Intercropping-derived SynCom members directly activate the plant-accessible soil phosphorus pool, increasing the phosphate available for rice roots in pot experiments.
+SynCom inoculation increased available soil phosphorus in the rice pot experiment, alongside lower rhizosphere pH and changes in phosphorus fractions. This is a measured inoculation response; contributions of particular strains or acids are not separately resolved.
@@ -686,7 +685,7 @@SynCom-driven phosphate activation contributes to the belowground phosphorus-acquisition program that also changes root morphology and up-regulates rice Pi transporter genes.
+PARTIAL: greater soil phosphorus availability is a proposed contributor to improved rice phosphorus acquisition. The comparisons do not isolate this contribution from root architectural and transport-associated responses.
SynCom members increase soil available phosphorus and support root-to-shoot phosphorus transport.
+SynCom-treated rice showed altered root architecture, phosphorus allocation and expression of phosphate-transporter genes. PARTIAL: these observations support the proposed acquisition/translocation pathway, but expression and endpoint concentrations do not independently establish transporter-mediated flux or necessity.
@@ -753,7 +751,7 @@Better available-phosphorus access, larger root absorptive surface, and higher root-to-shoot Pi transporter expression drive the measured increases in potted rice biomass and phosphorus uptake.
+PARTIAL: improved phosphorus access, root architecture and transport-associated responses are proposed contributors to the positive pot biomass/phosphorus outcome. Their separate contributions and necessity for that outcome remain unresolved.
The synthetic community significantly enhances rice biomass and phosphorus uptake in the pot assays, tying the soil-phosphorus and root-translocation effects to the plant-growth endpoint.
+The four-strain SynCom significantly increased rice dry biomass and phosphorus uptake in the pot comparison. This positive inoculation outcome is distinct from the field rice/soybean intercropping comparison, where rice yield and phosphorus uptake decreased. Benefit to rice is not evidence of reciprocal bacterial fitness.
@@ -807,10 +791,6 @@Metabolites: - phosphorus - (CHEBI:28659), - phosphate ion (CHEBI:35780) @@ -832,7 +812,7 @@
The complete primary main text distinguishes negative field intercropping effects on rice from positive SynCom pot effects. Soil-P fractions, root traits, root IAA and transporter expression support proposed pathways but do not establish each mediator as necessary. Preserve both existing directions as PARTIAL. MUTUALISM requires reciprocal benefit, not a plant response alone. Non-graph CROSS_FEEDER labels and aliased evidence are unchanged pending issue1764.
+ +Attaches to: ecological_interactions#Soil Available Phosphorus Activation, ecological_interactions#Phosphorus Acquisition Promotion, ecological_interactions#Rice Biomass and Phosphorus Uptake Increase
the yield and P uptake of intercropped rice were lower than those of rice grown in monoculture
+The field comparison must not be conflated with SynCom inoculation of potted rice.
+Leptospirillum group II oxidizes ferrous iron [Fe(II)] to ferric iron [Fe(III)] as the primary energy source for chemolithoautotrophic growth. This process generates reducing equivalents used for CO₂ fixation through the Calvin-Benson-Bassham cycle. The ferric iron produced serves as the oxidant for pyrite dissolution, creating a positive feedback loop that perpetuates extreme acidity. Iron oxidation is the predominant metabolism in the biofilm, reflected in Leptospirillum comprising 78% of detected clones. -
+Iron-oxidizing Leptospirillum populations contribute ferric iron to Richmond Mine mineral oxidation. Group II and III occurrence and dominance vary among samples and times; canonical member identifiers are retained without identifying every clone as the 5-way CG population. Clone fractions are not iron-oxidation rates. No Calvin-cycle pathway or direct nutrient cross-feeding is asserted.
+ + -Source Taxon: Leptospirillum group II
+Participating Taxa: + Leptospirillum group II, + Leptospirillum ferrodiazotrophum + +
@@ -854,23 +843,6 @@Biological Processes:
-Fe(III) oxidizes pyrite to generate more Fe(II) and sulfuric acid
+Leptospirillum iron oxidation contributes regenerated ferric oxidant to pyrite dissolution in the oxygen-supplied mine system. The source supports this community redox coupling, not a species-resolved dissolution rate or direct pairwise nutrient exchange.
