obsidian_pool_fermentor_opf_medium_modified_from_m_b_allen_1959

CultureMech:009237 bacterial COMPLEX LIQUID
Original name: Obsidian Pool fermentor (OPF) medium (modified from M. B. Allen, 1959)

Overview

External ontology
TOGO:M2682 — Obsidian Pool fermentor (OPF) medium (modified from M. B. Allen, 1959)
Applications
  • Microbial cultivation
Notes
TOGO M2682 imports the Obsidian Pool fermentor medium from Elkins et al. 2008. The source lists 1000 ml distilled water, modified Allen salts and organics, 1 ml Wolfe's Vitamin Solution (1000X), 10 uL/L LiCl/Na2WO4/NaSeO3/Ni(NH4)2(SO4) stock, and N2/CO2 (80:20) gas bubbling at 85 C.

Composition

flowchart LR
    CultureMech_009237["obsidian_pool_fermentor_opf_medium_modified_from_m_b_allen_1959"]
    ing0_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
    CultureMech_009237 --> ing0_Na2MoO4_x_2_H2O
    CHEBI_75213["CHEBI:75213"]
    ing0_Na2MoO4_x_2_H2O -.-> CHEBI_75213
    ing1_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
    CultureMech_009237 --> ing1_MnCl2_x_4_H2O
    CHEBI_86368["CHEBI:86368"]
    ing1_MnCl2_x_4_H2O -.-> CHEBI_86368
    ing2_ZnSO4_x_7_H2O["ZnSO4 x 7 H2O"]
    CultureMech_009237 --> ing2_ZnSO4_x_7_H2O
    CHEBI_32312["CHEBI:32312"]
    ing2_ZnSO4_x_7_H2O -.-> CHEBI_32312
    ing3_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
    CultureMech_009237 --> ing3_CuCl2_x_2_H2O
    CHEBI_86318["CHEBI:86318"]
    ing3_CuCl2_x_2_H2O -.-> CHEBI_86318
    ing4_CoSO4_x_7_H2O["CoSO4 x 7 H2O"]
    CultureMech_009237 --> ing4_CoSO4_x_7_H2O
    CHEBI_91244["CHEBI:91244"]
    ing4_CoSO4_x_7_H2O -.-> CHEBI_91244
    ing5_Na2B4O7_x_10_H2O["Na2B4O7 x 10 H2O"]
    CultureMech_009237 --> ing5_Na2B4O7_x_10_H2O
    CHEBI_131366["CHEBI:131366"]
    ing5_Na2B4O7_x_10_H2O -.-> CHEBI_131366
    ing6_VOSO4_x_5_H2O["VOSO4 x 5 H2O"]
    CultureMech_009237 --> ing6_VOSO4_x_5_H2O
    CHEBI_132758["CHEBI:132758"]
    ing6_VOSO4_x_5_H2O -.-> CHEBI_132758
    ing7_Distilled_water["Distilled water"]
    CultureMech_009237 --> ing7_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing7_Distilled_water -.-> CHEBI_15377
    ing8_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
    CultureMech_009237 --> ing8_MgSO4_x_7_H2O
    CHEBI_31795["CHEBI:31795"]
    ing8_MgSO4_x_7_H2O -.-> CHEBI_31795
    ing9_Yeast_Extract["Yeast Extract"]
    CultureMech_009237 --> ing9_Yeast_Extract
    ing10_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_009237 --> ing10_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing10_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing11_KH2PO4["KH2PO4"]
    CultureMech_009237 --> ing11_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing11_KH2PO4 -.-> CHEBI_63036
    ing12_Na2S_x_9_H2O["Na2S x 9 H2O"]
    CultureMech_009237 --> ing12_Na2S_x_9_H2O
    CHEBI_76209["CHEBI:76209"]
    ing12_Na2S_x_9_H2O -.-> CHEBI_76209
    ing13__NH4_2SO4["(NH4)2SO4"]
    CultureMech_009237 --> ing13__NH4_2SO4
    CHEBI_62946["CHEBI:62946"]
    ing13__NH4_2SO4 -.-> CHEBI_62946
    ing14_FeCl3_x_6_H2O["FeCl3 x 6 H2O"]
    CultureMech_009237 --> ing14_FeCl3_x_6_H2O
    CHEBI_86254["CHEBI:86254"]
    ing14_FeCl3_x_6_H2O -.-> CHEBI_86254
    ing15_Na2SO4["Na2SO4"]
    CultureMech_009237 --> ing15_Na2SO4
    CHEBI_32149["CHEBI:32149"]
    ing15_Na2SO4 -.-> CHEBI_32149
    ing16_KNO3["KNO3"]
    CultureMech_009237 --> ing16_KNO3
    CHEBI_63043["CHEBI:63043"]
    ing16_KNO3 -.-> CHEBI_63043
    ing17_CaSO4_x_2_H2O["CaSO4 x 2 H2O"]
    CultureMech_009237 --> ing17_CaSO4_x_2_H2O
    CHEBI_32583["CHEBI:32583"]
    ing17_CaSO4_x_2_H2O -.-> CHEBI_32583
    ing18_Na2S2O3["Na2S2O3"]
    CultureMech_009237 --> ing18_Na2S2O3
    CHEBI_132112["CHEBI:132112"]
    ing18_Na2S2O3 -.-> CHEBI_132112
    ing19_Peptone["Peptone"]
    CultureMech_009237 --> ing19_Peptone
    ing20_Carbon_dioxide_gas["Carbon dioxide gas"]
    CultureMech_009237 --> ing20_Carbon_dioxide_gas
    CHEBI_16526["CHEBI:16526"]
    ing20_Carbon_dioxide_gas -.-> CHEBI_16526
    ing21_Nitrogen_gas["Nitrogen gas"]
    CultureMech_009237 --> ing21_Nitrogen_gas
    CHEBI_17997["CHEBI:17997"]
    ing21_Nitrogen_gas -.-> CHEBI_17997

