGS-1 regolith on organics and nutrient recovery. +- name: Anaerobic-digestion nutrient outputs + value: ammonium production and organic-carbon removal + description: > + All three communities produced ammonium and removed organic carbon across the + tested media, the fertilizer-relevant outputs of the bioprocess. + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: All communities produced ammonium and removed organic carbon in all + explanation: States ammonium production and organic-carbon removal as the community outputs. +growth_media: +- name: Anabaena anaerobic-digestion assay (minimal medium / MGS-1 / water) + atmosphere: ANAEROBIC + preparation_notes: > + Three matrices were tested for anaerobic digestion of Anabaena sp. biomass: a + minimal medium, 200 g/L MGS-1 Mars regolith simulant, and water. Detailed medium + composition, temperature, pH, and incubation parameters are in the paper's Methods, + which is paywalled and therefore not asserted here. + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: digest the biomass of Anabaena sp. in minimal medium, + explanation: Names the minimal medium matrix used for the digestion assay. + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: simulant (MGS-1), and water. + explanation: Completes the set of three tested matrices (adds water) for the digestion assay. +external_resources: +- name: Primary publication - anaerobic digestion of cyanobacterial biomass for Mars fertilizer + repository: OTHER + resource_id: doi:10.1016/j.biortech.2025.132383 + url: https://doi.org/10.1016/j.biortech.2025.132383 + description: > + Ramalho et al. 2025, Bioresource Technology — tests three microbial communities for + anaerobic digestion of Anabaena sp. biomass in minimal medium, 200 g/L MGS-1 Mars + regolith simulant, and water, for Mars crop-fertilizer production. + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: this study suggests the viability of a bioprocess which could + explanation: Identifies this publication as the primary source describing the community and bioprocess. +- name: NCBI Taxonomy - Anabaena + repository: OTHER + resource_id: NCBITaxon:1163 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1163 + description: NCBI Taxonomy record for the genus Anabaena (cyanobacterial digestion feedstock). +related_ingredients: +- preferred_term: ammonium + chebi_term: + id: CHEBI:28938 + label: ammonium + relevance: > + Ammonium is the key fertilizer-relevant nutrient released by anaerobic digestion of + the Anabaena biomass; MGS-1 regolith reduced its recovery efficiency. + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: All communities produced ammonium and removed organic carbon in all + explanation: Names ammonium as a produced nutrient output of the digestion communities. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: > + Methane is the biogas product of the hydrogenotrophic methanogens in the syntrophic + minimal-medium community. + evidence: + - reference: PMID:40089033 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: hydrogenotrophic methanogens in minimal medium, but methanogens were outcompeted + explanation: Names hydrogenotrophic methanogens whose metabolic product is methane. +associated_datasets: [] +metals_present: [] +rare_earth_elements_present: [] +metal_relevance: NOT_APPLICABLE +metal_notes: > + Not a metals community. MGS-1 Mars regolith simulant is used here as a physical + digestion matrix, not for metal extraction or bioleaching; no metal or rare-earth + transformation role is curated. diff --git a/kb/communities/BioAsteroid_ISS_Chondrite_Biomining_Consortium.yaml b/kb/communities/BioAsteroid_ISS_Chondrite_Biomining_Consortium.yaml new file mode 100644 index 00000000..35da1ea1 --- /dev/null +++ b/kb/communities/BioAsteroid_ISS_Chondrite_Biomining_Consortium.yaml @@ -0,0 +1,468 @@ +id: CommunityMech:000305 +name: BioAsteroid ISS Chondrite Biomining Consortium +description: > + The BioAsteroid experiment tested microbial biomining of asteroidal + (L-chondrite) material under microgravity aboard the International Space + Station (ISS). Two heterotrophic microorganisms — the bacterium Sphingomonas + desiccabilis CP1D and the fungus Penicillium simplicissimum DSM 1078 — were + flown both as single strains and as an artificial two-member consortium on + crushed Northwest Africa (NWA) 869 L-chondrite meteorite fragments, in a 50% + v/v R2A medium, inside BioMining Reactors housed in KUBIK incubators. The + study measured leaching of 44 elements (including the platinum-group elements + ruthenium, palladium and platinum, and other elements of industrial interest) + from the meteorite and compared microbial versus abiotic (non-biological) + leaching under microgravity and terrestrial gravity. Penicillium + simplicissimum was the most effective bioleaching organism in microgravity, + enhancing release of palladium, platinum and other elements relative to + non-biological controls, while Sphingomonas desiccabilis formed a contiguous + biofilm on the rock surface but performed similarly or worse than the abiotic + control for most platinum-group elements. In the consortium, the fungus alone + outperformed the mixture for palladium, suggesting an antagonistic effect of + the bacterium. Metabolomic analysis showed distinct, microgravity-dependent + changes in microbial metabolism, particularly for P. simplicissimum, with + increased production of carboxylic acids and other molecules of potential + biomining or pharmaceutical interest. The work demonstrates proof of principle + for microbe-driven transformation of asteroidal material for in situ resource + utilization in space. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOMINING +engineering_design: + objective: > + Test whether heterotrophic microorganisms (a bacterium and a fungus), alone + and as an artificial consortium, can catalyse the release of technologically + and economically important elements — including platinum-group elements — + from L-chondrite asteroidal material under microgravity aboard the ISS, for + in situ resource utilization in space. + assembly_strategy: > + Defined two-member artificial consortium of the bacterium Sphingomonas + desiccabilis CP1D and the fungus Penicillium simplicissimum DSM 1078, + desiccated onto crushed sterile L-chondrite meteorite fragments and grown in + 50% v/v R2A medium; single-strain cultures and non-biological controls were + run in parallel, in microgravity (ISS) and terrestrial-gravity (Earth) + conditions. + perturbation_design: > + Compared microbial versus abiotic leaching and microgravity (ISS) versus + terrestrial gravity (Earth) for each treatment (bacterium, fungus, + consortium, non-biological control). + measurement_endpoints: + - Dissolution of 44 elements from the meteorite (ICP-MS/ICP-OES of the liquid + fraction), including platinum-group elements + - Microbe-mineral interaction and biofilm/mycelium formation (SEM/EDS) + - Microbial metabolome under microgravity versus terrestrial gravity + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: tested the use of microorganisms (bacteria and fungi) to extract 44 elements from L-chondrite asteroidal material + explanation: States the objective of extracting elements from L-chondrite asteroidal material with bacteria and fungi. + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: An artificial microbial consortium, a common strategy in terrestrial biomining + explanation: Supports the artificial-consortium assembly strategy. +environment_term: + preferred_term: BioAsteroid ISS microgravity biomining hardware + term: + id: ENVO:01001405 + label: laboratory environment + notes: > + The community is a controlled experimental cultivation rather than a sampled + natural community. Cultivation took place inside BioMining Reactors within + KUBIK incubators aboard the International Space Station under microgravity + (with terrestrial-gravity controls on Earth). The microbe-mineral substrate + was crushed Northwest Africa (NWA) 869 L-chondrite meteorite. The generic + laboratory-environment ENVO term is used because no ontology term captures + the spaceflight/microgravity biomining hardware context. +taxonomy: +- taxon_term: + preferred_term: Sphingomonas desiccabilis CP1D + term: + id: NCBITaxon:429134 + label: Sphingomonas desiccabilis + notes: > + Gram-negative, non-motile, non-spore-forming bacterium originally isolated + from soil crusts on the Colorado plateau, with demonstrated capacity to + extract metals during spaceflight. Ontology grounding is species-level; + the source uses strain designation CP1D. + strain_designation: + strain_name: CP1D + functional_role: + - PRIMARY_DEGRADER + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: a Gram-negative, non-motile and non-spore-forming bacterium, first isolated from soil crusts in the Colorado plateau + explanation: Identifies Sphingomonas desiccabilis CP1D as the bacterial member and its characteristics. + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: extract rare earth elements and vanadium from basalt rock under microgravity + explanation: Establishes S. desiccabilis as a metal-extracting bacterium used in space biomining. +- taxon_term: + preferred_term: Penicillium simplicissimum DSM 1078 + term: + id: NCBITaxon:69488 + label: Penicillium simplicissimum + notes: > + Ascomycete fungus (DSMZ strain DSM 1078) known for its capacity to perform + bioleaching. In this experiment it was the most effective bioleaching + organism under microgravity, enhancing release of platinum-group and other + elements. Ontology grounding is species-level. + strain_designation: + strain_name: DSM 1078 + culture_collections: + - collection: DSM + accession: '1078' + notes: DSMZ strain designation reported in the source (Penicillium simplicissimum DSM 1078). + functional_role: + - PRIMARY_DEGRADER + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: DSM 1078 (DSMZ), an Ascomycota known for its capacity to perform bioleaching + explanation: Identifies Penicillium simplicissimum DSM 1078 as the fungal member and its bioleaching capacity. + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Penicillium