diff --git a/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml b/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml index 66ea8c79..491dcc97 100644 --- a/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml +++ b/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml @@ -697,6 +697,58 @@ environmental_factors: devanaterra" reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments explanation: Demonstrates value of genomic data for understanding archaeal adaptations +related_ingredients: +- preferred_term: ammonia + chebi_term: + id: CHEBI:16134 + label: ammonia + relevance: Ammonia is the central energy substrate oxidized by the dominant ammonia-oxidizing + archaea (Ca. Nitrosotalea, Nitrososphaera-like) that define this community. At the + extremely low pH of AMD, free ammonia is reduced to nanomolar concentrations, and + the archaeal nitrifiers' extraordinary substrate affinity for ammonia is the adaptation + that lets them dominate nitrification where bacterial oxidizers cannot. + evidence: + - reference: PMID:21896746 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Growth at extremely low ammonia concentration (0.18 nM) also challenges accepted + views on ammonia uptake and metabolism and indicates novel mechanisms for ammonia + oxidation at low pH. + explanation: Anchors ammonia as the oxidized substrate driving acidophilic archaeal + growth at nanomolar concentrations. +- preferred_term: nitrite + chebi_term: + id: CHEBI:16301 + label: nitrite + relevance: Nitrite is the product of archaeal ammonia oxidation and the substrate handed + off to nitrite-oxidizing bacteria (Nitrospira), forming the syntrophic core of the + nitrification pathway in this community. Its low bioavailability at acidic pH is a + defining constraint shaping which nitrifiers persist in AMD sediments. + evidence: + - reference: PMID:29209281 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: ammonia (NH3) and nitrite (NO2-) concentrations are very low due to the chemical + equilibrium in solution + explanation: Anchors nitrite as a central, pH-limited intermediate of nitrification + in AMD sediments. +- preferred_term: urea + chebi_term: + id: CHEBI:16199 + label: urea + relevance: Urea is an alternative ammonia source the acidophilic AOA hydrolyze to generate + localized ammonia, overcoming the nanomolar free-ammonia limitation at low pH. Urea + hydrolysis is a key adaptation enabling archaeal nitrification to dominate in these + acidic environments. + evidence: + - reference: PMID:22592820 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The results strongly suggest that archaeal ammonia oxidation is supported by + hydrolysis of urea and that AOA, from the marine Group 1.1a-associated lineage, dominate + nitrification in two acidic soils tested. + explanation: Anchors urea as a central substrate whose hydrolysis sustains archaeal + nitrification at low pH. metals_present: - COPPER - IRON diff --git a/kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml b/kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml index 36e31646..afcf867a 100644 --- a/kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml +++ b/kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml @@ -244,6 +244,67 @@ environmental_factors: gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA explanation: Supports the wet-sedge-tundra and Alaska site identification. +related_ingredients: +- preferred_term: iron(3+) + chebi_term: + id: CHEBI:29034 + label: iron(3+) + relevance: Fe(III) is the terminal electron acceptor that defines this community. + Its dissimilatory reduction by the dominant Rhodoferax sp. drives the oxidation + of acetate and benzoate to CO2 and dominates microbial carbon degradation in the + thawing permafrost soils. + evidence: + - reference: PMID:37996661 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: pyruvate is used to generate acetate that can be oxidized, along with + benzoate, to CO2 when coupled with Fe(III) reduction + explanation: Anchors Fe(III) reduction as the electron-accepting half-reaction + coupled to organic carbon oxidation in this community. +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Fe(II) is the electron donor oxidized by the chemoautotrophic Gallionella + sp. to regenerate Fe(III), closing the iron redox cycle that sustains the + community's carbon-degradation activity during extended thaw. + evidence: + - reference: PMID:37996661 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) + oxidation (e.g., Cyc1) increased concurrently + explanation: Anchors Fe(II) oxidation as the donor half-reaction that increases + in lockstep with Fe(III) reduction, defining the iron redox couple. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Acetate is the central organic carbon substrate generated from pyruvate + and oxidized to CO2 when coupled to Fe(III) reduction; it also links the iron + cyclers to acetoclastic methanogens that they competitively suppress. + evidence: + - reference: PMID:37996661 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: pyruvate is used to generate acetate that can be oxidized, along with + benzoate, to CO2 when coupled with Fe(III) reduction + explanation: Anchors acetate as the carbon donor produced from pyruvate and + oxidized via Fe(III) reduction. +- preferred_term: benzoate + chebi_term: + id: CHEBI:16150 + label: benzoate + relevance: Benzoate is a key aromatic carbon substrate whose degradation genes rise + concurrently with Fe(III) reduction; it is oxidized to CO2 coupled to iron + reduction, contributing to the iron-dominated carbon degradation in this community. + evidence: + - reference: PMID:37996661 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: with genes for benzoate degradation and pyruvate metabolism + explanation: Anchors benzoate degradation as a carbon-cycling pathway increasing + alongside iron redox gene abundance. metals_present: - IRON rare_earth_elements_present: [] diff --git a/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml b/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml index d5b90b41..ae1fe8a0 100644 --- a/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml +++ b/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml @@ -964,6 +964,51 @@ environmental_factors: snippet: Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill explanation: Documents long-term weathering profile development +related_ingredients: +- preferred_term: zinc(2+) + chebi_term: + id: CHEBI:29105 + label: zinc(2+) + relevance: Zinc is the most abundant toxic metal in these Pb-Zn tailings (2000-8000 mg/kg solid, + 50-500 mg/L dissolved), released as Zn(2+) by oxidative weathering of sphalerite (ZnS) and + a primary driver of community structure and metal-resistance selection in the consortium. + evidence: + - reference: PMID:22092956 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Analysis of mobile salts showed that E.C. values were driven by ionic S, Zn, Cl and Al + explanation: Identifies dissolved zinc as a key mobile-phase element shaping the tailings bacterial + community. +- preferred_term: lead(2+) + chebi_term: + id: CHEBI:49807 + label: lead(2+) + relevance: Lead, mobilized as Pb(2+) from galena (PbS) during sulfide oxidation, is the defining + contaminant of this Pb-Zn polymetallic system (200-800 mg/kg solid, 5-50 mg/L dissolved) and + a key selective pressure on the acidophilic populations. + evidence: + - reference: doi:10.1128/aem.02458-10 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Analysis of spatial and temporal variations in the microbial community in the abandoned tailings + impoundment of a Pb-Zn mine revealed distinct microbial populations associated with the different + oxidation stages of the tailings + explanation: Anchors lead as a central contaminant of the Pb-Zn mine tailings the community inhabits. +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Ferrous iron is the central energy substrate and redox currency of the tailings, oxidized + by Acidithiobacillus and Leptospirillum to ferric iron that attacks sulfide minerals and regenerated + by Geobacter-mediated reduction in deep anoxic layers, driving the stratified iron cycle. + evidence: + - reference: PMID:22092956 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal + down a face of the tailings hill + explanation: Establishes the high iron (and sulfur) content that fuels the iron-oxidizing acidophile + community. metals_present: - COPPER - IRON diff --git a/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml b/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml index adc73801..cf4fb249 100644 --- a/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml +++ b/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml @@ -543,6 +543,36 @@ environmental_factors: snippet: Finally, an outline of the existing challenges and future prospects on this exciting field was narrated for plausible real-world use explanation: Describes REE mineralogy at Bayan Obo +related_ingredients: +- preferred_term: cerium(3+) + chebi_term: + id: CHEBI:48782 + label: cerium(3+) + relevance: Cerium is the dominant rare-earth element in the bastnaesite (REE(CO3)F) + that makes up the Bayan Obo tailings, and Ce3+ is one of the five light REE the + consortium mobilizes through acidolysis and organic-acid complexation, achieving + 82-83% recovery. + evidence: + - reference: doi:10.1016/j.cej.2024.153492 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: rare-earth metals acid bioleaching from the rare-earth-rich tailings + explanation: Anchors the rare-earth metals (dominated by Ce) as the central target + compounds recovered by acid bioleaching from the tailings. +- preferred_term: lanthanum(3+) + chebi_term: + id: CHEBI:49701 + label: lanthanum(3+) + relevance: Lanthanum co-dominates the bastnaesite ore alongside cerium and is one + of the five light REE (La, Ce, Pr, Nd, Sm) released as La3+ during consortium + bioleaching of the rare-earth-rich tailings. + evidence: + - reference: doi:10.1016/j.cej.2024.153492 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: rare-earth metals acid bioleaching from the rare-earth-rich tailings + explanation: Anchors