Ferroplasma acidarmanus oxidizes ferrous iron microaerophilically in extremely acidic microniches (pH approaching 0.5). This archaeon thrives where pH is too low for bacterial competitors, filling an ecological niche unavailable to Leptospirillum and Acidithiobacillus. Ferroplasma maintains cytoplasmic pH ~5.6 through specialized proton-pumping mechanisms while oxidizing Fe(II) in near-zero pH environments. The organism exhibits extreme metal resistance, tolerating high concentrations of arsenic and copper that would inhibit bacterial iron oxidizers. -
+Ferroplasma is an iron-oxidizing contributor to the Richmond Mine ferric-iron pool. Comparative culture evidence supports iron-oxidizing mixotrophy and an organic-carbon requirement for F. acidarmanus Fer1. Field geochemistry supports its community role, not autotrophic carbon fixation, a measured species-specific flux or competitive exclusion of bacterial iron oxidizers.
+ -Source Taxon: Ferroplasma acidarmanus
+Participating Taxa: + Ferroplasma acidarmanus + +
@@ -947,17 +921,6 @@Biological Processes:
-Fe(III) from Ferroplasma contributes to pyrite oxidation
+Ferroplasma iron oxidation contributes ferric oxidant to pyrite dissolution in the site-level redox model. Isolate physiology does not apportion that field flux or establish reciprocal fitness with Leptospirillum.
Ferric iron generated by Leptospirillum and Ferroplasma oxidizes pyrite (FeS₂) minerals according to: FeS₂ + 14Fe³⁺ + 8H₂O → 15Fe²⁺ + 2SO₄²⁻ + 16H⁺. This process releases ferrous iron, sulfate, and protons, generating extreme acidity (pH 0.5-1.0) and solubilizing metals. The Richmond Mine community oxidizes approximately 1-2 × 10⁵ moles of pyrite per day, demonstrating the massive scale of microbially-mediated mineral dissolution. Sulfate concentrations increase dramatically, and the released Fe(II) is re-oxidized by the microbial community, creating a closed iron redox cycle. -
+Microbially regenerated ferric iron oxidizes pyrite, releasing ferrous iron for subsequent microbial oxidation and contributing sulfate and acidity. The reported approximately 1-2 x 10^5 moles pyrite/day is a mine-outflow-derived estimate at the sampled times, not the rate of this particular biofilm or any pair of species. The coupled cycle depends on external oxygen and mineral supply; it is not closed or self-sustaining.
-Source Taxon: Leptospirillum group II
+Participating Taxa: -
Target Taxon: Ferroplasma acidarmanus
+ Leptospirillum group II, + + Leptospirillum ferrodiazotrophum, + + Ferroplasma acidarmanus + + @@ -1047,7 +1014,7 @@Released Fe(II) is re-oxidized by iron-oxidizing community
+Pyrite oxidation reduces ferric iron and releases ferrous iron that supports subsequent Leptospirillum iron oxidation. This existing feedback is chemically grounded and depends on external oxygen/mineral supply; it is not proof of ecological mutualism.
Leptospirillum ferrodiazotrophum (group III) fixes atmospheric nitrogen through nitrogenase activity, providing fixed nitrogen to the nitrogen-limited biofilm community. This organism is the only Leptospirillum capable of nitrogen fixation, making it a keystone species despite not being numerically dominant. Fixed nitrogen is released through cell lysis, excretion, or after predation, becoming available to other community members including groups II Leptospirillum and Ferroplasma that lack nitrogen fixation genes. Group III typically appears in later stages of biofilm development, suggesting nitrogen limitation shapes community succession. -
- - -Source Taxon: Leptospirillum ferrodiazotrophum
- - - - - -Metabolites: - - dinitrogen - (CHEBI:17997), - - ammonia - (CHEBI:16134) - -
- - - -Biological Processes:
-Ultrasmall ARMAN archaea occur with Thermoplasmatales in Richmond Mine acid biofilms; 3D cryo-electron tomography showed Thermoplasmatales protuberances penetrating ARMAN cell walls and cytoplasmic membranes, indicating direct interspecies contact that could support parasitic or syntrophic exchange. -
+The primary abstract reports direct contact in a small subset of cryo-electron tomographic reconstructions: Thermoplasmatales protuberances penetrate ARMAN cell envelopes. It does not identify those imaged pairs as F. acidarmanus with a particular Micrarchaeota or Parvarchaeota subgroup. Observed contact is retained, without a demonstrated nutrient exchange, fitness effect or syntrophic metabolic feedback.