simplicissimum enhanced the release of palladium, platinum and other elements in microgravity + explanation: Establishes the fungus as the primary bioleaching driver for platinum-group elements in microgravity. +ecological_interactions: +- name: Fungal bioleaching of platinum-group and critical elements from L-chondrite + description: > + Penicillium simplicissimum catalyses the release of platinum-group elements + (palladium, platinum, ruthenium) and other critical elements (including + phosphorus, vanadium and copper) from the L-chondrite meteorite, enhancing + leaching relative to non-biological controls under microgravity. This is + interpreted as heterotrophic bioleaching through proton, organic-acid and + complexing-compound release. + interaction_type: CROSS_FEEDING + scope: PAIRWISE + source_taxon: + preferred_term: Penicillium simplicissimum DSM 1078 + term: + id: NCBITaxon:69488 + label: Penicillium simplicissimum + metabolites: + - preferred_term: palladium + term: + id: CHEBI:33363 + label: palladium + - preferred_term: vanadium + term: + id: CHEBI:27698 + label: vanadium atom + - preferred_term: copper(2+) + term: + id: CHEBI:29036 + label: copper(2+) + - preferred_term: carboxylic acid + term: + id: CHEBI:33575 + label: carboxylic acid + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Penicillium simplicissimum enhanced the release of palladium, platinum and other elements in microgravity + explanation: Documents fungal enhancement of platinum-group element release in microgravity. + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: enhanced bioleaching of phosphorus, vanadium and copper compared to the bacterium + explanation: Documents fungal enhancement of phosphorus, vanadium and copper leaching. + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: increased production of carboxylic acids + explanation: Links the fungus to increased carboxylic acid production, a candidate leaching mechanism. +- name: Bacterial and fungal biofilm colonization of the meteorite surface + description: > + Both the bacterium Sphingomonas desiccabilis and the fungus Penicillium + simplicissimum colonize the L-chondrite surface. In consortium, the bacterium + and the fungus interact in a similar fashion in both gravity conditions, + forming a mixed filamentous (fungus) and rod-shaped-cell (bacterium) biofilm + on the rock, providing the physical microbe-mineral contact required for + bioleaching. + interaction_type: COLONIZATION_FACILITATION + scope: PAIRWISE + source_taxon: + preferred_term: Sphingomonas desiccabilis CP1D + term: + id: NCBITaxon:429134 + label: Sphingomonas desiccabilis + target_taxon: + preferred_term: Penicillium simplicissimum DSM 1078 + term: + id: NCBITaxon:69488 + label: Penicillium simplicissimum + biological_processes: + - preferred_term: biofilm formation + term: + id: GO:0042710 + label: biofilm formation + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: formed a contiguous biofilm across many areas of the rock + explanation: Documents S. desiccabilis biofilm formation on the meteorite surface. + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the bacterium and the fungus interacting in a similar fashion in both gravity conditions + explanation: Documents co-colonization of the rock by the bacterium and the fungus in the consortium. +- name: Bacterial antagonism of fungal palladium leaching in the consortium + description: > + In the two-member consortium, palladium leaching was lower than for the + fungus alone: Penicillium simplicissimum alone outperformed the consortium + for palladium, an outcome the authors attribute to an antagonistic effect of + the bacterium Sphingomonas desiccabilis on fungal palladium extraction. + interaction_type: COMPETITION + scope: PAIRWISE + source_taxon: + preferred_term: Sphingomonas desiccabilis CP1D + term: + id: NCBITaxon:429134 + label: Sphingomonas desiccabilis + target_taxon: + preferred_term: Penicillium simplicissimum DSM 1078 + term: + id: NCBITaxon:69488 + label: Penicillium simplicissimum + metabolites: + - preferred_term: palladium + term: + id: CHEBI:33363 + label: palladium + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the fungus alone outperformed the consortium, possibly due to the antagonistic effects of the bacterium + explanation: Documents bacterial antagonism of fungal palladium leaching in the consortium. +environmental_factors: +- name: Microgravity (ISS spaceflight) + value: microgravity + description: > + The experiment was conducted under microgravity aboard the International + Space Station, with samples installed in non-centrifuged (microgravity) + slots of KUBIK incubators; terrestrial-gravity controls were run on Earth. + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: installation into the microgravity (non-centrifuged) slots within the two KUBIK (ESA) incubators + explanation: Documents the microgravity cultivation condition aboard the ISS. +- name: Meteorite substrate (L-chondrite, NWA 869) + value: Northwest Africa (NWA) 869 L3-6 chondrite regolith breccia + description: > + The microbe-mineral substrate was crushed Northwest Africa (NWA) 869 + meteorite, an L3-6 (L-chondrite) regolith breccia, fragmented to ~1-3.5 mm + pieces; its dominant mineral phases are olivine and pyroxene with minor + feldspar, melilite and iron sulfides. + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: was the Northwest Africa (NWA) 869 meteorite, a L3-6 chondrite regolith breccia + explanation: Identifies the L-chondrite meteorite used as the leaching substrate. +- name: Incubation temperature and duration + value: ~19.5-20 °C for 19 days + description: > + Samples were incubated for 19 days at approximately 19.5-20 °C (ISS incubator + setpoint 20 °C; logged flight temperature 19.5 °C). + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Samples grew for 19 days at 19.5 + explanation: Documents the 19-day incubation at ~19.5 °C. +- name: Medium pH + value: '7.2' + unit: pH + description: > + Cultivation used a near-neutral 50% v/v R2A medium at pH 7.2, chosen to + encourage the microorganisms to extract nutrients from the meteorite + (heterotrophic, non-acidophilic bioleaching). + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The medium used for this experiment was a solution of 50% v/v R2A medium + explanation: Documents the 50% v/v R2A medium; the source reports its pH as 7.2. +growth_media: +- name: BioAsteroid 50% v/v R2A biomining medium + ph: '7.2' + temperature: '20' + temperature_unit: °C + atmosphere: AEROBIC + incubation_time: '19' + incubation_time_unit: days + vessel_type: BioMining Reactor (BMR) within KUBIK incubator + inoculum_source: > + Sphingomonas desiccabilis CP1D stationary-phase R2A culture and/or + sonicated/filtered Penicillium simplicissimum mycelial suspension desiccated + onto crushed sterile meteorite fragments + preparation_notes: > + 50% v/v R2A medium, 5 mL per sample. Reported composition (g/L): yeast + extract 0.25; peptone 0.25; casamino acids 0.25; glucose 0.25; soluble starch + 0.25; Na-pyruvate 0.15; K2HPO4 0.15; MgSO4.7H2O 0.025; pH 7.2. + composition: + - name: glucose + concentration: '0.25' + unit: g/L + chebi_term: + preferred_term: glucose + term: + id: CHEBI:17234 + label: glucose + - name: soluble starch + concentration: '0.25' + unit: g/L + chebi_term: + preferred_term: starch + term: + id: CHEBI:28017 + label: starch + - name: sodium pyruvate + concentration: '0.15' + unit: g/L + chebi_term: + preferred_term: pyruvate + term: + id: CHEBI:15361 + label: pyruvate + - name: yeast extract + concentration: '0.25' + unit: g/L + - name: peptone + concentration: '0.25' + unit: g/L + - name: casamino acids + concentration: '0.25' + unit: g/L + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The medium used for this experiment was a solution of 50% v/v R2A medium + explanation: Documents the 50% v/v R2A cultivation medium. + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'yeast extract 0.25; peptone 0.25; casamino acids 0.25; glucose 0.25, soluble starch 0.25, Na-pyruvate 0.15' + explanation: Documents the medium composition (g/L). +cultivation_setup: +- cultivation_mode: BATCH + system_type: OTHER + instrument_detail: > + BioMining Reactor (BMR) culture chamber inside an Experiment Unit + (KEU-RK, Kayser Italia), incubated in KUBIK (ESA) incubators aboard the ISS; + 5 mL medium injected once and 1 mL fixative injected at the end. + manufacturer_model: Kayser Italia KEU-RK Experiment Unit; ESA KUBIK incubator + working_volume: 5.0 + working_volume_unit: mL + operating_temperature: 20.0 + operating_temperature_unit: °C + temperature_controlled: true + notes: > + Closed batch cultivation under microgravity (non-centrifuged KUBIK slots) on + the ISS, with terrestrial-gravity controls on Earth; 19-day incubation. + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: installation into the microgravity (non-centrifuged) slots within the two KUBIK (ESA) incubators + explanation: Documents the KUBIK incubator hardware used for cultivation aboard the ISS. + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Samples grew for 19 days at 19.5 + explanation: Documents the 19-day batch incubation. +external_resources: +- name: Primary publication - BioAsteroid ISS microbial biomining (npj Microgravity 2026) + repository: OTHER + resource_id: doi:10.1038/s41526-026-00567-3 + url: https://doi.org/10.1038/s41526-026-00567-3 + description: > + Version-of-record publication reporting the BioAsteroid experiment: microbial + biomining of 44 elements from L-chondrite asteroidal material aboard the ISS + under microgravity (PMID:41617698). + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: tested the use of microorganisms (bacteria and fungi) to extract 44 elements from L-chondrite asteroidal material + explanation: Primary source for the BioAsteroid community record. +- name: bioRxiv preprint - BioAsteroid experiment + repository: OTHER + resource_id: doi:10.1101/2024.01.13.575412 + url: https://doi.org/10.1101/2024.01.13.575412 + description: > + bioRxiv preprint of the same BioAsteroid experiment; the