the rare-earth metals (La among the light REE) as the central + target compounds recovered from the tailings. metals_present: - IRON rare_earth_elements_present: diff --git a/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml b/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml index 7aff5da7..01f68735 100644 --- a/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml +++ b/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml @@ -607,6 +607,53 @@ environmental_factors: supports: SUPPORT evidence_source: IN_VITRO snippet: actinobacterium isolated from manganese mining soil +related_ingredients: +- preferred_term: chromate(2-) + chebi_term: + id: CHEBI:35404 + label: chromate(2-) + relevance: Chromate is the toxic hexavalent chromium species [Cr(VI), CrO4(2-)] that this + enrichment was selected to detoxify, serving as the central electron acceptor reduced + to insoluble Cr(III) by Intrasporangiaceae sp. SOCrRB. + evidence: + - reference: doi:10.1021/acs.est.8b05053 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Chromate (Cr(VI)), as one of ubiquitous contaminants in groundwater, has posed + a major threat to public health and ecological environment. + explanation: Anchors chromate as the central toxic Cr(VI) contaminant targeted for microbial + reduction. +- preferred_term: elemental sulfur + chebi_term: + id: CHEBI:33403 + label: elemental sulfur + relevance: Reduced sulfur, including elemental sulfur, is the inorganic electron donor whose + oxidation is coupled to Cr(VI) reduction in this enrichment, enhancing chromate reduction + rates relative to organic-carbon-dependent reduction alone. + evidence: + - reference: doi:10.1021/acs.est.8b05053 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: little is known for microbial chromate reduction coupled to elemental sulfur (S(0)) + or zerovalent iron (Fe(0)) oxidation + explanation: Anchors elemental sulfur as the inorganic electron donor coupled to chromate + reduction. +- preferred_term: sulfate + chebi_term: + id: CHEBI:16189 + label: sulfate + relevance: Sulfate is the fully oxidized end product of the microbial sulfur cycle that + closes the coupled sulfur-oxidation/Cr(VI)-reduction metabolism, and is also abundant in + the chromite-processing tailings from which the community derives. + evidence: + - reference: doi:10.1016/j.cej.2020.124801 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Microbial sulphur cycle is of great importance to anaerobic degradation of organic + pollutants coupled with metal reduction, which however is usually limited by the poor + oxidation of the elemental sulphur to sulphate + explanation: Anchors sulfate as the oxidation product of the sulfur cycle coupled to metal + reduction. metals_present: - CHROMIUM - IRON diff --git a/kb/communities/Copper_Biomining_Heap_Leach.yaml b/kb/communities/Copper_Biomining_Heap_Leach.yaml index 860a3ded..ad8fddde 100644 --- a/kb/communities/Copper_Biomining_Heap_Leach.yaml +++ b/kb/communities/Copper_Biomining_Heap_Leach.yaml @@ -563,6 +563,64 @@ environmental_factors: snippet: Acidithiobacillus thiooxidans kept constant throughout the leaching cycle, and Firmicutes group showed a low and a patchy distribution in the heap explanation: Describes aerated heap leaching operation +related_ingredients: +- preferred_term: chalcopyrite + chebi_term: + id: CHEBI:86202 + label: chalcopyrite + relevance: Chalcopyrite (CuFeS2) is the primary copper sulfide mineral substrate of this heap-leach + consortium. The community generates ferric iron and acid that oxidatively dissolve chalcopyrite, + releasing copper for recovery, making it the central target ore for the entire bioleaching process. + evidence: + - reference: doi:10.3389/fmicb.2022.820052 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: were selected to perform bioleaching of chalcopyrite waste rock in the presence of the SX + reagent + explanation: Names chalcopyrite as the explicit mineral substrate being bioleached by the consortium + members. +- preferred_term: copper(2+) + chebi_term: + id: CHEBI:29036 + label: copper(2+) + relevance: Copper(2+) ions are the economically valuable product solubilized from chalcopyrite during + bioleaching. Recovery of dissolved Cu2+ from low-grade ores via heap bioleaching, solvent extraction, + and electrowinning is the defining objective of this engineered community. + evidence: + - reference: doi:10.3389/fmicb.2022.820052 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: is often combined with solvent extraction (SX) and electrowinning to recover, e.g., copper + from low-grade ores + explanation: Establishes solubilized copper as the recovered product of the heap bioleaching process. +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Ferrous iron is the key electron donor oxidized by the iron-oxidizing members (Acidithiobacillus + ferrooxidans, Leptospirillum, Ferroplasma) to regenerate the ferric iron oxidant that dissolves + copper sulfides, closing the iron redox cycle that drives leaching. + evidence: + - reference: doi:10.1038/s41598-021-95324-9 + supports: SUPPORT + evidence_source: REVIEW + snippet: oxidation of iron(II)-ions and inorganic sulfur compounds + explanation: Anchors iron(II) as the substrate oxidized by acidophiles to catalyze metal sulfide + dissolution. +- preferred_term: pyrite + chebi_term: + id: CHEBI:86471 + label: pyrite + relevance: Pyrite (FeS2) is a co-occurring iron sulfide mineral and energy source for the Leptospirillum + iron oxidizers central to aged heaps; growth on pyrite supports the iron oxidation that sustains + chalcopyrite leaching in this consortium. + evidence: + - reference: doi:10.1038/s41598-021-95324-9 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: that produces (Z)-11-methyl-2-dodecenoic acid when grown with pyrite as energy source + explanation: Documents pyrite as the energy substrate for Leptospirillum spp. growth in this bioleaching + community. metals_present: - COPPER - IRON diff --git a/kb/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml b/kb/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml index bbf3b230..6a8197dc 100644 --- a/kb/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml +++ b/kb/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml @@ -144,6 +144,54 @@ environmental_factors: enrichment of Actinobacteria explanation: Supports the iron-amendment perturbation design. growth_media: [] +related_ingredients: +- preferred_term: iron + chebi_term: + id: CHEBI:18248 + label: iron atom + relevance: Iron is the central metabolite of this community. Bacterial iron + transport and metabolism functionality is highly correlated with drought + enrichment, and exogenous iron application disrupts the drought-induced + enrichment of Actinobacteria, implicating iron as the microbiome-drought axis. + evidence: + - reference: PMID:34050180 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: bacterial iron transport and metabolism functionality is highly + correlated with drought enrichment + explanation: Anchors iron as the metabolite whose transport and metabolism + correlate with drought enrichment. +- preferred_term: phytosiderophore + chebi_term: + id: CHEBI:38155 + label: phytosiderophore + relevance: Phytosiderophore-mediated iron acquisition is the host control point + linking root iron homeostasis to community composition. Loss of a plant + phytosiderophore iron transporter increases abundance of the drought-enriched + Actinobacteria lineage. + evidence: + - reference: PMID:34050180 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: loss of a plant phytosiderophore iron transporter impacts microbial + community composition + explanation: Anchors the phytosiderophore as the iron-chelating compound whose + transporter loss reshapes the microbiome. +- preferred_term: carbohydrate + chebi_term: + id: CHEBI:16646 + label: carbohydrate + relevance: Carbohydrate transport functions are overrepresented in drought- + enriched taxa, reflecting the root-exudate carbon resources that, alongside + iron, structure the drought-enriched rhizosphere community. + evidence: + - reference: PMID:34050180 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: carbohydrate and secondary metabolite transport functionalities are + overrepresented within drought-enriched taxa + explanation: Anchors carbohydrate transport as an overrepresented function in + drought-enriched taxa. external_resources: - name: Primary publication for the drought rhizosphere iron community repository: OTHER diff --git a/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml b/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml index 7983384e..48db3fbd 100644 --- a/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml +++ b/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml @@ -669,6 +669,37 @@ environmental_factors: recovery relevant to circular economy and green technology applications. ' +related_ingredients: +- preferred_term: teichoic acid + chebi_term: + id: CHEBI:30049 + label: teichoic acid + relevance: Teichoic acids in the cell walls of Gram-positive Bacillus and Micrococcus + are the primary binding sites driving the community's selective adsorption and + fractionation of heavy rare earth elements, the defining function of this ion-adsorption + REE deposit community. + evidence: + - reference: PMID:35708325 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: teichoic acids in the cell wall served as the main sites for HREE adsorption, + leading to an enrichment of HREEs in the deposit + explanation: Names teichoic acids verbatim as the main HREE-adsorption sites responsible + for deposit-scale HREE enrichment, anchoring this compound to the community. +- preferred_term: phosphate + chebi_term: + id: CHEBI:26020 + label: phosphate + relevance: Surface phosphate groups (and carboxyl groups) on bacterial cell walls + act as active sites for REE adsorption, providing the coordination chemistry that + underlies selective heavy-REE binding and fractionation in this community. + evidence: + - reference: PMID:35708325 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: the surface carboxyl and phosphate groups are active sites for