Ingredients (22)

# Ingredient Concentration Ontology Notes
1 Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
0.03 MG_PER_L CHEBI:75213
sodium molybdate dihydrate
 TOGO M2682 adds 30 uL of 1 mg/ml Na2MoO4 x 2 H2O per liter, equivalent to 0.03 mg/L.
2 MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
1.8 MG_PER_L CHEBI:86368
manganese(II) chloride tetrahydrate
 TOGO M2682 adds 180 uL of 10 mg/ml MnCl2 x 4 H2O per liter, equivalent to 1.8 mg/L.
3 ZnSO4 x 7 H2O
7H2O.O4S.Zn 287.558 g/mol
0.22 MG_PER_L CHEBI:32312
zinc sulfate heptahydrate
 TOGO M2682 adds 22 uL of 10 mg/ml ZnSO4 x 7 H2O per liter, equivalent to 0.22 mg/L.
4 CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
0.05 MG_PER_L CHEBI:86318
copper(II) chloride dihydrate
 TOGO M2682 adds 5 uL of 10 mg/ml CuCl2 x 2 H2O per liter, equivalent to 0.05 mg/L.
5 CoSO4 x 7 H2O
Co.7H2O.O4S 281.101 g/mol
0.01 MG_PER_L CHEBI:91244
cobalt(2+) sulfate heptahydrate
 TOGO M2682 adds 10 uL of 1 mg/ml CoSO4 x 7 H2O per liter, equivalent to 0.01 mg/L.
6 Na2B4O7 x 10 H2O
10H2O.H4B4O9.2Na 417.401 g/mol
4.5 MG_PER_L CHEBI:131366
disodium tetraborate decahydrate
 TOGO M2682 adds 180 uL of 25 mg/ml Na2B4O7 x 10 H2O per liter, equivalent to 4.5 mg/L.
7 VOSO4 x 5 H2O
5H2O.O4S.OV 253.081 g/mol
0.03 MG_PER_L CHEBI:132758
vanadyl sulfate pentahydrate
 TOGO M2682 adds 30 uL of 1 mg/ml VOSO4 x 5 H2O per liter, equivalent to 0.03 mg/L.
8 Distilled water
H2O 18.015 g/mol
1000.0 ML_PER_L CHEBI:15377
water
 TOGO M2682 makes the final medium with 1000 ml distilled water.
9 MgSO4 x 7 H2O
7H2O.Mg.O4S 246.473 g/mol
0.25 G_PER_L CHEBI:31795
magnesium sulfate heptahydrate
 TOGO M2682 lists 0.25 g MgSO4 x 7 H2O in the final liter.
10 Yeast Extract 0.1 G_PER_L FOODON:03315426
Yeast extract
 TOGO M2682 lists 0.1 g Yeast Extract in the final liter.
11 CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
0.07 G_PER_L CHEBI:86158
calcium chloride dihydrate
 TOGO M2682 lists 0.07 g CaCl2 x 2 H2O in the final liter.
12 KH2PO4
H2O4P.K 136.084 g/mol
0.28 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
 TOGO M2682 lists 0.28 g KH2PO4 in the final liter.
13 Na2S x 9 H2O
9H2O.2Na.S 240.182 g/mol
0.13 G_PER_L CHEBI:76209
sodium sulfide nonahydrate
 TOGO M2682 lists 0.13 g Na2S x 9 H2O in the final liter.
14 (NH4)2SO4
2H4N.O4S 132.141 g/mol
1.3 G_PER_L CHEBI:62946
ammonium sulfate
 TOGO M2682 lists 1.3 g (NH4)2SO4 in the final liter.
15 FeCl3 x 6 H2O
Cl3Fe.6H2O 270.294 g/mol
0.02 G_PER_L CHEBI:86254
iron trichloride hexahydrate
 TOGO M2682 lists 0.02 g FeCl3 x 6 H2O in the final liter.
16 Na2SO4
2Na.O4S 142.043 g/mol
0.07 G_PER_L CHEBI:32149
sodium sulfate
 TOGO M2682 lists 0.07 g Na2SO4 in the final liter.
17 KNO3
K.NO3 101.102 g/mol
0.1 G_PER_L CHEBI:63043
potassium nitrate
 TOGO M2682 lists 0.1 g KNO3 in the final liter.
18 CaSO4 x 2 H2O
Ca.2H2O.O4S 172.171 g/mol
0.17 G_PER_L CHEBI:32583
calcium sulfate dihydrate
 TOGO M2682 lists 0.17 g CaSO4 x 2 H2O in the final liter.
19 Na2S2O3
2Na.O3S2 158.111 g/mol
0.78 G_PER_L CHEBI:132112
sodium thiosulfate
 TOGO M2682 lists 0.78 g Na2S2O3 in the final liter.
20 Peptone 0.5 G_PER_L MICRO:0000178 (source link unavailable)
Peptone
 TOGO M2682 lists 0.5 g Peptone in the final liter.
21 Carbon dioxide gas
CO2 44.009 g/mol
variable VARIABLE CHEBI:16526
carbon dioxide
 TOGO M2682 lists CO2 gas; source comments specify N2/CO2 (80:20) bubbling.
22 Nitrogen gas
N2 28.014 g/mol
variable VARIABLE CHEBI:17997
dinitrogen
 TOGO M2682 lists N2 gas; source comments specify N2/CO2 (80:20) bubbling.

