Overview
- External ontology
- mediadive.medium:J747 (source link unavailable) — FRESHWATER MEDIUM WITH TOLUENE
- Applications
-
- Microbial cultivation
- pH
- 7.0
- High-metal flag
- True
- Notes
- Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=747
Composition
flowchart LR
CultureMech_003090["freshwater_medium_with_toluene"]
ing0_Iron_III__citrate["Iron(III) citrate"]
CultureMech_003090 --> ing0_Iron_III__citrate
CHEBI_144421["CHEBI:144421"]
ing0_Iron_III__citrate -.-> CHEBI_144421
ing1_NaCl["NaCl"]
CultureMech_003090 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_KCl["KCl"]
CultureMech_003090 --> ing2_KCl
CHEBI_32588["CHEBI:32588"]
ing2_KCl -.-> CHEBI_32588
ing3_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
CultureMech_003090 --> ing3_MgCl2_x_6_H2O
CHEBI_86345["CHEBI:86345"]
ing3_MgCl2_x_6_H2O -.-> CHEBI_86345
ing4_NH4Cl["NH4Cl"]
CultureMech_003090 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_KH2PO4["KH2PO4"]
CultureMech_003090 --> ing5_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing5_KH2PO4 -.-> CHEBI_63036
ing6_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
CultureMech_003090 --> ing6_CaCl2_x_2_H2O
CHEBI_86158["CHEBI:86158"]
ing6_CaCl2_x_2_H2O -.-> CHEBI_86158
ing7_Na2SO4["Na2SO4"]
CultureMech_003090 --> ing7_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing7_Na2SO4 -.-> CHEBI_32149
ing8_Sodium_acetate_x_3_H2O["Sodium acetate x 3 H2O"]
CultureMech_003090 --> ing8_Sodium_acetate_x_3_H2O
CHEBI_32954["CHEBI:32954"]
ing8_Sodium_acetate_x_3_H2O -.-> CHEBI_32954
ing9_NaHCO3["NaHCO3"]
CultureMech_003090 --> ing9_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing9_NaHCO3 -.-> CHEBI_32139
ing10_FeCl2["FeCl2"]
CultureMech_003090 --> ing10_FeCl2
CHEBI_30812["CHEBI:30812"]
ing10_FeCl2 -.-> CHEBI_30812
ing11_Toluene["Toluene"]
CultureMech_003090 --> ing11_Toluene
CHEBI_17578["CHEBI:17578"]
ing11_Toluene -.-> CHEBI_17578
ing12_HCl["HCl"]
CultureMech_003090 --> ing12_HCl
CHEBI_17883["CHEBI:17883"]
ing12_HCl -.-> CHEBI_17883
ing13_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
CultureMech_003090 --> ing13_FeCl2_x_4_H2O
CHEBI_86249["CHEBI:86249"]
ing13_FeCl2_x_4_H2O -.-> CHEBI_86249
ing14_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_003090 --> ing14_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing14_p_Aminobenzoic_acid -.-> CHEBI_30753
ing15_Biotin["Biotin"]
CultureMech_003090 --> ing15_Biotin
CHEBI_15956["CHEBI:15956"]
ing15_Biotin -.-> CHEBI_15956
ing16_Nicotinic_acid["Nicotinic acid"]
CultureMech_003090 --> ing16_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing16_Nicotinic_acid -.-> CHEBI_15940
ing17_DL_Calcium_pantothenate["DL-Calcium pantothenate"]
CultureMech_003090 --> ing17_DL_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing17_DL_Calcium_pantothenate -.-> CHEBI_31345
ing18_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
CultureMech_003090 --> ing18_Pyridoxine_hydrochloride
CHEBI_30961["CHEBI:30961"]
ing18_Pyridoxine_hydrochloride -.-> CHEBI_30961
ing19_Sodium_phosphate_buffer["Sodium phosphate buffer"]
CultureMech_003090 --> ing19_Sodium_phosphate_buffer
ing20_Thiamine_HCl["Thiamine HCl"]
CultureMech_003090 --> ing20_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing20_Thiamine_HCl -.-> CHEBI_49105
ing21_Vitamin_B12["Vitamin B12"]
CultureMech_003090 --> ing21_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing21_Vitamin_B12 -.-> CHEBI_176843
ing22_NaOH["NaOH"]
CultureMech_003090 --> ing22_NaOH
CHEBI_32145["CHEBI:32145"]
ing22_NaOH -.-> CHEBI_32145
ing23_Na2SeO3_x_5_H2O["Na2SeO3 x 5 H2O"]
CultureMech_003090 --> ing23_Na2SeO3_x_5_H2O
CHEBI_131361["CHEBI:131361"]
ing23_Na2SeO3_x_5_H2O -.-> CHEBI_131361
ing24_Na2WO4_x_2_H2O["Na2WO4 x 2 H2O"]
CultureMech_003090 --> ing24_Na2WO4_x_2_H2O
CHEBI_63939["CHEBI:63939"]
ing24_Na2WO4_x_2_H2O -.-> CHEBI_63939
Ingredients (25)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Iron(III) citrate
C6H5FeO7 244.944 g/mol
|
333.333 G_PER_L |
CHEBI:144421
iron(III) citrate
|
|
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
27.7778 G_PER_L |
CHEBI:26710
sodium chloride
|
|
| 3 |
KCl
Cl.K 74.551 g/mol
|
13.8889 G_PER_L |
CHEBI:32588
potassium chloride
|
|
| 4 |
MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