REE adsorption + explanation: Names phosphate groups verbatim as active sites for REE adsorption, + anchoring this compound to the community's biosorption mechanism. metals_present: - IRON rare_earth_elements_present: diff --git a/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml b/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml index 350c0ed3..4fc9ac07 100644 --- a/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml +++ b/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml @@ -92,3 +92,47 @@ environmental_factors: description: Live versus dead SynCom inoculation, with and without Miscanthus plants in tailing soil. evidence: - *id001 +related_ingredients: +- preferred_term: ammonium sulfate + chebi_term: + id: CHEBI:62946 + label: ammonium sulfate + relevance: Ammonium sulfate is the primary leaching agent used in ionic rare earth mining and is the + root cause of the nitrogen pollution this SynCom is engineered to remediate. It is the upstream + source of the high ammonia nitrogen burden in the tailing soil. + evidence: + - reference: PMID:39481489 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Ammonium sulfate, as the primary leaching agent, has caused significant nitrogen pollution + in rare earth elements (REEs) mining areas. + explanation: The snippet names ammonium sulfate explicitly as the leaching agent driving nitrogen + pollution in the REE mining context of this community. +- preferred_term: ammonia + chebi_term: + id: CHEBI:16134 + label: ammonia + relevance: Ammonia nitrogen is the target pollutant the SynCom removes via its nitrification and + denitrification capabilities, converting it into plant nutrients. Its reduction is the primary + measured endpoint of the community's bioremediation function. + evidence: + - reference: PMID:39481489 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: in a REEs tailing soil containing a high ammonia nitrogen (AN) concentration + explanation: The snippet anchors ammonia (ammonia nitrogen) as the high-concentration pollutant in + the tailing soil that the community acts upon. +- preferred_term: ammonium + chebi_term: + id: CHEBI:28938 + label: ammonium + relevance: Ammonium is the cationic nitrogen species released from the ammonium sulfate leaching agent + and serves as the nitrification substrate that the root-derived strains transform during nitrogen + cycling in the tailings. + evidence: + - reference: PMID:39481489 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Ammonium sulfate, as the primary leaching agent, has caused significant nitrogen pollution + explanation: The snippet anchors the ammonium ion via the ammonium sulfate source compound that + supplies the ammonium driving the community's nitrogen transformation. diff --git a/kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml b/kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml index c577d197..175253ca 100644 --- a/kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml +++ b/kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml @@ -810,6 +810,73 @@ environmental_factors: biogenic thiosulfate sourced from a bioreactor used for biogas biodesulfurization, is proposed as a sustainable alternative to conventional methods explanation: Establishes application to multiple catalyst waste streams +related_ingredients: +- preferred_term: thiosulfate + chebi_term: + id: CHEBI:16094 + label: thiosulfate(2-) + relevance: Biogenic thiosulfate is the central lixiviant of this community, produced as an + intermediate of bacterial sulfur oxidation and forming stable Pd(S2O3)2(2-) complexes that + mobilize platinum-group metals from spent catalysts. Its biological generation replaces toxic + cyanide leaching, integrating lixiviant production with the bioleaching process itself. + evidence: + - reference: PMID:38138568 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Bioleaching of palladium (Pd) using the thiosulfate-copper-ammonia leaching processes, + with biogenic thiosulfate sourced from a bioreactor used for biogas biodesulfurization, is + proposed as a sustainable alternative to conventional methods + explanation: Abstract names thiosulfate as the biogenic leaching agent for Pd, anchoring it as + the central lixiviant of this community. +- preferred_term: palladium + chebi_term: + id: CHEBI:33363 + label: palladium + relevance: Palladium is the primary platinum-group metal target recovered by this consortium from + spent automotive three-way catalysts and petroleum hydroprocessing catalysts. It is mobilized as + a Pd-thiosulfate complex after alumina-support dissolution, with reported extraction reaching + 93.2%. + evidence: + - reference: PMID:38138568 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: A remarkable 96.2 and 93.2% of the total Pd was successfully extracted from the solid at + 5% pulp density using both commercially available and biogenic thiosulfate, highlighting the + method's versatility for Pd bioleaching from both thiosulfate sources. + explanation: Abstract quantifies Pd extraction, anchoring palladium as the principal recovered + PGM of