-Source Taxon: Ferroplasma acidarmanus
-Target Taxon: Micrarchaeota (ARMAN-1/2)
- - @@ -1220,33 +1104,22 @@Ultrasmall ARMAN-4 and ARMAN-5 Parvarchaeota co-occur with Thermoplasmatales in Richmond Mine acid biofilms; 3D cryo-electron tomography showed Thermoplasmatales projections penetrating ARMAN cell envelopes, consistent with direct interspecies contact. -
- +A. ferrooxidans was detected and predominated in the higher-pH Red Pool during the reported Richmond Mine survey. Community composition covaried with pH, temperature and solution chemistry. This supports a spatial distribution observation, not competitive exclusion, a pH optimum at 1.4 or measured iron/sulfur flux by the same population.
-Source Taxon: Ferroplasma acidarmanus
-Target Taxon: Parvarchaeota (ARMAN-4/5)
- +Participating Taxa: + Acidithiobacillus ferrooxidans +
-Biological Processes:
-Acidithiobacillus ferrooxidans occupies higher pH niches (pH >1.0) such as the Red Pool (pH 1.4) where it can outcompete Leptospirillum and Ferroplasma. This versatile chemolithoautotroph oxidizes both ferrous iron and reduced sulfur compounds, fixing carbon and nitrogen from the atmosphere. At pH 1.4, A. ferrooxidans grows optimally while Ferroplasma activity declines. This spatial partitioning by pH creates distinct microenvironments within the mine where different iron oxidizers dominate, expanding the overall metabolic capacity and pH range of the biofilm ecosystem. A. ferrooxidans contributes to pyrite dissolution in moderate pH zones while Leptospirillum and Ferroplasma dominate at extreme acidity (pH <1.0). -
+ -Source Taxon: Acidithiobacillus ferrooxidans
+ +The primary isolation abstract supports a free-living nitrogen-fixing organism. The biofilm proteomic abstract reports nitrogen-fixation proteins were not identified. Neither accessible primary abstract resolves nitrogen release, uptake by another member or the asserted succession/keystone mechanism. Remove the transfer node without treating nondetection as proof of no capacity. Complete main texts for these sources were not accessible in this pass; non-graph roles remain issue1764.
-Target Taxon: Leptospirillum group II
+Attaches to: ecological_interactions#Ferrous Iron Oxidation by Leptospirillum, ecological_interactions#Ferrous Iron Oxidation by Ferroplasma, ecological_interactions#Pyrite Dissolution, ecological_interactions#Thermoplasmatales-ARMAN Cell Contact, ecological_interactions#Higher-pH Acidithiobacillus Distribution
Metabolites:
+ iron-oxidizing, free-living diazotroph The isolated organism has positive diazotrophic capacity, not demonstrated nitrogen delivery to other members. Biological Processes: Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics Protein nondetection constrains claims about demonstrated nitrogen fixation in the sampled biofilms.2 evidence item(s)
- Fe(II)
- (CHEBI:29033),
+
+
Retain direct generic ARMAN contact, but leave exact imaged partners and metabolic/fitness consequences unresolved. Current SYNTROPHY does not require obligacy; contact alone does not demonstrate the required metabolic feedback. The coarse COMMUNITY_LEVEL contact has unspecified participants and must not be read as an observation for every canonical member. The geochemical primary sections support a real iron/mineral feedback, variable field populations and higher-pH A. ferrooxidans distribution, not a closed loop, competition or species-resolved flux. The Ferroplasma review and reference Acidithiobacillus genome are not exact-system functional tests. Taxonomy and non-graph claims remain unchanged pending issue1764.
- doi:10.1186/1467-4866-5-13 +Attaches to: ecological_interactions#Ferrous Iron Oxidation by Leptospirillum, ecological_interactions#Ferrous Iron Oxidation by Ferroplasma, ecological_interactions#Pyrite Dissolution, ecological_interactions#Thermoplasmatales-ARMAN Cell Contact, ecological_interactions#Higher-pH Acidithiobacillus Distribution
A small subset of 3D cryo-electron tomographic reconstructions
+The primary abstract limits the observed contacts to a subset of reconstructions.
