{
  "id": "AssayMech:ax17-extracted-feii-ferrozine",
  "name": "Oxalate-extracted Fe(II) ferrozine assay in Ax17 ferrihydrite cultures",
  "record_kind": "OPERATIONAL_ASSAY",
  "categories": [
    "BIOTRANSFORMATION"
  ],
  "description": "Measure extraction-defined Fe(II) during laboratory growth of D. ferrireducens Ax17 with synthetic two-line ferrihydrite, using ferrozine spectrophotometry after oxalate dissolution.",
  "limitations": [
    "Oxalate extraction measures an operational Fe(II) pool; the unfiltered preparation is not a dissolved-iron measurement.",
    "Ferrozine Fe(II) alone cannot identify magnetite or another mineral phase; the paper uses separate complementary mineral analyses.",
    "Added FeCl2 and cysteine create a background requiring the matched abiotic controls.",
    "The iron and ferrihydrite links describe the same experiment and do not constitute independent replication.",
    "The Methods specifies 0.22 micrometre filtration, whereas the Results uses 0.2 micrometre wording; this record preserves the Methods value without inferring equivalence."
  ],
  "evidence": [
    {
      "reference": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1272245/full",
      "title": "Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens",
      "claim": "Primary methods measure Fe(II) with ferrozine after oxalate dissolution, including unfiltered and pre-dissolution-filtered fractions and uninoculated controls.",
      "locator": "html:#s2",
      "source_license": "CC-BY-4.0"
    },
    {
      "reference": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1272245/full",
      "title": "Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens",
      "claim": "The results report extracted Fe(II) in millimolar units; this is not a direct mineral identification.",
      "locator": "html:#s3",
      "source_license": "CC-BY-4.0"
    }
  ],
  "ontology_groundings": [
    {
      "term_id": "METPO:2000017",
      "term_name": "reduces",
      "entity_type": "OBJECT_PROPERTY",
      "relation": "TESTS_PREDICATE",
      "source_version": "800c9d27913158efdf466edf2cd710dbf1ce893f",
      "source_path": "metpo.json",
      "source_url": "https://github.com/berkeleybop/metpo/blob/800c9d27913158efdf466edf2cd710dbf1ce893f/metpo.json",
      "evidence": [
        {
          "reference": "https://github.com/berkeleybop/metpo/blob/800c9d27913158efdf466edf2cd710dbf1ce893f/metpo.json",
          "title": "METPO ontology at commit 800c9d27913158efdf466edf2cd710dbf1ce893f",
          "claim": "METPO reduces is an object property; the controlled Fe(II) assay can assess the scoped iron-redox process but is not identical to that predicate.",
          "locator": "/graphs/0/nodes/1472",
          "source_license": "CC-BY-4.0"
        }
      ]
    }
  ],
  "method": {
    "summary": "Dissolve samples with oxalate before ferrozine spectrophotometry; compare unfiltered preparations with preparations passed through 0.22 micrometre PES filters before dissolution.",
    "evidence": [
      {
        "reference": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1272245/full",
        "title": "Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens",
        "claim": "Primary methods measure Fe(II) with ferrozine after oxalate dissolution, including unfiltered and pre-dissolution-filtered fractions and uninoculated controls.",
        "locator": "html:#s2",
        "source_license": "CC-BY-4.0"
      }
    ]
  },
  "measurement": {
    "target": "Oxalate-extractable Fe(II) in the selected sample fraction.",
    "readout": "Ferrozine spectrophotometric response reported as Fe(II) concentration.",
    "unit": "mmol/L",
    "interpretation": "Interpret against matched uninoculated controls; extraction and filtration define the measured fraction, without assigning mineral identity.",
    "evidence": [
      {
        "reference": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1272245/full",
        "title": "Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens",
        "claim": "Primary methods measure Fe(II) with ferrozine after oxalate dissolution, including unfiltered and pre-dissolution-filtered fractions and uninoculated controls.",
        "locator": "html:#s2",
        "source_license": "CC-BY-4.0"
      },
      {
        "reference": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1272245/full",
        "title": "Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens",
        "claim": "The results report extracted Fe(II) in millimolar units; this is not a direct mineral identification.",
        "locator": "html:#s3",
