#30 backfill batch 3: finish AMD/biomining/REE cohort (14 communities)

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

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: []

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

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:

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

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

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