Overview
- External ontology
- mediadive.medium:J594 (source link unavailable) — ALICYCLIPHILUS DENITRIFICANS MEDIUM
- Applications
-
- Microbial cultivation
- pH
- 7.3
- High-metal flag
- True
- Notes
- Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=594
Composition
flowchart LR
CultureMech_002942["alicycliphilus_denitrificans_medium"]
ing0_Na2HPO4_x_2_H2O["Na2HPO4 x 2 H2O"]
CultureMech_002942 --> ing0_Na2HPO4_x_2_H2O
CHEBI_91258["CHEBI:91258"]
ing0_Na2HPO4_x_2_H2O -.-> CHEBI_91258
ing1_KH2PO4["KH2PO4"]
CultureMech_002942 --> ing1_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing1_KH2PO4 -.-> CHEBI_63036
ing2_NaNO3["NaNO3"]
CultureMech_002942 --> ing2_NaNO3
CHEBI_63005["CHEBI:63005"]
ing2_NaNO3 -.-> CHEBI_63005
ing3_Sodium_acetate_x_3_H2O["Sodium acetate x 3 H2O"]
CultureMech_002942 --> ing3_Sodium_acetate_x_3_H2O
CHEBI_32954["CHEBI:32954"]
ing3_Sodium_acetate_x_3_H2O -.-> CHEBI_32954
ing4_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
CultureMech_002942 --> ing4_CaCl2_x_2_H2O
CHEBI_86158["CHEBI:86158"]
ing4_CaCl2_x_2_H2O -.-> CHEBI_86158
ing5_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
CultureMech_002942 --> ing5_MgCl2_x_6_H2O
CHEBI_86345["CHEBI:86345"]
ing5_MgCl2_x_6_H2O -.-> CHEBI_86345
ing6_NH4HCO3["NH4HCO3"]
CultureMech_002942 --> ing6_NH4HCO3
CHEBI_184335["CHEBI:184335"]
ing6_NH4HCO3 -.-> CHEBI_184335
ing7_NaHCO3["NaHCO3"]
CultureMech_002942 --> ing7_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing7_NaHCO3 -.-> CHEBI_32139
ing8_Na2SO4["Na2SO4"]
CultureMech_002942 --> ing8_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing8_Na2SO4 -.-> CHEBI_32149
ing9_Sodium_acetate["Sodium acetate"]
CultureMech_002942 --> ing9_Sodium_acetate
ing9_Sodium_acetate -.-> CHEBI_32954
ing10_HCl["HCl"]
CultureMech_002942 --> ing10_HCl
CHEBI_17883["CHEBI:17883"]
ing10_HCl -.-> CHEBI_17883
ing11_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
CultureMech_002942 --> ing11_FeCl2_x_4_H2O
CHEBI_86249["CHEBI:86249"]
ing11_FeCl2_x_4_H2O -.-> CHEBI_86249
ing12_ZnCl2["ZnCl2"]
CultureMech_002942 --> ing12_ZnCl2
CHEBI_49976["CHEBI:49976"]
ing12_ZnCl2 -.-> CHEBI_49976
ing13_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
CultureMech_002942 --> ing13_MnCl2_x_4_H2O
CHEBI_86368["CHEBI:86368"]
ing13_MnCl2_x_4_H2O -.-> CHEBI_86368
ing14_H3BO3["H3BO3"]
CultureMech_002942 --> ing14_H3BO3
CHEBI_33118["CHEBI:33118"]
ing14_H3BO3 -.-> CHEBI_33118
ing15_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
CultureMech_002942 --> ing15_CoCl2_x_6_H2O
CHEBI_53503["CHEBI:53503"]
ing15_CoCl2_x_6_H2O -.-> CHEBI_53503
ing16_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
CultureMech_002942 --> ing16_CuCl2_x_2_H2O
CHEBI_86318["CHEBI:86318"]
ing16_CuCl2_x_2_H2O -.-> CHEBI_86318
ing17_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
CultureMech_002942 --> ing17_NiCl2_x_6_H2O
CHEBI_34887["CHEBI:34887"]
ing17_NiCl2_x_6_H2O -.-> CHEBI_34887
ing18_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
CultureMech_002942 --> ing18_Na2MoO4_x_2_H2O
CHEBI_75213["CHEBI:75213"]
ing18_Na2MoO4_x_2_H2O -.-> CHEBI_75213