+Microbial electrochemical cells inoculated with Rifle aquifer material were fed acetate as the sole carbon source and poised at iron-oxide-like anode potentials for years, enriching electrode-attached biofilms whose growth depended on extracellular electron transfer to the anode. -
+Acetate-fed microbial electrochemical cells enriched electroactive consortia from Rifle aquifer material. Electrode-attached biofilm and planktonic communities differed, and the systems produced current. This is an observed community response to the enrichment environment, not proof that every member directly respires the anode or occupies a demonstrated partitioned niche.
@@ -853,14 +846,7 @@The acetate bioanodes selected a novel MHC-rich Geobacter as the dominant electrode-attached organism. -
-The same enrichments also recovered diverse non-Geobacter organisms with MHCs, candidate porin-cytochrome complexes, and e-pili. -
+PARTIAL: the acetate-fed electrode environment enriched a biofilm dominated by the novel Geobacter population. The observed enrichment supports selection in this system, but does not establish competitive exclusion, a single causal contribution of its MHC inventory or dominance throughout the natural aquifer.
Six near-complete and one partial Geobacter genomes dominated the electrode-attached biofilm DNA, with the leading S0_RifleGW_Geobacter_53_40 genome encoding 72 candidate multiheme c-type cytochromes. -
+A novel Geobacter population dominated the sampled electrode-attached community, and its recovered genome encoded at least 72 putative multiheme c-type cytochromes. This combines observed biofilm composition with predicted genomic capacity; it does not establish competition, conductivity of each candidate protein or the organism's natural aquifer niche.
@@ -908,29 +892,7 @@Biological Processes:
-Geobacter genomes had the greatest number and diversity of candidate porin-cytochrome complex porin types. -
-Beyond the dominant Geobacter, Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, and Beta- and Gammaproteobacteria genomes also encoded large multiheme c-type cytochromes, candidate porin-cytochrome complexes, and/or putative conductive e-pili. -
- - - - -Participating Taxa: - - EET-capable Rifle aquifer Actinobacteria, - - EET-capable Rifle aquifer Ignavibacteria, - - EET-capable Rifle aquifer Chloroflexi, - - EET-capable Rifle aquifer Acidobacteria, - - EET-capable Rifle aquifer Firmicutes, - - EET-capable Rifle aquifer Beta- and Gammaproteobacteria - -
- - - - - -Biological Processes:
-Acidobacteria, Betaproteobacteria, and Ignavibacteria were among the high-MHC genomes encoding candidate porin-cytochrome complexes. -
-Twelve high-MHC near-complete genomes encoded at least one candidate outer-membrane porin-cytochrome complex, extending potential trans-outer membrane electron conduits from Geobacter into Acidobacteria, Betaproteobacteria, and Ignavibacteria. -
- - - - - - - - -Biological Processes:
-Putative conductive type-IV pilins were detected in 16 of the 31 EET-related genomes under strict aromatic-residue criteria, and cytochrome OmcS homolog searches recovered 22 sequences, nearly all from Geobacter, that could support conductive extracellular filaments. -
- - - - - - - - -Biological Processes:
-Only a small subset of the thousands of organisms previously detected in the Rifle aquifer have the genetic potential to mediate mineral redox transformations.
+ + +The complete primary main text supports community current, enrichment and biofilm dominance. Non-Geobacter MHCs, candidate PCCs, e-pili and OmcS homologs are valuable genomic predictions, not demonstrated niche partitioning, conductivity, mineral flux or syntrophic partnerships. The candidate-set conclusion does not exclude EET potential in all other aquifer organisms. Remove four inventory/conclusion nodes and three analysis-order arrows while preserving the environmental-selection observation and one PARTIAL dominance direction. The source leaves the dominant organism's environmental niche unresolved and gives inconsistent near-complete-genome denominators in the PCC caption versus main text; no denominator is silently adjudicated. Non-graph functional-role labels and canonical taxonomy remain issue1764; cultivation setup is unchanged.
+Attaches to: ecological_interactions#Acetate-Fed Iron-Oxide-Like Bioanode Selection, ecological_interactions#Multiheme Geobacter Electrode Dominance
Biological Processes:
-may have the potential to mediate mineral redox transformations
+The primary abstract explicitly describes potential, not experimentally measured natural-community flux.
+