|
11.1111 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
|
| 5 |
NH4Cl
Cl.H4N 53.492 g/mol
|
6.94444 G_PER_L |
CHEBI:31206
ammonium chloride
|
|
| 6 |
KH2PO4
H2O4P.K 136.084 g/mol
|
5.55556 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
|
| 7 |
CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
|
2.77778 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
|
| 8 |
Na2SO4
2Na.O4S 142.043 g/mol
|
0.0394444 G_PER_L |
CHEBI:32149
sodium sulfate
|
|
| 9 |
Sodium acetate x 3 H2O
C2H3O2.Na 82.034 g/mol
|
37.7778 G_PER_L |
CHEBI:32954
sodium acetate
|
|
| 10 |
NaHCO3
CHO3.Na 84.006 g/mol
|
30 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
|
| 11 |
FeCl2
Cl2Fe 126.751 g/mol
|
0.5 G_PER_L |
CHEBI:30812
iron dichloride
|
|
| 12 |
Toluene
C7H8 92.141 g/mol
|
5 G_PER_L |
CHEBI:17578
toluene
|
|
| 13 |
HCl
HCl 36.461 g/mol
|
2.5 G_PER_L |
CHEBI:17883
hydrogen chloride
|
|
| 14 |
FeCl2 x 4 H2O
Cl2Fe.4H2O 198.811 g/mol
|
1.5 G_PER_L |
CHEBI:86249
iron dichloride tetrahydrate
|
|
| 15 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
0.04 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
|
| 16 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.01 G_PER_L |
CHEBI:15956
biotin
|
|
| 17 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
0.1 G_PER_L |
CHEBI:15940
nicotinic acid
|
|
| 18 |
DL-Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.05 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
|
| 19 |
Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
|
0.1 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
|
| 20 | Sodium phosphate buffer | 100.0 G_PER_L | [Collapsed 2 identical duplicates: 100.0, 100.0] | |
| 21 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.1 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
|
| 22 | Vitamin B12 | 0.05 G_PER_L |
CHEBI:176843
vitamin B12
|
|
| 23 |
NaOH
HO.Na 39.997 g/mol
|
0.4 G_PER_L |
CHEBI:32145
sodium hydroxide
|
|
| 24 |
Na2SeO3 x 5 H2O
5H2O.2Na.O3Se 263.012 g/mol
|
0.006 G_PER_L |
CHEBI:131361
disodium selenite pentahydrate
|
|
| 25 |
Na2WO4 x 2 H2O
2H2O.2Na.O4W 329.846 g/mol
|
0.008 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Preparation
- First dissolve iron(III) citrate in 800 ml distilled water and adjust pH to 7.0 with 10 N NaOH. Then, add the remaining minerals, bring volume to 970 ml and autoclave under a N2 atmosphere. Add aseptically and anaerobically the following filter-sterilized solutions:
- Distribute the medium into sterile culture vessels (e.g., 50 ml per 120 ml bottle) under a N2-CO2 (4:1, v/v) gas mixture, and seal with sterile butyl rubber stoppers. Then add per 50 ml the following solutions from anaerobic stocks:
- Check the final pH of the medium to be around 7.0.
Solutions
Trace element solution (see Medium No. 187
Dose: 1 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-26T17:53:17.470110Z | mediadive-import | Imported from MediaDive | Source: JCM, ID: J747 |
| 2026-03-09T08:05:04.932644+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 1 solution(s) from ingredients |
| 2026-03-13T03:09:36.896495Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:19:17.726566Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:003090 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name |
| 2026-03-17T06:30:48.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:45:31.480415+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "FRESHWATER MEDIUM WITH TOLUENE" to "freshwater_medium_with_toluene" for consistent matching |
| 2026-05-16T09:03:35.209348+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=1 |
| 2026-06-05T07:41:05.524500+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 23 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:46:58.821138+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 3 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-09-02T07:38:08.634898+00:00 | repair_merged_duplicates.py | REPAIRED_SUMMED_DUPLICATE_MERGE | Collapsed 1 ingredient row(s) whose concentration was the SUM of identical duplicate values written by cleanup_media_quality.py. Every merged part was the same value, so the pre-merge value is unambiguous and no source lookup was needed. Rows whose merged parts differ were left untouched. |