this community. +- preferred_term: copper(2+) + chebi_term: + id: CHEBI:29036 + label: copper(2+) + relevance: Copper ions act as the redox co-catalyst in the thiosulfate-copper-ammonia leaching + system, accelerating oxidative dissolution of palladium and stabilizing the PGM-thiosulfate + complexes. Optimal recovery in this community used a defined CuSO4 concentration alongside + thiosulfate and ammonium sulfate. + evidence: + - reference: PMID:38138568 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'indicating the optimal conditions to be Na2S2O3 1.2 M, CuSO4 0.03 M, (NH4)2SO4 1.5 M, + Na2SO3 0.2 M, pH 8, and 60 °C' + explanation: Abstract specifies the CuSO4 concentration in the optimized leaching system, + anchoring copper(2+) as the co-catalyst of this community. +- preferred_term: ammonia + chebi_term: + id: CHEBI:16134 + label: ammonia + relevance: Ammonia (supplied as ammonium sulfate) is the third component of the + thiosulfate-copper-ammonia leaching system, buffering pH and providing secondary ligand effects + that enhance the stability and selectivity of PGM-thiosulfate complexation in this community. + evidence: + - reference: PMID:38138568 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Bioleaching of palladium (Pd) using the thiosulfate-copper-ammonia leaching processes, + with biogenic thiosulfate sourced from a bioreactor used for biogas biodesulfurization, is + proposed as a sustainable alternative to conventional methods + explanation: Abstract names ammonia as part of the leaching system, anchoring it as a co-reagent + central to PGM mobilization in this community. metals_present: - COPPER - IRON diff --git a/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml b/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml index 9f64f111..57b5b04d 100644 --- a/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml +++ b/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml @@ -846,6 +846,71 @@ environmental_factors: evidence_source: IN_VIVO snippet: Altogether 67% of the bacteria produced indoleacetic acid (IAA) explanation: Documents plant growth promotion prevalence +related_ingredients: +- preferred_term: vanadate(3-) + chebi_term: + id: CHEBI:46442 + label: vanadate(3-) + relevance: Soluble pentavalent vanadium (V(V), as vanadate) is the defining contaminant of the + Panzhihua V-Ti magnetite tailings (340 mg/kg total V). Its high mobility and toxicity drive both + the ecological risk and the central microbial detoxification process, in which V-reducing bacteria + reduce mobile V(V) to less soluble V(IV), immobilizing vanadium in the tailings. + evidence: + - reference: doi:10.1021/acs.est.3c04508 + supports: SUPPORT + evidence_source: REVIEW + snippet: Vanadium(V) is a highly toxic multivalent, redox-sensitive element. + explanation: Anchors vanadate (V(V)) as the redox-sensitive, toxic vanadium species central to this + community. + - reference: PMID:33125214 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: environment and human health. Microorganisms can reduce the more toxic and + explanation: Confirms microbial reduction of mobile, toxic V(V) (vanadate) as the key detoxification + pathway in vanadium tailings. +- preferred_term: iron(3+) + chebi_term: + id: CHEBI:29034 + label: iron(3+) + relevance: Iron is the dominant ore-forming element of the V-Ti magnetite tailings, hosting vanadium + within iron oxide minerals. Ferric iron supports siderophore-mediated iron acquisition and Fe(III) + redox cycling by indigenous bacteria, which couples to vanadium mobility and detoxification in the + tailings. + evidence: + - reference: doi:10.3389/fmicb.2018.01853 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: build symbiotic relationships with native rhizobia in the iron-vanadium-titanium + explanation: Names iron as a primary constituent of the iron-vanadium-titanium (V-Ti magnetite) mine + tailing matrix. +- preferred_term: copper(2+) + chebi_term: + id: CHEBI:29036 + label: copper(2+) + relevance: Copper (127 mg/kg) is one of the key polymetallic contaminants selecting for metal-tolerant + rhizobia in the tailings, and is a primary target of rhizobia-enhanced phytoextraction (Cu uptake + increased ~600% with inoculation). + evidence: + - reference: doi:10.3389/fmicb.2023.1078333 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: different levels of tolerance to copper (Cu), nickel (Ni), manganese (Mn) and zinc (Zn) + explanation: Anchors copper as a heavy metal that tailings rhizobia tolerate, central to metal-tolerance + selection in this community. +- preferred_term: nickel(2+) + chebi_term: + id: CHEBI:49786 + label: nickel(2+) + relevance: Nickel (60 mg/kg) is a polymetallic contaminant of the tailings and a co-target of rhizobia-mediated + phytoextraction (Ni uptake increased ~576% with inoculation), shaping the multi-metal tolerance + phenotype of the indigenous community. + evidence: + - reference: doi:10.3389/fmicb.2023.1078333 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: different levels of tolerance to copper (Cu), nickel (Ni), manganese (Mn) and zinc (Zn) + explanation: Anchors nickel as a heavy metal tolerated by tailings rhizobia, central to multi-metal + tolerance in this community. metals_present: - COPPER - IRON diff --git a/kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml b/kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml index df9ad4e2..8729c5d3 100644 --- a/kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml +++ b/kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml @@ -489,6 +489,74 @@ environmental_factors: metals and critical raw materials and the transformation of the residual in clean mineral fraction to be used for the mass production of cement, concrete and construction products explanation: Documents cobalt mineralogy and accessibility to bioleaching +related_ingredients: +- preferred_term: cobalt(2+) + chebi_term: + id: CHEBI:48828 + label: cobalt(2+) + relevance: Cobalt is the primary target metal of this bioleaching community, occurring + on the surface of framboidal pyrite in the Rammelsberg tailings. Microbial activity + by the Acidithiobacillus consortium mobilizes Co into solution, achieving high + cobalt recovery and supporting critical battery-material supply chains. + evidence: + - reference: doi:10.1016/j.hydromet.2020.105484 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Cobalt dissolution kinetics were highly improved by the bacterial activity, + whatever the consortium. This is consistent with the presence of Co in the pyrite + in the secondary ore. + explanation: Anchors cobalt as the central leached metal whose dissolution depends + on the bacterial consortium and is tied to Co-bearing pyrite. +- preferred_term: nickel(2+) + chebi_term: + id: CHEBI:49786 + label: nickel(2+) + relevance: Nickel is a co-recovered critical metal in the sulfidic polymetallic + tailings processed by this consortium, released rapidly during bioleaching from + Ni-bearing sulfide minerals such as pentlandite and violarite. + evidence: + - reference: doi:10.1016/j.hydromet.2020.105484 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Nickel was released very quickly, suggesting that part of Ni dissolved + in the primary heap was re-precipitated and remained in the secondary ore. + explanation: Anchors nickel as a key mobilized metal with rapid release kinetics + during bioleaching of the secondary ore. +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Ferrous iron is the energy substrate for Acidithiobacillus ferrooxidans, + whose oxidation of Fe(II) to Fe(III) generates the ferric oxidant that chemically + attacks the cobalt-bearing sulfide minerals, making iron cycling the engine of + this bioleaching community. + evidence: + - reference: PMID:39770610 + supports: SUPPORT + evidence_source: REVIEW + snippet: It has emerged as a key player in biomining and bioleaching technologies + thanks to its unique ability to mobilize a wide spectrum of elements, such as + Li, P, V, Cr, Fe, Ni, Cu, Zn, Ga, As, Mo, W, Pb, U, and its role in ferrous + iron oxidation and reduction + explanation: Anchors ferrous iron oxidation as the central metabolic role driving + element mobilization in this consortium. +- preferred_term: sulfate + chebi_term: + id: CHEBI:16189 + label: sulfate + relevance: Sulfate is the terminal oxidation product of reduced sulfur compounds + released when ferric iron attacks the tailings' sulfide minerals; sulfur oxidation + to sulfate by Acidithiobacillus thiooxidans produces the sulfuric acid that maintains + the low pH required for ferric iron stability and continued metal leaching. + evidence: + - reference: doi:10.1016/j.hydromet.2020.105484 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This material still contains several sulfide minerals (pyrrhotite, pyrite, + sphalerite, pentlandite, violarite, chalcopyrite) and significant amounts of + metals (Zn, Ni, Cu, Co, rare earth elements) + explanation: Anchors the sulfide-mineral matrix whose oxidation yields sulfate + and the metals targeted by the consortium. metals_present: - COBALT - COPPER diff --git a/kb/communities/Richmond_Mine_AMD_Biofilm.yaml b/kb/communities/Richmond_Mine_AMD_Biofilm.yaml index 65068145..7af584e9 100644 --- a/kb/communities/Richmond_Mine_AMD_Biofilm.yaml +++ b/kb/communities/Richmond_Mine_AMD_Biofilm.yaml @@ -368,7 +368,7 @@ ecological_interactions: metabolites: - preferred_term: pyrite term: - id: CHEBI:51905 + id: CHEBI:86471 label: pyrite notes: FeS₂ mineral substrate - preferred_term: sulfate @@ -680,6 +680,69 @@ environmental_factors: snippet: Unexpectedly, sequences that affiliated within the delta subdivision of the Proteobacteria were detected explanation: Suggests anaerobic microniches despite subaerial location +related_ingredients: +- preferred_term: pyrite + chebi_term: + id: CHEBI:86471 + label: pyrite + relevance: Pyrite (FeS2) is the massive sulfide ore the biofilm develops on and the + primary substrate of the entire ecosystem. Microbially-mediated oxidation of roughly + 1-2 x 10^5 moles of pyrite per day generates the sulfuric acid and dissolved metals + that define this extreme habitat. + evidence: + - reference: PMID:10966399 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: An unusually thick ( approximately 1 cm) slime developed on a slump of + finely disseminated pyrite ore within an extreme acid mine drainage site at Iron + Mountain, near Redding, Calif + explanation: Anchors pyrite ore as the mineral substrate the biofilm colonizes. +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Ferrous iron [Fe(II)], reaching up to 24 g/L in the drainage, is the sole + energy source oxidized by the dominant chemolithoautotrophs (Leptospirillum, Ferroplasma) + that drive this community. + evidence: + - reference: doi:10.1186/1467-4866-5-13 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Extremely acidic effluent (pH between 0.5 and 0.9) resulting from oxidation + of approximately 1 × 105 to 2 × 105 moles pyrite/day contains up to 24 g/1 Fe, + several g/1 Zn and hundreds of mg/l Cu + explanation: Documents the very high dissolved iron concentration available as the + central substrate for iron-oxidizing metabolism. +- preferred_term: iron(3+) + chebi_term: + id: CHEBI:29034 + label: iron(3+) + relevance: Ferric iron [Fe(III)] generated by microbial iron oxidation is the chemical + oxidant that attacks pyrite, sustaining the closed iron redox cycle that perpetuates + extreme acidity and mineral dissolution. + evidence: + - reference: doi:10.1186/1467-4866-5-13 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: data suggest that Fe3+ oxidizes the majority of sulfur to sulfate on the + surface of pyrite + explanation: Anchors ferric iron as the oxidant driving pyrite sulfur oxidation + in this AMD system. +- preferred_term: sulfate + chebi_term: + id: CHEBI:16189 + label: sulfate + relevance: Sulfate is the major product of pyrite oxidation, accumulating as Fe(III) + converts pyritic sulfide to sulfate and contributing to the extreme acidity and + high ionic load of the drainage. + evidence: + - reference: doi:10.1186/1467-4866-5-13 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Sulfobacillus spp. and Acidithiobacillus caldus may metabolize elemental + sulfur as an intermediate species in the oxidation of pyritic sulfide to sulfate + explanation: Anchors sulfate as the terminal oxidation product of pyritic sulfur + in this community. metals_present: - COPPER - IRON diff --git a/kb/communities/Rifle_Uranium_Reducing_Community.yaml b/kb/communities/Rifle_Uranium_Reducing_Community.yaml index ac809398..6999e0f5 100644 --- a/kb/communities/Rifle_Uranium_Reducing_Community.yaml +++ b/kb/communities/Rifle_Uranium_Reducing_Community.yaml @@ -615,6 +615,60 @@ environmental_factors: evidence_source: IN_VIVO snippet: Within 50 days uranium had declined below the prescribed treatment level explanation: Quantifies time to achieve treatment goals +related_ingredients: +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Acetate is the injected electron donor and carbon source that drives the entire + bioremediation strategy at the Rifle site. Amendment at 1-3 mM stimulates Geobacter proliferation + and the coupled Fe(III)/U(VI) reduction that immobilizes uranium, then sustains the later + sulfate-reducing phase. + evidence: + - reference: PMID:14532040 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period + explanation: Anchors acetate as the amendment injected to stimulate in situ uranium reduction +- preferred_term: iron(3+) + chebi_term: + id: CHEBI:29034 + label: iron(3+) + relevance: Fe(III) in the aquifer sediments is the dominant terminal electron acceptor during + Phase I, supporting Geobacter respiration that is coincident with and drives U(VI) reduction. + Its depletion triggers the succession to sulfate reduction. + evidence: + - reference: PMID:14532040 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: suggesting that U(VI) reduction was coincident with Fe(III) reduction + explanation: Links Fe(III) reduction to the coincident uranium reduction central to this community +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Fe(II) accumulation in the groundwater is the geochemical signature of active dissimilatory + Fe(III) reduction by Geobacter during Phase I, marking the reducing conditions under which U(VI) + is reduced and immobilized. + evidence: + - reference: PMID:14532040 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Fe(II) in the groundwater also increased during this period + explanation: Documents Fe(II) accumulation as the marker of the Fe(III)-reducing activity tied to U removal +- preferred_term: sulfate + chebi_term: + id: CHEBI:16189 + label: sulfate + relevance: Sulfate becomes the dominant terminal electron acceptor in Phase II after Fe(III) depletion, + when sulfate-reducing bacteria become predominant and contribute to uranium removal via enzymatic + and sulfide-mediated reduction. + evidence: + - reference: PMID:14532040 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: there was a loss of sulfate from the groundwater and an accumulation of sulfide + explanation: Anchors sulfate as the electron acceptor consumed during the Phase II succession metals_present: - IRON - URANIUM