npj Microgravity + version of record (doi:10.1038/s41526-026-00567-3) is preferred for evidence. +- name: NCBI Taxonomy - Sphingomonas desiccabilis + repository: OTHER + resource_id: NCBITaxon:429134 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=429134 + description: NCBI Taxonomy record for Sphingomonas desiccabilis. +- name: NCBI Taxonomy - Penicillium simplicissimum + repository: OTHER + resource_id: NCBITaxon:69488 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=69488 + description: NCBI Taxonomy record for Penicillium simplicissimum. +related_ingredients: +- preferred_term: palladium + chebi_term: + id: CHEBI:33363 + label: palladium + relevance: > + Palladium is a platinum-group element and a primary target of the BioAsteroid + biomining experiment; Penicillium simplicissimum enhanced its release from the + L-chondrite in microgravity relative to non-biological controls. + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Penicillium simplicissimum enhanced the release of palladium, platinum and other elements in microgravity + explanation: Names palladium as a fungally enhanced leaching target. +- preferred_term: carboxylic acid + chebi_term: + id: CHEBI:33575 + label: carboxylic acid + relevance: > + Carboxylic acids were produced at increased levels by the fungus in + microgravity and are a candidate mechanism (organic-acid leaching) for + heterotrophic bioleaching of the meteorite. + evidence: + - reference: PMID:41617698 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: increased production of carboxylic acids + explanation: Names carboxylic acids as fungal metabolites increased in microgravity. +associated_datasets: [] +metals_present: +- PALLADIUM +- IRON +- COPPER +- NICKEL +- COBALT +- VANADIUM +- ZINC +rare_earth_elements_present: +- EUROPIUM +- LUTETIUM +metal_relevance: PRIMARY +metal_notes: > + Biomining of asteroidal L-chondrite material. The platinum-group element + palladium was a primary target, with Penicillium simplicissimum enhancing its + release in microgravity. Other elements with reported microbial leaching + effects include iron, copper, nickel, cobalt, vanadium and zinc; only the + metal/REE elements that map to schema enum values are listed here. Two rare + earth elements — europium and lutetium — were bioleached in this study. + Platinum, ruthenium, molybdenum and manganese are also reported in the source + but have no corresponding schema enum value and are therefore omitted from the + structured metal lists. diff --git a/kb/communities/BioRock_ISS_Basalt_Biomining_Consortium.yaml b/kb/communities/BioRock_ISS_Basalt_Biomining_Consortium.yaml new file mode 100644 index 00000000..f544adec --- /dev/null +++ b/kb/communities/BioRock_ISS_Basalt_Biomining_Consortium.yaml @@ -0,0 +1,479 @@ +id: CommunityMech:000303 +name: BioRock ISS Basalt Biomining Consortium +description: > + A defined three-species bacterial panel flown as the ESA BioRock experiment on + board the International Space Station to test microbial bioleaching of economically + important elements from basaltic rock under microgravity, simulated Mars gravity, + and simulated Earth gravity (with ground 1 x g controls). Sphingomonas desiccabilis + CP1D (DSM 16792), Bacillus subtilis NCIB 3610 (DSM 10), and Cupriavidus metallidurans + CH34 (DSM 2839) were each cultivated on slides of olivine basalt (collected near + Gufunes, Reykjavik, Iceland; chosen as an analogue of Moon/Mars surface material) + inside a purposely designed miniature biomining reactor housed in the KUBIK + incubator. Sphingomonas desiccabilis enhanced mean leached concentrations of rare + earth elements (the lanthanides plus yttrium) relative to non-biological controls + in all gravity regimes, while Bacillus subtilis reduced REE bioleaching efficacy and + Cupriavidus metallidurans showed no difference, demonstrating the microbial + specificity of the process as on Earth. A companion analysis showed that + Sphingomonas desiccabilis and Bacillus subtilis both enhanced vanadium leaching by + 184.92 to 283.22% relative to sterile controls, and a third study found no + significant differences in final bacterial cell concentrations between gravity + regimes. Gravity level had no significant effect on mean leaching in any case, + establishing the principle of biomining and associated bioindustrial processes on + Solar System bodies with non-1 x g gravity. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOMINING +engineering_design: + objective: > + Test whether microbial bioleaching of rare earth elements and vanadium from + basaltic rock can be achieved under extraterrestrial (microgravity and simulated + Mars) gravity, using a defined panel of three bacteria in a miniature space + biomining reactor. + assembly_strategy: > + A defined panel of three bacterial species (Sphingomonas desiccabilis CP1D, + Bacillus subtilis NCIB 3610, Cupriavidus metallidurans CH34), each grown as a + single-strain culture on identical basalt slides in an identical medium and + hardware, was compared against non-biological (sterile) controls across gravity + regimes. + perturbation_design: > + Gravity regime was the primary designed variable: true microgravity, simulated + Mars gravity, and simulated Earth gravity generated by an onboard centrifuge in the + KUBIK incubator, plus ground 1 x g controls. + measurement_endpoints: + - Leached concentrations of rare earth elements in chamber fluid vs non-biological controls + - Leached vanadium concentration vs sterile controls + - Final bacterial cell counts and optical densities across gravity regimes + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: test hypotheses on the bioleaching of REEs from basaltic rock in microgravity and simulated Mars and Earth gravities using three microorganisms and a purposely designed biomining reactor + explanation: States the experimental objective, the three-organism panel, the basalt substrate, and the purpose-built biomining reactor. + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: conducted the ESA BioRock experiment on board the International Space Station + explanation: Identifies the community as the ESA BioRock ISS biomining experiment. +environment_term: + preferred_term: BioRock ISS basalt biomining reactor (laboratory/spaceflight culture) + term: + id: ENVO:01001405 + label: laboratory environment + notes: > + The community is a controlled spaceflight cultivation rather than a sampled natural + community. Bacteria were grown on slides of olivine basalt (a Moon/Mars surface + analogue collected near Gufunes, Reykjavik, Iceland) inside a purpose-built + miniature biomining reactor in the KUBIK incubator in the Columbus module of the + International Space Station, under microgravity, simulated Mars gravity, and + simulated Earth gravity, with ground 1 x g controls. +taxonomy: +- taxon_term: + preferred_term: Sphingomonas desiccabilis CP1D + term: + id: NCBITaxon:429134 + label: Sphingomonas desiccabilis + notes: > + Type strain CP1D (DSM 16792); the only panel member that significantly enhanced + rare earth element bioleaching from basalt across all gravity regimes, and (with + B. subtilis) enhanced vanadium leaching. + strain_designation: + strain_name: CP1D + culture_collections: + - collection: DSM + accession: '16792' + notes: Type strain deposited as DSM 16792; sourced from the University of Edinburgh for the BioRock experiment. + functional_role: + - PRIMARY_DEGRADER + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Sphingomonas desiccabilis CP1D (DSM 16792; Type strain) + explanation: Names the strain and culture-collection accession of the primary REE-leaching member. + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Sphingomonas desiccabilis enhanced mean leached concentrations of REEs compared to non-biological controls in all gravity conditions + explanation: Establishes S. desiccabilis as the member that enhanced REE bioleaching in all gravity regimes. +- taxon_term: + preferred_term: Bacillus subtilis NCIB 3610 + term: + id: NCBITaxon:1423 + label: Bacillus subtilis + notes: > + Type strain NCIB 3610 (DSM 10), a Gram-positive, spore- and biofilm-forming + bacterium introduced into the experiment as spores desiccated on the basalt. It + reduced REE bioleaching efficacy relative to controls but (with S. desiccabilis) + enhanced vanadium leaching. + strain_designation: + strain_name: NCIB 3610 + culture_collections: + - collection: DSM + accession: '10' + notes: Type strain NCIB 3610, deposited as DSM 10; provided by DLR Cologne for the BioRock experiment. + functional_role: + - PRIMARY_DEGRADER + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Bacillus subtilis NCIB 3610 (DSM 10; Type strain) + explanation: Names the strain and culture-collection accession of the B. subtilis member. + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Sphingomonas desiccabilis and Bacillus subtilis enhanced the leaching of vanadium under the three gravity conditions compared to sterile controls by 184.92 to 283.22% + explanation: Establishes B. subtilis as a vanadium-leaching member of the panel. +- taxon_term: + preferred_term: Cupriavidus metallidurans CH34 + term: + id: NCBITaxon:119219 + label: Cupriavidus metallidurans + notes: > + Type strain CH34 (DSM 2839), a Gram-negative, motile, metal-resistant bacterium + often used in space experiments. In BioRock it showed no significant difference in + REE bioleaching compared to non-biological controls, illustrating the microbial + specificity of the process. + strain_designation: + strain_name: CH34 + culture_collections: + - collection: DSM + accession: '2839' + notes: Type strain CH34, deposited as DSM 2839. + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Cupriavidus metallidurans CH34 (DSM 2839; Type strain) + explanation: Names the strain and culture-collection accession of the C. metallidurans member. + - reference: PMID:33154740 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Cupriavidus metallidurans CH34 + explanation: Confirms C. metallidurans CH34 as one of the three panel members in the cell-concentration study. +ecological_interactions: +- name: Sphingomonas desiccabilis rare-earth-element bioleaching from basalt + description: > + Sphingomonas desiccabilis colonised basalt slides and mobilised rare earth + elements (the lanthanides plus yttrium) into the chamber fluid, raising mean leached + REE concentrations above non-biological controls under microgravity, simulated Mars + gravity, and simulated Earth gravity. Gravity regime had no significant effect on + the final yields, demonstrating that microbe-mineral REE bioleaching proceeds with + comparable efficacy across gravitational conditions. The basalt substrate contained + all measured lanthanides (La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu). + interaction_type: CROSS_FEEDING + source_taxon: + preferred_term: Sphingomonas desiccabilis CP1D + term: + id: NCBITaxon:429134 + label: Sphingomonas desiccabilis + metabolites: + - preferred_term: lanthanum(3+) + term: + id: CHEBI:49701 + label: lanthanum(3+) + - preferred_term: cerium(3+) + term: + id: CHEBI:48782 + label: cerium(3+) + - preferred_term: neodymium(3+) + term: + id: CHEBI:229785 + label: neodymium(3+) + - preferred_term: yttrium(3+) + term: + id: CHEBI:49962 + label: yttrium(3+) + biological_processes: + - preferred_term: response to metal ion + term: + id: GO:0010038 + label: response to metal ion + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Sphingomonas desiccabilis enhanced mean leached concentrations of REEs compared to non-biological controls in all gravity conditions + explanation: Documents S. desiccabilis enhancing REE leaching from basalt across gravity regimes. + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Content of rare earth elements (REEs; reported as μg/g + explanation: Anchors the basalt REE content table quantifying the leached lanthanides. +- name: Vanadium bioleaching by Sphingomonas desiccabilis and Bacillus subtilis + description: > + Both Sphingomonas desiccabilis and Bacillus subtilis enhanced leaching of vanadium + from basalt relative to sterile controls (by 184.92 to 283.22%) under microgravity, + simulated Mars gravity, and simulated Earth gravity. Vanadium is a valuable steel + additive, and its microbial mobilisation from basalt without a significant gravity + effect supports biomining and bioremediation on other Solar System bodies. + interaction_type: CROSS_FEEDING + source_taxon: + preferred_term: Bacillus subtilis NCIB 3610 + term: + id: NCBITaxon:1423 + label: Bacillus subtilis + biological_processes: + - preferred_term: response to metal ion + term: + id: GO:0010038 + label: response to metal ion + evidence: + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Sphingomonas desiccabilis and Bacillus subtilis enhanced the leaching of vanadium under the three gravity conditions compared to sterile controls by 184.92 to 283.22% + explanation: Quantifies vanadium bioleaching by both S. desiccabilis and B. subtilis. + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: One element of interest in mining is vanadium (V) + explanation: Identifies vanadium as the target element for this bioleaching interaction. +- name: Microbial specificity of basalt bioleaching among panel members + description: > + The three panel members differed in bioleaching outcome: Sphingomonas desiccabilis + enhanced REE leaching, Bacillus subtilis reduced REE bioleaching efficacy, and + Cupriavidus metallidurans showed no difference from non-biological controls. This + species-dependent partitioning of bioleaching activity mirrors the microbial + specificity of the process observed on Earth. + interaction_type: NICHE_PARTITIONING + source_taxon: + preferred_term: Sphingomonas desiccabilis CP1D + term: + id: NCBITaxon:429134 + label: Sphingomonas desiccabilis + target_taxon: + preferred_term: Cupriavidus metallidurans CH34 + term: + id: NCBITaxon:119219 + label: Cupriavidus metallidurans + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Bacillus subtilis exhibited a reduction in bioleaching efficacy and Cupriavidus metallidurans showed no difference compared to non-biological controls + explanation: Documents the species-specific differences in bioleaching outcome among the three members. + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: showing the microbial specificity of the process, as on Earth + explanation: States that bioleaching is microbially specific, supporting niche partitioning among members. +environmental_factors: +- name: Gravity regime + value: microgravity, simulated Mars gravity, and simulated Earth gravity (plus ground 1 x g controls) + description: > + The experiment compared true microgravity with simulated Mars and simulated Earth + gravity generated by an onboard centrifuge in the KUBIK incubator, alongside ground + 1 x g controls. Gravity had no significant effect on mean leaching or on final cell + concentrations. + evidence: + - reference: PMID:33154740 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: microbe-mineral interactions in microgravity, simulated Mars gravity and simulated Earth gravity + explanation: Documents the three gravity regimes tested for microbe-mineral interaction. +- name: Basalt substrate + value: olivine basalt slides (Gufunes, Reykjavik, Iceland) + description: > + Bacteria were cultivated on slides of olivine basalt collected near Gufunes, + Reykjavik, Iceland, chosen as an analogue of Moon/Mars surface material and as the + source rock for the leached rare earth elements and vanadium. + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: olivine basalt rock collected near Gufunes, Reykjavik in Iceland + explanation: Identifies the basalt substrate and its geographic source. +- name: Incubation temperature and duration + value: 21 days at ~20 C + description: > + Cultures were grown for 21 days at approximately 20 C (temperature loggers recorded + 20.16 C; strains were pre-grown at 20-22 C), before fixative injection ended the + experiment. + evidence: + - reference: PMID:33154740 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Samples grew for 21 days at 20.16°C + explanation: Documents the incubation duration and logged temperature of the ISS cultivation. +growth_media: +- name: 50% R2A medium (BioRock spaceflight cultivation) + temperature: '20.16' + temperature_unit: °C + atmosphere: AEROBIC + vessel_type: miniature biomining reactor culture chamber (KUBIK incubator, ISS) + inoculum_source: single-strain cultures pre-grown in R2A, applied to olivine basalt slides + preparation_notes: > + The medium used for the BioRock experiment was R2A at 50% v/v of the published + component concentrations, approved for spaceflight and supporting growth of all + three panel members. Overnight cultures were pre-grown in 100% v/v R2A at 20-22 C to + stationary phase; five millilitres of 50% R2A were used per sample chamber. + evidence: + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The medium used for the BioRock experiment was R2A + explanation: Identifies R2A as the cultivation medium. + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: at 50% v/v of the published component concentrations + explanation: Documents that R2A was used at 50% v/v strength. + - reference: PMID:33154740 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Five milliliters of a 50% v/v solution of R2A growth medium + explanation: Documents the 5 mL per-sample volume of 50% R2A used in the flight hardware. +cultivation_setup: +- cultivation_mode: BATCH + system_type: BIOREACTOR_UNSPECIFIED + operating_temperature: 20.16 + operating_temperature_unit: °C + temperature_controlled: true + notes: > + Purpose-built miniature space biomining reactor: culture chambers holding basalt + slides submerged in medium, housed in the KUBIK incubator in the Columbus module of + the ISS. Run as a closed 21-day batch cultivation ended by fixative injection. + evidence: + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: a miniature space biomining reactor was successfully used + explanation: Documents the miniature biomining reactor hardware. + - reference: PMID:33154740 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: KUBIK incubator located in the Columbus module onboard the ISS + explanation: Documents that the reactor was housed in the KUBIK incubator on the ISS. + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The experiment was conducted for 21 days + explanation: Documents the 21-day batch cultivation duration. +external_resources: +- name: Primary publication - REE extraction in microgravity and Mars gravity + repository: OTHER + resource_id: doi:10.1038/s41467-020-19276-w + url: https://doi.org/10.1038/s41467-020-19276-w + description: > + Nature Communications 2020 primary publication reporting rare earth element + bioleaching from basalt by the BioRock panel on the ISS. + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: bioleaching of REEs from basaltic rock + explanation: Lists the primary REE-extraction publication for this community. +- name: Companion publication - vanadium mining and bioremediation + repository: OTHER + resource_id: doi:10.3389/fmicb.2021.641387 + url: https://doi.org/10.3389/fmicb.2021.641387 + description: > + Frontiers in Microbiology 2021 companion publication reporting microbially-enhanced + vanadium leaching by the BioRock panel under micro- and Mars gravity. + evidence: + - reference: PMID:33868198 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: One element of interest in mining is vanadium (V) + explanation: Lists the vanadium-mining companion publication for this community. +- name: Companion publication - final bacterial cell concentrations + repository: OTHER + resource_id: doi:10.3389/fmicb.2020.579156 + url: https://doi.org/10.3389/fmicb.2020.579156 + description: > + Frontiers in Microbiology 2020 companion publication reporting no significant effect + of microgravity or simulated Mars gravity on final bacterial cell concentrations, + with detailed cultivation methods for the three-species panel. + evidence: + - reference: PMID:33154740 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: no significant differences in final cell counts and optical densities between