saltwater_iron_oxidizing_bacteria_medium

CultureMech:010043 bacterial COMPLEX SOLID_AGAR
Original name: Saltwater Iron-Oxidizing Bacteria Medium

Overview

External ontology
TOGO:M642 — Saltwater Iron-Oxidizing Bacteria Medium
Applications
  • Microbial cultivation
Notes
Source: https://togomedium.org/medium/M642 Original source: JCM - JCM_M629 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=629

Composition

flowchart LR
    CultureMech_010043["saltwater_iron_oxidizing_bacteria_medium"]
    ing0_Bottom_layer["Bottom layer"]
    CultureMech_010043 --> ing0_Bottom_layer
    ing1_Top_layer["Top layer"]
    CultureMech_010043 --> ing1_Top_layer
    ing2_Agarose["Agarose"]
    CultureMech_010043 --> ing2_Agarose
    CHEBI_2511["CHEBI:2511"]
    ing2_Agarose -.-> CHEBI_2511
    ing3_Artificial_saltwater__see_below_["Artificial saltwater (see below)"]
    CultureMech_010043 --> ing3_Artificial_saltwater__see_below_
    ing4_NaHCO3["NaHCO3"]
    CultureMech_010043 --> ing4_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing4_NaHCO3 -.-> CHEBI_32139
    ing5_MES["MES"]
    CultureMech_010043 --> ing5_MES
    CHEBI_39010["CHEBI:39010"]
    ing5_MES -.-> CHEBI_39010
    ing6_Carbon_dioxide_gas["Carbon dioxide gas"]
    CultureMech_010043 --> ing6_Carbon_dioxide_gas
    CHEBI_16526["CHEBI:16526"]
    ing6_Carbon_dioxide_gas -.-> CHEBI_16526
    ing7_Nitrogen_gas["Nitrogen gas"]
    CultureMech_010043 --> ing7_Nitrogen_gas
    CHEBI_17997["CHEBI:17997"]
    ing7_Nitrogen_gas -.-> CHEBI_17997
    ing8_Oxygen_gas["Oxygen gas"]
    CultureMech_010043 --> ing8_Oxygen_gas
    ing9_Distilled_water["Distilled water"]
    CultureMech_010043 --> ing9_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing9_Distilled_water -.-> CHEBI_15377
    ing10_MgSO4_7H2O["MgSO4・7H2O"]
    CultureMech_010043 --> ing10_MgSO4_7H2O
    CHEBI_31795["CHEBI:31795"]
    ing10_MgSO4_7H2O -.-> CHEBI_31795
    ing11_NaCl["NaCl"]
    CultureMech_010043 --> ing11_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing11_NaCl -.-> CHEBI_26710
    ing12_CaCl2_2H2O["CaCl2・2H2O"]
    CultureMech_010043 --> ing12_CaCl2_2H2O
    CHEBI_86158["CHEBI:86158"]
    ing12_CaCl2_2H2O -.-> CHEBI_86158
    ing13_KH2PO4["KH2PO4"]
    CultureMech_010043 --> ing13_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing13_KH2PO4 -.-> CHEBI_63036
    ing14_NH4Cl["NH4Cl"]
    CultureMech_010043 --> ing14_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing14_NH4Cl -.-> CHEBI_31206
    ing15_MgCl2_6H2O["MgCl2・6H2O"]
    CultureMech_010043 --> ing15_MgCl2_6H2O
    CHEBI_86345["CHEBI:86345"]
    ing15_MgCl2_6H2O -.-> CHEBI_86345
    ing16_KCl["KCl"]
    CultureMech_010043 --> ing16_KCl
    CHEBI_32588["CHEBI:32588"]
    ing16_KCl -.-> CHEBI_32588

Ingredients (17)