Solutions

Wolfe's Vitamin Solution (1000X)

Dose: 1.0 ML_PER_L

TOGO M2682 adds 1.0 ml/L Wolfe's Vitamin Solution (1000X); this source does not disclose its composition.

LiCl/Na2WO4/NaSeO3/Ni(NH4)2(SO4) stock

Dose: 0.01 ML_PER_L

Stock composition
IngredientConcentrationNotes
Na2WO4 1.0 G_PER_L TOGO M2682 defines the Li/W/Se/Ni stock with 1 mg/ml Na2WO4.
Na2SeO3 1.0 G_PER_L TOGO M2682 defines the Li/W/Se/Ni stock with 1 mg/ml Na2SeO3.
LiCl 1.0 G_PER_L TOGO M2682 defines the Li/W/Se/Ni stock with 1 mg/ml LiCl.
Ni(NH4)2(SO4) 1.0 G_PER_L TOGO M2682 defines the Li/W/Se/Ni stock with 1 mg/ml Ni(NH4)2(SO4). This source formula is retained ungrounded because it does not specify nickel sulfate stoichiometry or hydrate state.
TOGO M2682 adds 10 uL/L of a stock containing 1 mg/ml each LiCl, Na2WO4, NaSeO3, and Ni(NH4)2(SO4).

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-27T06:35:57.051406Z togo-import Imported from TOGO Medium Source: TOGO, ID: M2682
2026-01-28T19:48:11.272425Z 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
2026-03-09T08:04:18.478308+00:00 solution-migrator-v1.0 Migrated solutions from ingredients to solutions array Moved 1 solution(s) from ingredients
2026-03-13T06:20:04.564494Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:009237
2026-03-14T00:00:00+00:00 schema-defaulter-v1.0 Applied schema defaults and normalizations Added default solution name
2026-03-17T06:29:49.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:23.309006+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "Obsidian Pool fermentor (OPF) medium (modified from M. B. Allen, 1959)" to "obsidian_pool_fermentor_opf_medium_modified_from_m_b_allen_1959" for consistent matching
2026-05-16T09:04:28.049022+00:00 migrate_legacy_fields.py MIGRATED_LEGACY_FIELDS curation_history.date->timestamp=2
2026-06-05T07:41:40.341642+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 9 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T06:58:28.595564+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.
2026-06-10T07:47:09.711767+00:00 primary-term-label-canonicalization-v1.0 Canonicalized primary term label to OBO canonical (OAK) 4 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.
2026-09-12T00:00:00-07:00 repair_togo_m2682_obsidian_pool_score15.py RESOLVED_TOGO_M2682_OBSIDIAN_POOL_SCORE15 Corrected microliter stock additions from g/L to mg/L final concentrations, moved the LiCl/Na2WO4/NaSeO3/Ni stock solutes under an inline stock solution, fixed Na2S2O3 and hydrated salt groundings, and added the 85 C N2/CO2 incubation conditions.