        "source_license": "CC-BY-4.0"
      }
    ]
  },
  "controls": [
    {
      "description": "Composition-matched uninoculated treatments incubated at 55 degrees Celsius and at room temperature.",
      "evidence": [
        {
          "reference": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1272245/full",
          "title": "Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens",
          "claim": "Primary methods measure Fe(II) with ferrozine after oxalate dissolution, including unfiltered and pre-dissolution-filtered fractions and uninoculated controls.",
          "locator": "html:#s2",
          "source_license": "CC-BY-4.0"
        }
      ]
    }
  ],
  "related_records": [
    {
      "corpus": "cmmmech",
      "identifier": "cmmmech:iron",
      "relation": "MEASURES_PROCESS",
      "basis": "The selected Ax17 mechanism explicitly cites Sklute 2023 and the extraction-based ferrozine endpoint; this measures its Fe-redox component only.",
      "source_version": "df061de720fb9884dcc6e41369a3049cef52a059",
      "source_path": "data/records/iron.yaml",
      "source_url": "https://github.com/CultureBotAI/CMMMech/blob/df061de720fb9884dcc6e41369a3049cef52a059/data/records/iron.yaml",
      "target_locator": "/mechanisms/0",
      "scope": "D. ferrireducens Ax17 (DSM 111878), synthetic two-line ferrihydrite; oxalate-extractable Fe(II) with matched abiotic controls.",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/CMMMech/blob/df061de720fb9884dcc6e41369a3049cef52a059/data/records/iron.yaml",
          "title": "CMMMech iron mechanism at df061de720fb9884dcc6e41369a3049cef52a059",
          "claim": "The selected Ax17 mechanism explicitly cites Sklute 2023 and the extraction-based ferrozine endpoint; this measures its Fe-redox component only.",
          "locator": "/mechanisms/0",
          "source_license": "CC-BY-4.0"
        },
        {
          "reference": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1272245/full",
          "title": "Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens",
          "claim": "Primary methods measure Fe(II) with ferrozine after oxalate dissolution, including unfiltered and pre-dissolution-filtered fractions and uninoculated controls.",
          "locator": "html:#s2",
          "source_license": "CC-BY-4.0"
        }
      ]
    },
    {
      "corpus": "cmmmech",
      "identifier": "cmmmech:ferrihydrite",
      "relation": "MEASURES_PROCESS",
      "basis": "The selected Ax17 mechanism explicitly cites Sklute 2023 and the extraction-based ferrozine endpoint; this measures its Fe-redox component only.",
      "source_version": "df061de720fb9884dcc6e41369a3049cef52a059",
      "source_path": "data/records/ferrihydrite.yaml",
      "source_url": "https://github.com/CultureBotAI/CMMMech/blob/df061de720fb9884dcc6e41369a3049cef52a059/data/records/ferrihydrite.yaml",
      "target_locator": "/mechanisms/0",
      "scope": "D. ferrireducens Ax17 (DSM 111878), synthetic two-line ferrihydrite; oxalate-extractable Fe(II) with matched abiotic controls.",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/CMMMech/blob/df061de720fb9884dcc6e41369a3049cef52a059/data/records/ferrihydrite.yaml",
          "title": "CMMMech ferrihydrite mechanism at df061de720fb9884dcc6e41369a3049cef52a059",
          "claim": "The selected Ax17 mechanism explicitly cites Sklute 2023 and the extraction-based ferrozine endpoint; this measures its Fe-redox component only.",
          "locator": "/mechanisms/0",
          "source_license": "CC-BY-4.0"
        },
        {
          "reference": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1272245/full",
          "title": "Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens",
          "claim": "Primary methods measure Fe(II) with ferrozine after oxalate dissolution, including unfiltered and pre-dissolution-filtered fractions and uninoculated controls.",
          "locator": "html:#s2",
          "source_license": "CC-BY-4.0"
        }
      ]
    }
  ],
  "research_gaps": [
    {
      "scope": "protocol_parameters",
      "reason": "A complete ferrozine reagent/calibration recipe is not reproduced; the cited primary method and its referenced analytical protocol are required for execution."
    }
  ],
  "curation_history": [
    {
      "timestamp": "2026-11-09T02:38:32Z",
      "curator": "assay-stream-c",
      "action": "CREATE",
      "summary": "Curate initial sourced assay concept or scoped operational assay",
      "history_file": "history/records/ax17-extracted-feii-ferrozine/2026-11-09T023832Z-assay-stream-c-381808.yaml"
    }
  ]
}