# Ingredient Concentration Ontology Notes
1 Bottom layer 100 G_PER_L
2 Top layer 101 G_PER_L
3 Agarose
(C12H18O9)n.C12H20O10 630.549 g/mol
1.15 G_PER_L CHEBI:2511
agarose
 Role: Solidifying component [Merged 2 duplicates: 1.0, 0.15]
4 Artificial saltwater (see below) 150.0 G_PER_L [Merged 2 duplicates: 50.0, 100.0]
5 NaHCO3
CHO3.Na 84.006 g/mol
0.24200000000000002 G_PER_L CHEBI:32139
sodium hydrogencarbonate
 Role: Buffer; Properties: Simple component, Inorganic compound, Defined component [Merged 2 duplicates: 0.042, 0.2]
6 MES 0.195 G_PER_L CHEBI:39010
MES
 Role: Buffer; Properties: Defined component, Organic compound, Simple component
7 Carbon dioxide gas
CO2 44.009 g/mol
variable VARIABLE CHEBI:16526
carbon dioxide
 Properties: ガス
8 Nitrogen gas
N2 28.014 g/mol
variable VARIABLE CHEBI:17997
dinitrogen
 Properties: ガス
9 Oxygen gas variable VARIABLE Properties: ガス
10 Distilled water
H2O 18.015 g/mol
1 G_PER_L CHEBI:15377
water
 Role: Solvating media; Properties: Defined component, Inorganic compound, Simple component
11 MgSO4・7H2O
7H2O.Mg.O4S 246.473 g/mol
6.78 G_PER_L CHEBI:31795
magnesium sulfate heptahydrate
 Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
12 NaCl
Cl.Na 58.443 g/mol
27.5 G_PER_L CHEBI:26710
sodium chloride
 Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component
13 CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
1.4 G_PER_L CHEBI:86158
calcium chloride dihydrate
 Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component
14 KH2PO4
H2O4P.K 136.084 g/mol
0.05 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
 Role: Buffer; Properties: Defined component, Simple component, Inorganic compound
15 NH4Cl
Cl.H4N 53.492 g/mol
1 G_PER_L CHEBI:31206
ammonium chloride
 Role: Nitrogen source; Properties: Defined component, Inorganic compound, Simple component
16 MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
5.38 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
 Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component
17 KCl
Cl.K 74.551 g/mol
0.72 G_PER_L CHEBI:32588
potassium chloride
 Role: Mineral source; Properties: Simple component, Defined component, Inorganic compound

Solutions

FeS solution (see Medium [M641])

Dose: 50 G_PER_L

Cross-reference to Medium M641

Trace mineral solution (see Medium [M190])

Dose: 1 G_PER_L

Cross-reference to Medium M190

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-27T06:35:55.452010Z togo-import Imported from TOGO Medium Source: JCM, ID: M642
2026-01-28T19:48:41.031996Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-03T00:00:00+00:00 schema-defaulter-v1.0 Applied schema defaults and normalizations Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas; Added default concentration for ingredient: Oxygen gas
2026-03-09T08:05:09.092204+00:00 solution-migrator-v1.0 Migrated solutions from ingredients to solutions array Moved 2 solution(s) from ingredients
2026-03-13T03:09:40.844284Z data-quality-cleanup-v1.0 Data quality fixes Merged 3 duplicate ingredient(s)
2026-03-13T06:20:10.910702Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:010043
2026-03-14T00:00:00+00:00 schema-defaulter-v1.0 Applied schema defaults and normalizations Added default solution name; Added default solution name
2026-03-17T06:30:53.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:29.838485+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "Saltwater Iron-Oxidizing Bacteria Medium" to "saltwater_iron_oxidizing_bacteria_medium" for consistent matching
2026-05-16T09:03:19.712987+00:00 migrate_legacy_fields.py MIGRATED_LEGACY_FIELDS curation_history.date->timestamp=2
2026-06-05T07:40:43.205438+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 8 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T06:57:32.023894+00:00 mgso4-heptahydrate-term-fix-v1.0 Corrected MgSO4·7H2O primary term grounding to heptahydrate Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched.
2026-06-10T07:46:51.219199+00:00 primary-term-label-canonicalization-v1.0 Canonicalized primary term label to OBO canonical (OAK) 2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.