the three gravity regimens on the ISS + explanation: Lists the cell-concentration companion publication and its main finding. +- name: NCBI Taxonomy - Sphingomonas desiccabilis + repository: OTHER + resource_id: NCBITaxon:429134 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=429134 + description: NCBI Taxonomy record for Sphingomonas desiccabilis. +- name: NCBI Taxonomy - Bacillus subtilis + repository: OTHER + resource_id: NCBITaxon:1423 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1423 + description: NCBI Taxonomy record for Bacillus subtilis. +- name: NCBI Taxonomy - Cupriavidus metallidurans + repository: OTHER + resource_id: NCBITaxon:119219 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=119219 + description: NCBI Taxonomy record for Cupriavidus metallidurans. +related_ingredients: +- preferred_term: cerium(3+) + chebi_term: + id: CHEBI:48782 + label: cerium(3+) + relevance: > + Cerium is one of the most abundant rare earth elements in the basalt substrate and + among the REEs leached into the chamber fluid by S. desiccabilis in the BioRock + experiment. + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Content of rare earth elements (REEs; reported as μg/g + explanation: Anchors cerium among the basalt REEs quantified and leached. +- preferred_term: neodymium(3+) + chebi_term: + id: CHEBI:229785 + label: neodymium(3+) + relevance: > + Neodymium is an economically important rare earth element present in the basalt and + among the REEs mobilised by S. desiccabilis bioleaching in microgravity and Mars + gravity. + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Sphingomonas desiccabilis enhanced mean leached concentrations of REEs compared to non-biological controls in all gravity conditions + explanation: Anchors neodymium among the REEs enhanced by S. desiccabilis leaching. +- preferred_term: yttrium(3+) + chebi_term: + id: CHEBI:49962 + label: yttrium(3+) + relevance: > + Yttrium is a rare earth element (grouped with the lanthanides and scandium) targeted + in the basalt bioleaching experiment. + evidence: + - reference: PMID:33173035 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: REEs), which include the lanthanides, scandium and yttrium + explanation: States that the targeted REEs include yttrium alongside the lanthanides and scandium. +associated_datasets: [] +metals_present: +- IRON +- VANADIUM +rare_earth_elements_present: +- LANTHANUM +- CERIUM +- PRASEODYMIUM +- NEODYMIUM +- SAMARIUM +- EUROPIUM +- GADOLINIUM +- TERBIUM +- DYSPROSIUM +- HOLMIUM +- ERBIUM +- THULIUM +- YTTERBIUM +- LUTETIUM +- YTTRIUM +metal_relevance: PRIMARY +metal_notes: > + Primary function is biomining: bioleaching of rare earth elements and vanadium from + basalt on the ISS. The basalt REE content table quantified all fourteen lanthanides + (La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu); yttrium is listed as a + targeted REE (scandium is mentioned generally but was not quantified in the leaching + table). Vanadium was actively leached by S. desiccabilis and B. subtilis (enhanced + 184.92-283.22% over sterile controls). Iron is a major constituent of the olivine + basalt substrate rather than a specific mining target. diff --git a/kb/communities/Lunar_Martian_Simulant_PGPB_Lettuce_SynCom.yaml b/kb/communities/Lunar_Martian_Simulant_PGPB_Lettuce_SynCom.yaml new file mode 100644 index 00000000..e4abcac3 --- /dev/null +++ b/kb/communities/Lunar_Martian_Simulant_PGPB_Lettuce_SynCom.yaml @@ -0,0 +1,449 @@ +id: CommunityMech:000304 +name: Lunar and Martian Simulant PGPB Lettuce SynCom +description: > + A defined four-strain plant growth-promoting bacterial (PGPB) consortium + designed for space-agriculture (In-Situ Resource Utilization) research, + composed of Azotobacter chroococcum 76A, Priestia megaterium EL5, + Methylobacterium populi VP2, and Kosakonia pseudosacchari TL13. The strains + belong to the microbial collection of the Department of Agricultural Sciences + of the University of Naples Federico II and were selected for complementary + plant growth-promoting traits (nitrogen fixation, phosphate solubilization, + phytohormone biosynthesis) and for mutual non-antagonism in dual-culture + assays. In a greenhouse pot experiment, the consortium was combined with + green compost derived from plant residues (pH 8.25, low C/N ratio) to improve + lettuce (Lactuca sativa cv. Grand Rapids) growth on commercial Lunar + (LHS-1) and Martian (MMS-1) regolith simulants with zero external chemical + input aside from the compost. Compost amendment increased lettuce biomass and + nutrient bioavailability, and PGPB inoculation enhanced leaf biomass and + mineral nutritional content while significantly increasing the copy number of + functional marker genes for nitrogen fixation (nifH), alkaline phosphatase + (phoD), and phytase (BPP) in non-amended substrates. The system is a + Bioregenerative Life Support System model relevant to regolith-agriculture and + long-term space missions. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: > + Test whether a selected consortium of plant growth-promoting bacteria, + combined with green compost, can improve lettuce growth and nutrient + bioavailability on Lunar and Martian regolith simulants with zero external + input aside from the compost. + assembly_strategy: > + Assemble a four-member PGPB consortium (Azotobacter chroococcum 76A, + Priestia megaterium EL5, Methylobacterium populi VP2, Kosakonia + pseudosacchari TL13) from an in-house microbial collection, selecting + strains for plant growth-promoting traits and for complete absence of + mutual inhibition in dual-culture antagonism assays; produce freeze-dried + inocula by fermentor cultivation and apply to lettuce grown on regolith + simulants with and without compost amendment. + measurement_endpoints: + - Lettuce leaf biomass, leaf number, leaf area, and growth index + - Foliar and substrate macro- and micro-nutrient content and bioavailability + - Copy number of nifH, phoD, and BPP functional marker genes in the rhizosphere + - Bacterial diversity and community composition by high-throughput 16S sequencing + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: role of selected consortium of plant growth-promoting + explanation: States the design goal of testing a selected PGPB consortium for space agriculture. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: zero external input aside from green compost + explanation: Supports the zero-external-input design constraint with green compost as the only amendment. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: absence of antagonism, assessed + explanation: Supports the assembly strategy of selecting mutually non-antagonistic strains. +environment_term: + preferred_term: greenhouse regolith-simulant pot cultivation + term: + id: ENVO:01001405 + label: laboratory environment + notes: > + The community was studied in a controlled greenhouse pot experiment using + commercial Lunar (LHS-1) and Martian (MMS-1) regolith simulants amended with + green compost, as an Earth-based model of In-Situ Resource Utilization space + agriculture. The ENVO grounding reflects the controlled experimental + (laboratory/greenhouse) setting; the extraterrestrial simulant context is + captured in the description and environmental_factors. +taxonomy: +- taxon_term: + preferred_term: Azotobacter chroococcum 76A + term: + id: NCBITaxon:353 + label: Azotobacter chroococcum + notes: > + Source identifies strain 76A; ontology grounding is species-level to the + stable NCBI Taxonomy term Azotobacter chroococcum. + strain_designation: + strain_name: 76A + notes: > + Strain from the microbial collection of the Department of Agricultural + Sciences, University of Naples Federico II. A free-living aerobic + rhizobacterium reported to fix N2, produce exopolysaccharide and + phytohormone, and (for several strains) solubilize phosphorus. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Azotobacter chroococcum 76A, Priestia megaterium EL5, Methylobacterium populi VP2, and Kosakonia + explanation: Names Azotobacter chroococcum 76A as a member of the consortium. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: REVIEW + snippet: showed multiple PGP activities + explanation: Supports Azotobacter's plant growth-promoting activities in the introduction's account of the genus. +- taxon_term: + preferred_term: Priestia megaterium EL5 + term: + id: NCBITaxon:1404 + label: Priestia megaterium + notes: > + Source identifies strain EL5; ontology grounding is species-level to the + stable NCBI Taxonomy term Priestia megaterium (formerly Bacillus + megaterium). + strain_designation: + strain_name: EL5 + notes: > + Strain from the microbial collection of the Department of Agricultural + Sciences, University of Naples Federico II. Priestia megaterium is + reported to have strong phosphate solubilization capability, including in + extraterrestrial simulants. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Priestia megaterium EL5, Methylobacterium populi VP2, and Kosakonia + explanation: Names Priestia megaterium EL5 as a member of the consortium. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: REVIEW + snippet: strong phosphate solubilization capabilities, even in + explanation: Supports the phosphate-solubilizing role attributed to Priestia megaterium. +- taxon_term: + preferred_term: Methylobacterium populi VP2 + term: + id: NCBITaxon:223967 + label: Methylorubrum populi + notes: > + Source names the strain Methylobacterium populi VP2; NCBI Taxonomy has + reclassified this species as Methylorubrum populi (NCBITaxon:223967), so + the canonical ontology label used here is Methylorubrum populi. The strain + was isolated from a polluted environment. + strain_designation: + strain_name: VP2 + isolation_source: polluted environment + notes: > + Strain from the microbial collection of the Department of Agricultural + Sciences, University of Naples Federico II. Methylobacterium species are + phytosymbionts contributing to plant development through phytohormone + biosynthesis, nitrogen fixation, and ethylene biosynthesis suppression. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Methylobacterium populi VP2, and Kosakonia + explanation: Names Methylobacterium populi VP2 as a member of the consortium. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: REVIEW + snippet: phytohormone biosynthesis, nitrogen fixa + explanation: Supports the plant-development mechanisms (phytohormone biosynthesis, nitrogen fixation) attributed to Methylobacterium. +- taxon_term: + preferred_term: Kosakonia pseudosacchari TL13 + term: + id: NCBITaxon:1646340 + label: Kosakonia pseudosacchari + notes: > + Source identifies strain TL13; ontology grounding is species-level to the + stable NCBI Taxonomy term Kosakonia pseudosacchari. + strain_designation: + strain_name: TL13 + notes: > + Strain from the microbial collection of the Department of Agricultural + Sciences, University of Naples Federico II. Kosakonia species are + endophytes with plant growth-promoting traits; K. pseudosacchari TL13 + shows freeze-drying resistance, ease of cultivation, and ability to use + alternative carbon sources. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Kosakonia pseudosacchari + explanation: Names Kosakonia pseudosacchari (strain TL13) as a member of the consortium. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: REVIEW + snippet: freeze-drying resistance, ease + explanation: Supports the freeze-drying resistance and cultivation traits attributed to K. pseudosacchari TL13. +ecological_interactions: +- name: Non-antagonistic PGPB consortium assembly + description: > + The four consortium members were combined only after dual-culture antagonism + testing showed a complete absence of inhibition zones, i.e., the strains + coexist without mutual antagonism. This compatibility was a selection + criterion for building the multi-strain inoculant. + interaction_type: COMMENSALISM + scope: COMMUNITY_LEVEL + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: absence of antagonism, assessed + explanation: Supports selection of strains showing absence of antagonism for the consortium. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: of inhibition zones were used for consortium + explanation: Supports that only strains with no inhibition zones were combined into the consortium. +- name: PGPB rhizosphere colonization and functional-gene enrichment + description: > + Inoculation with the PGPB consortium significantly increased the copy number + of nitrogen-fixation (nifH) and phosphate-solubilization/mineralization + marker genes (phoD alkaline phosphatase, BPP phytase) in the lettuce + rhizosphere of non-amended regolith simulants, consistent with colonization + of the rhizosphere and enrichment of nitrogen-fixation and + phosphorus-cycling functions. + interaction_type: COLONIZATION_FACILITATION + scope: COMMUNITY_LEVEL + target_taxon: + preferred_term: Lactuca sativa (lettuce host) + term: + id: NCBITaxon:4236 + label: Lactuca sativa + biological_processes: + - preferred_term: nitrogen fixation + term: + id: GO:0009399 + label: nitrogen fixation + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: significantly increased the relative abun + explanation: Supports that PGPB inoculation increased the relative abundance of marker functional genes. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: increase in functional genes linked with nitrogen fixation and phosphorus + explanation: Supports enrichment of nitrogen-fixation and phosphorus-solubilization functional genes upon inoculation. +- name: PGPB-enhanced lettuce growth and mineral nutrition + description: > + On nutrient-limited regolith simulants, the PGPB consortium enhanced lettuce + leaf biomass and mineral nutritional content, a beneficial plant-microbe + interaction in which the bacteria promote host growth in the rhizosphere. + interaction_type: MUTUALISM + scope: COMMUNITY_LEVEL + target_taxon: + preferred_term: Lactuca sativa (lettuce host) + term: + id: NCBITaxon:4236 + label: Lactuca sativa + biological_processes: + - preferred_term: indoleacetic acid biosynthetic process + term: + id: GO:0009684 + label: indoleacetic acid biosynthetic process + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: PGPB treatment enhanced leaf biomass by 35% + explanation: Supports enhancement of lettuce leaf biomass by PGPB inoculation. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: microbial consortium could exert positive impact on plants grown in nutrient-limited substrates + explanation: Supports a positive impact of the consortium on plants in nutrient-limited regolith substrates. +environmental_factors: +- name: Regolith simulant substrate + value: Lunar Highlands Simulant (LHS-1) and Mojave Mars Simulant (MMS-1) + description: > + Lettuce was grown on commercial Lunar (LHS-1, Exolith Lab) and Martian + (MMS-1, The Martian Garden) regolith simulants, with quartz sand as an inert + control substrate. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: commercial Lunar (LHS-1) and Martian (MMS-1) + explanation: Supports the use of LHS-1 and MMS-1 regolith simulants as substrates. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Mojave Mars Simulant (MMS-1 + explanation: Identifies MMS-1 as the Mojave Mars Simulant used in the experiment. +- name: Regolith alkalinity and nutrient limitation + value: alkaline pH (9 to 10), organic-matter-poor + description: > + Regolith simulants are alkaline (pH 9 to 10), lack organic matter, and carry + anomalous or toxic chemical species (e.g., perchlorates in Mars regolith), + making them nutrient-deficient substrates for plant growth. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: REVIEW + snippet: alkaline pH (9 to 10) + explanation: Supports the alkaline pH range characteristic of regolith. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: REVIEW + snippet: perchlorates in Mars rego + explanation: Supports the presence of toxic perchlorates in Mars regolith. +- name: Green compost amendment + value: green compost, pH 8.25, low C/N ratio, 20% v/v + description: > + A commercial green compost derived from pruning waste and grass cuttings + (alkaline pH 8.25, low C/N ratio indicating good nitrogen availability) was + incorporated at 20% (v/v) as the only external amendment, simulating in-situ + recycling of plant residues. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: alkaline pH (8.25) and a low C/N ratio + explanation: Supports the compost pH and low C/N ratio. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: zero external input aside from green compost + explanation: Supports green compost as the sole external amendment. +- name: Greenhouse climate + value: mean air temperature 13 C; 10/14 photoperiod + description: > + The pot experiment was conducted in a greenhouse with mean air temperature + 13 C (min 8, max 17) and a 10/14 photoperiod. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 10/14 photoperiod + explanation: Supports the greenhouse photoperiod used during cultivation. +growth_media: +- name: PGPB inoculum production media (per-strain fermentor cultivation) + atmosphere: AEROBIC + ph: '7.00' + shaking_speed: '130' + shaking_speed_unit: rpm + inoculum_size: 2% (v/v) of ~1e8 CFU/mL cell suspension + preparation_notes: > + Each strain was cultivated separately in a strain-specific complex medium: + Brain Heart Infusion (BHI) for K. pseudosacchari TL13, Yeast Mannitol Broth + (YMB) for A. chroococcum 76A, Plate Count Broth (PCB) for P. megaterium EL5, + and Nutrient Broth (NB) for M. populi VP2. Fermentations were run at 30 C + (K. pseudosacchari, P. megaterium), 28 C (A. chroococcum), and for M. populi, + at pH 7.00, 130 rpm agitation, air sparging 0.5 vvm, with antifoam added. + Biomass was centrifuged and freeze-dried; inocula were resuspended to 1e6 + CFU/mL per strain and applied to lettuce by a root-dip method plus repeated + collar application after transplanting. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: pH 7.00, agitation at 130 rpm, air sparging at 0.5 + explanation: Supports the fermentation pH, agitation, and aeration conditions for inoculum production. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: freeze-dried for long term + explanation: Supports freeze-drying of the biomass for inoculum storage. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: root dip method + explanation: Supports the root-dip inoculation method used to apply the consortium to lettuce. +cultivation_setup: +- cultivation_mode: BATCH + system_type: STIRRED_TANK_BIOREACTOR + instrument_detail: 14 L fermentor used to produce each strain's biomass for the inoculum + manufacturer_model: New Brunswick BioFlo/CelliGen 115 (Eppendorf) + working_volume: 8.0 + working_volume_unit: L + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 14 L fermentor + explanation: Supports the fermentor used to cultivate the strains. + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: working volume of 8 L + explanation: Supports the 8 L working volume of the fermentor. +external_resources: +- name: Primary publication - PGPB consortia and green compost on regolith simulants + repository: OTHER + resource_id: doi:10.1007/s00374-025-01923-3 + url: https://doi.org/10.1007/s00374-025-01923-3 + description: > + Duri et al. 2025, Biology and Fertility of Soils - primary source describing + the four-strain PGPB consortium and green compost improving lettuce growth + on Lunar and Martian regolith simulants. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: application of microbial consortium along with green compost is a promising strategy + explanation: Identifies this publication as the primary source and summarizes its central finding. +- name: NCBI Taxonomy - Azotobacter chroococcum + repository: OTHER + resource_id: NCBITaxon:353 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=353 + description: NCBI Taxonomy record for Azotobacter chroococcum. +- name: NCBI Taxonomy - Priestia megaterium + repository: OTHER + resource_id: NCBITaxon:1404 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1404 + description: NCBI Taxonomy record for Priestia megaterium. +- name: NCBI Taxonomy - Methylorubrum populi + repository: OTHER + resource_id: NCBITaxon:223967 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=223967 + description: NCBI Taxonomy record for Methylorubrum populi (formerly Methylobacterium populi). +- name: NCBI Taxonomy - Kosakonia pseudosacchari + repository: OTHER + resource_id: NCBITaxon:1646340 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1646340 + description: NCBI Taxonomy record for Kosakonia pseudosacchari. +related_ingredients: +- preferred_term: indole-3-acetic acid + chebi_term: + id: CHEBI:16411 + label: indole-3-acetic acid + relevance: > + Indole-3-acetic acid is the phytohormone whose biosynthesis is a key + plant growth-promoting mechanism of the consortium members (e.g., + Azotobacter and Methylobacterium), contributing to enhanced lettuce growth. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: REVIEW + snippet: phytohormone biosynthesis, nitrogen fixa + explanation: Names phytohormone biosynthesis as a PGPB mechanism of consortium members. +- preferred_term: perchlorate + chebi_term: + id: CHEBI:49706 + label: perchlorate + relevance: > + Perchlorate is an anomalous, toxic chemical species present in Mars regolith, + part of the nutrient-deficient and hostile substrate chemistry that the + PGPB-plus-compost strategy is designed to overcome. + evidence: + - reference: doi:10.1007/s00374-025-01923-3 + supports: SUPPORT + evidence_source: REVIEW + snippet: perchlorates in Mars rego + explanation: Names perchlorates as toxic species in Mars regolith. +associated_datasets: [] +metals_present: [] +rare_earth_elements_present: [] +metal_relevance: NOT_APPLICABLE +metal_notes: > + This is a regolith-agriculture / plant growth-promotion community; no metal or + rare earth element extraction, leaching, or cycling role is curated. Regolith + and compost mineral nutrients (e.g., N, P) are relevant to plant nutrition but + do not constitute a metals-focused community function. diff --git a/kb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml b/kb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml new file mode 100644 index 00000000..3ee386aa --- /dev/null +++ b/kb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml @@ -0,0 +1,412 @@ +id: CommunityMech:000306 +name: Lunar Regolith Simulant Phosphorus-Solubilizing Bacteria for Nicotiana benthamiana +description: > + A defined set of phosphorus-solubilizing bacteria (PSBs) assembled to improve + the fertility of lunar regolith simulant for in-situ resource utilization (ISRU) + agriculture in bioregenerative life support systems. Five commonly used + microbial-fertilizer strains were tested on a CAS-1 lunar soil simulant: + Bacillus mucilaginosus (AS1.232), Bacillus megaterium (AS1.217), Bacillus + subtilis (CMCC 63501), Bacillus licheniformis (ATCC 11946), and Pseudomonas + fluorescens (ATCC 13525). In a 21-day bio-improving experiment followed by a + 24-day Nicotiana benthamiana cultivation experiment, three of the strains - + Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens - + tolerated the lunar regolith simulant conditions and dissociated insoluble + inorganic phosphorus from the simulant. The mechanism is chemolithoheterotrophic + organic-acid production: the bacteria synthesize organic acids (e.g. oxalic, + citric, tartaric acids) from carbon sources in the medium, lowering the pH and + chelating metal ions in insoluble phosphates such as Ca3(PO4)2, FePO4, and + AlPO4, thereby releasing available phosphate. PSB treatment raised the available + phosphorus content of the simulant and promoted Nicotiana benthamiana growth, + with the largest improvement when the simulant was pre-cultured with PSBs 18 + days before sowing. The work establishes a microbiological route to convert + lunar regolith into a plant-cultivation substrate for future lunar bases. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: > + Explore a microbiological method to transform lunar regolith simulant into a + fertile substrate for higher-plant cultivation by using phosphorus-solubilizing + bacteria to mobilize insoluble inorganic phosphorus, supporting self-sufficient + bioregenerative life support for future lunar bases. + assembly_strategy: > + Screen five microbial-fertilizer PSB strains (Bacillus mucilaginosus, Bacillus + megaterium, Bacillus subtilis, Bacillus licheniformis, Pseudomonas fluorescens) + for tolerance to and phosphorus solubilization on CAS-1 lunar regolith simulant, + then apply the effective strains to bio-improve the simulant before sowing. + perturbation_design: > + A 21-day bio-improving (regolith pre-culture) phase followed by a 24-day + Nicotiana benthamiana cultivation phase, comparing PSB treatments (including a + "pre-cultured for 18 days" treatment) against sterilized-control and + horticultural-soil references. + measurement_endpoints: + - Bacterial tolerance and growth (OD600) on lunar regolith simulant + - Available / soluble inorganic phosphorus content of the simulant and medium + - Regolith and culture-medium pH + - Nicotiana benthamiana growth (seedling length, fresh weight, chlorophyll content) + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: In-situ utilization of lunar soil resources will effectively improve the self-sufficiency of bioregenerative life support systems for future lunar bases + explanation: States the ISRU / bioregenerative-life-support objective motivating the community design. + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: a 21-day bio-improving experiment with another 24-day Nicotiana benthamiana cultivation experiment are carried out on lunar regolith + explanation: Documents the two-phase experimental design (bio-improving then plant cultivation) on lunar regolith simulant. +environment_term: + preferred_term: lunar regolith simulant plant-cultivation laboratory experiment + term: + id: ENVO:01001405 + label: laboratory environment + notes: > + Controlled laboratory experiment on a CAS-1 lunar soil simulant (a terrestrial + copy of lunar regolith), not a sampled natural community. The simulant provides + insoluble inorganic phosphorus (Ca3(PO4)2, FePO4, AlPO4) that the PSBs mobilize; + the space / lunar-base ISRU context is captured in the description. +taxonomy: +- taxon_term: + preferred_term: Bacillus mucilaginosus (AS1.232) + term: + id: NCBITaxon:61624 + label: Paenibacillus mucilaginosus + notes: > + Reported by the source as Bacillus mucilaginosus (strain AS1.232); the stable + NCBI Taxonomy term for this organism is Paenibacillus mucilaginosus. One of the + three PSBs that tolerated the lunar regolith simulant and dissociated insoluble + inorganic phosphorus. + strain_designation: + strain_name: AS1.232 + culture_collections: + - collection: OTHER + accession: AS1.232 + notes: Provided by the Shanghai Bioresource collection center; AS accession number. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the phosphorus-solublizing bacteria Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens can tolerate the lunar regolith simulant conditions and dissociate the insoluble phosphorus from the regolith simulant + explanation: Names Bacillus mucilaginosus as one of the effective phosphorus-solubilizing members. + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232) + explanation: Provides the strain designation AS1.232 for Bacillus mucilaginosus. +- taxon_term: + preferred_term: Bacillus megaterium (AS1.217) + term: + id: NCBITaxon:1404 + label: Priestia megaterium + notes: > + Reported by the source as Bacillus megaterium (strain AS1.217); the stable NCBI + Taxonomy term for this organism is Priestia megaterium. One of the three PSBs + that tolerated the lunar regolith simulant and dissociated insoluble inorganic + phosphorus. + strain_designation: + strain_name: AS1.217 + culture_collections: + - collection: OTHER + accession: AS1.217 + notes: Provided by the Shanghai Bioresource collection center; AS accession number. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the phosphorus-solublizing bacteria Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens can tolerate the lunar regolith simulant conditions and dissociate the insoluble phosphorus from the regolith simulant + explanation: Names Bacillus megaterium as one of the effective phosphorus-solubilizing members. + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232) + explanation: Provides the strain designation AS1.217 for Bacillus megaterium. +- taxon_term: + preferred_term: Pseudomonas fluorescens (ATCC 13525) + term: + id: NCBITaxon:294 + label: Pseudomonas fluorescens + notes: > + Strain ATCC 13525. One of the three PSBs that tolerated the lunar regolith + simulant and dissociated insoluble inorganic phosphorus. + strain_designation: + strain_name: ATCC 13525 + culture_collections: + - collection: ATCC + accession: '13525' + notes: Type strain accession; strains provided by the Shanghai Bioresource collection center. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the phosphorus-solublizing bacteria Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens can tolerate the lunar regolith simulant conditions and dissociate the insoluble phosphorus from the regolith simulant + explanation: Names Pseudomonas fluorescens as one of the effective phosphorus-solubilizing members. + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232) + explanation: Provides the strain designation ATCC 13525 for Pseudomonas fluorescens. +- taxon_term: + preferred_term: Bacillus subtilis (CMCC 63501) + term: + id: NCBITaxon:1423 + label: Bacillus subtilis + notes: > + Strain CMCC 63501. Tested as a candidate PSB but did not effectively dissociate + insoluble inorganic phosphorus from the lunar regolith simulant under the study + conditions. + strain_designation: + strain_name: CMCC 63501 + culture_collections: + - collection: OTHER + accession: CMCC 63501 + notes: Provided by the Shanghai Bioresource collection center; CMCC accession number. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232) + explanation: Names Bacillus subtilis (CMCC 63501) as one of the five tested PSB strains. +- taxon_term: + preferred_term: Bacillus licheniformis (ATCC 11946) + term: + id: NCBITaxon:1402 + label: Bacillus licheniformis + notes: > + Strain ATCC 11946. Tested as a candidate PSB but did not effectively dissociate + insoluble inorganic phosphorus from the lunar regolith simulant under the study + conditions. + strain_designation: + strain_name: ATCC 11946 + culture_collections: + - collection: ATCC + accession: '11946' + notes: Strains provided by the Shanghai Bioresource collection center. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: B. megaterium (AS1.217), B. subtilis (CMCC 63501), P. fluorescens (ATCC 13525), B. licheniformis (ATCC 11946), and B. mucilaginosus (AS1.232) + explanation: Names Bacillus licheniformis (ATCC 11946) as one of the five tested PSB strains. +ecological_interactions: +- name: Phosphorus solubilization from lunar regolith simulant via organic-acid secretion + description: > + The phosphorus-solubilizing bacteria synthesize organic acids from carbon + sources in the medium, lowering the pH and chelating metal ions in insoluble + phosphate minerals (Ca3(PO4)2, FePO4, AlPO4), thereby dissociating insoluble + inorganic phosphorus and increasing the soluble/available phosphorus available + to plants. This microbe-mineral process, driven by the whole PSB treatment, is + the core mechanism improving the fertility of the lunar regolith simulant. + interaction_type: CROSS_FEEDING + scope: COMMUNITY_LEVEL + metabolites: + - preferred_term: phosphate + term: + id: CHEBI:18367 + label: phosphate(3-) + - preferred_term: oxalic acid + term: + id: CHEBI:16995 + label: oxalic acid + - preferred_term: citrate + term: + id: CHEBI:16947 + label: citrate(3-) + biological_processes: + - preferred_term: organic acid biosynthetic process + term: + id: GO:0016053 + label: organic acid biosynthetic process + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: PSBs to synthesize organic acids by using carbon sources in the medium to reduce regolith pH, thus activating insoluble inorganic phosphorus in lunar regolith simulant + explanation: States the organic-acid / pH-reduction mechanism of phosphorus mobilization from the simulant. + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: organic acid ions also facilitate the dissolution of phosphate minerals through chelating with the metal ions in Ca 3 (PO 4 ) 2 , FePO 4 , AlPO 4 + explanation: Documents metal-ion chelation of insoluble phosphate minerals by secreted organic acids. +- name: Phosphorus-enabled promotion of Nicotiana benthamiana growth + description: > + By raising the available phosphorus content of the lunar regolith simulant, + the PSB treatment promotes the growth of the higher plant Nicotiana benthamiana, + a plant-beneficial outcome that is strongest when the simulant is pre-cultured + with PSBs 18 days before sowing. + interaction_type: COLONIZATION_FACILITATION + scope: COMMUNITY_LEVEL + target_taxon: + preferred_term: Nicotiana benthamiana + term: + id: NCBITaxon:4100 + label: Nicotiana benthamiana + metabolites: + - preferred_term: phosphate + term: + id: CHEBI:18367 + label: phosphate(3-) + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The phosphorus-solubilizing bacteria treatment improves the available phosphorus content of the regolith simulant, promoting the growth of Nicotiana benthamiana + explanation: Links PSB-driven available-phosphorus increase to promotion of Nicotiana benthamiana growth. + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the growth of Nicotiana benthamiana could be most improved by treating the regolith simulant with PSBs 18 days before sowing + explanation: Documents the strongest plant-growth improvement from an 18-day pre-culture treatment. +environmental_factors: +- name: Lunar regolith simulant substrate + value: CAS-1 lunar soil simulant + description: > + The cultivation substrate is a terrestrial copy of the CAS-1 lunar soil + simulant, which supplies insoluble inorganic phosphorus that the PSBs mobilize. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The simulant used in our study is a copy of the CAS-1 lunar soil simulant + explanation: Identifies the CAS-1 lunar soil simulant as the experimental substrate. +- name: Available phosphorus increase in liquid medium + value: soluble inorganic phosphorus increased by 212 percent + description: > + In the shaking-flask solubilization test, the concentration of soluble + inorganic phosphorus in the liquid medium was significantly increased by the + effective PSBs, indicating active dissociation of insoluble phosphorus. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: soluble inorganic phosphorus in the liquid medium was significantly increased by 212 + explanation: Quantifies the increase in soluble inorganic phosphorus driven by PSB solubilization. +- name: Acidification as the phosphorus-dissolving factor + value: bacterial acidic substances lower pH + description: > + Acidic substances secreted by the bacteria were identified as the key factor + dissolving inorganic phosphorus from the simulant, consistent with the + organic-acid solubilization mechanism. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the acidic substances were the key factor in dissolving inorganic phosphorus from the simulant + explanation: Identifies bacterial acidic substances as the controlling factor in phosphorus dissolution. +growth_media: +- name: PSB phosphorus-solubilization liquid medium (shaking-flask assay) + temperature: '30' + temperature_unit: °C + ph: '7.0' + atmosphere: AEROBIC + shaking_speed: '180' + shaking_speed_unit: rpm + vessel_type: shaking flask + preparation_notes: > + Strains were cultured overnight in a shaking flask at 180 rpm and 30 C. The + phosphorus-solubilization assay used a liquid medium containing glucose 10 g/L, + (NH4)2SO4 0.5 g/L, Ca3(PO4)2 5 g/L (insoluble inorganic phosphorus source), + NaCl 0.3 g/L, FeSO4 0.03 g/L, KCl 0.3 g/L, MgSO4 0.3 g/L, MnSO4 0.03 g/L, at + pH 7.0. + composition: + - name: glucose + concentration: '10' + unit: g/L + - name: Ca3(PO4)2 (insoluble inorganic phosphorus source) + concentration: '5' + unit: g/L + chebi_term: + preferred_term: phosphate + term: + id: CHEBI:18367 + label: phosphate(3-) + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: cultured overnight in a shaking flask at 180 rpm and 30 °C + explanation: Documents the 30 C, 180 rpm shaking-flask cultivation conditions. + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: glucose 10 g/L + explanation: Documents glucose as the carbon source (10 g/L) in the solubilization assay medium. +external_resources: +- name: Primary publication - phosphorus-solubilizing bacteria improve Nicotiana benthamiana on lunar regolith simulant + repository: OTHER + resource_id: doi:10.1038/s42003-023-05391-z + url: https://doi.org/10.1038/s42003-023-05391-z + description: > + Xia et al., Communications Biology (2023). Primary source describing the five + tested PSB strains, phosphorus solubilization from CAS-1 lunar regolith + simulant, and improved Nicotiana benthamiana growth. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: five species of phosphorus-solubilizing bacteria are used as test strains + explanation: Identifies the publication as the primary source describing the five-strain PSB community. +- name: NCBI Taxonomy - Paenibacillus mucilaginosus + repository: OTHER + resource_id: NCBITaxon:61624 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=61624 + description: NCBI Taxonomy record for Paenibacillus mucilaginosus (reported as Bacillus mucilaginosus). +- name: NCBI Taxonomy - Priestia megaterium + repository: OTHER + resource_id: NCBITaxon:1404 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1404 + description: NCBI Taxonomy record for Priestia megaterium (reported as Bacillus megaterium). +- name: NCBI Taxonomy - Pseudomonas fluorescens + repository: OTHER + resource_id: NCBITaxon:294 + url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=294 + description: NCBI Taxonomy record for Pseudomonas fluorescens. +related_ingredients: +- preferred_term: phosphate + chebi_term: + id: CHEBI:18367 + label: phosphate(3-) + relevance: > + Available phosphate is the nutrient the PSBs mobilize from insoluble inorganic + phosphorus in the lunar regolith simulant; its increase drives improved plant + growth. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The phosphorus-solubilizing bacteria treatment improves the available phosphorus content of the regolith simulant, promoting the growth of Nicotiana benthamiana + explanation: Names available phosphorus as the mobilized nutrient central to the community's function. +- preferred_term: oxalic acid + chebi_term: + id: CHEBI:16995 + label: oxalic acid + relevance: > + Oxalic acid is one of the organic acids secreted by PSBs that lowers pH and + chelates metal ions to dissolve insoluble phosphate minerals. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: organic acid ions also facilitate the dissolution of phosphate minerals through chelating with the metal ions in Ca 3 (PO 4 ) 2 , FePO 4 , AlPO 4 + explanation: Documents organic acids (including oxalic acid) as the phosphate-mineral-dissolving lixiviants. +- preferred_term: citrate + chebi_term: + id: CHEBI:16947 + label: citrate(3-) + relevance: > + Citric acid / citrate is among the organic acids that solubilize insoluble + phosphate minerals through metal-ion chelation and acidification. + evidence: + - reference: PMID:37945659 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: PSBs to synthesize organic acids by using carbon sources in the medium to reduce regolith pH, thus activating insoluble inorganic phosphorus in lunar regolith simulant + explanation: Supports secreted organic acids (including citric acid) as the mechanism of phosphorus activation. +associated_datasets: [] +metals_present: [] +rare_earth_elements_present: [] +metal_relevance: NOT_APPLICABLE +metal_notes: > + This is a phosphorus-mobilization / ISRU-agriculture community, not a metals + community. The relevant transformation is dissolution of insoluble inorganic + phosphate minerals to release available phosphate; no metal or rare-earth-element + recovery role is curated.