ing19_NaOH["NaOH"]
CultureMech_002942 --> ing19_NaOH
CHEBI_32145["CHEBI:32145"]
ing19_NaOH -.-> CHEBI_32145
ing20_Na2SeO3_x_5_H2O["Na2SeO3 x 5 H2O"]
CultureMech_002942 --> ing20_Na2SeO3_x_5_H2O
CHEBI_131361["CHEBI:131361"]
ing20_Na2SeO3_x_5_H2O -.-> CHEBI_131361
ing21_Na2WO4_x_2_H2O["Na2WO4 x 2 H2O"]
CultureMech_002942 --> ing21_Na2WO4_x_2_H2O
CHEBI_63939["CHEBI:63939"]
ing21_Na2WO4_x_2_H2O -.-> CHEBI_63939
ing22_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_002942 --> ing22_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing22_p_Aminobenzoic_acid -.-> CHEBI_30753
ing23_Biotin["Biotin"]
CultureMech_002942 --> ing23_Biotin
CHEBI_15956["CHEBI:15956"]
ing23_Biotin -.-> CHEBI_15956
ing24_Nicotinic_acid["Nicotinic acid"]
CultureMech_002942 --> ing24_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing24_Nicotinic_acid -.-> CHEBI_15940
ing25_DL_Calcium_pantothenate["DL-Calcium pantothenate"]
CultureMech_002942 --> ing25_DL_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing25_DL_Calcium_pantothenate -.-> CHEBI_31345
ing26_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
CultureMech_002942 --> ing26_Pyridoxine_hydrochloride
CHEBI_30961["CHEBI:30961"]
ing26_Pyridoxine_hydrochloride -.-> CHEBI_30961
ing27_Sodium_phosphate_buffer["Sodium phosphate buffer"]
CultureMech_002942 --> ing27_Sodium_phosphate_buffer
ing28_Thiamine_HCl["Thiamine HCl"]
CultureMech_002942 --> ing28_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing28_Thiamine_HCl -.-> CHEBI_49105
ing29_Vitamin_B12["Vitamin B12"]
CultureMech_002942 --> ing29_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing29_Vitamin_B12 -.-> CHEBI_176843
Ingredients (30)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Na2HPO4 x 2 H2O
2H2O.HO4P.2Na 177.988 g/mol
|
0.586932 G_PER_L |
CHEBI:91258
disodium hydrogenphosphate dihydrate
|
|
| 2 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.454042 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
|
| 3 |
NaNO3
NO3.Na 84.994 g/mol
|
0.941307 G_PER_L |
CHEBI:63005
sodium nitrate
|
|
| 4 |
Sodium acetate x 3 H2O
C2H3O2.Na 82.034 g/mol
|
0.150609 G_PER_L |
CHEBI:32954
sodium acetate
|
|
| 5 |
CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
|
2.2 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
|
| 6 |
MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
|
2 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
|
| 7 |
NH4HCO3
CHO3.H4N 79.055 g/mol
|
6.98413 G_PER_L |
CHEBI:184335
Ammonium bicarbonate
|
|
| 8 |
NaHCO3
CHO3.Na 84.006 g/mol
|
59.2063 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
|
| 9 |
Na2SO4
2Na.O4S 142.043 g/mol
|
3.1746 G_PER_L |
CHEBI:32149
sodium sulfate
|
|
| 10 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
10 G_PER_L |
CHEBI:32954
sodium acetate
|
|
| 11 |
HCl
HCl 36.461 g/mol
|
2.5 G_PER_L |
CHEBI:17883
hydrogen chloride
|
|
| 12 |
FeCl2 x 4 H2O
Cl2Fe.4H2O 198.811 g/mol
|
1.5 G_PER_L |
CHEBI:86249
iron dichloride tetrahydrate
|
|
| 13 |
ZnCl2
2Cl.Zn 136.296 g/mol
|
0.07 G_PER_L |
CHEBI:49976
zinc dichloride
|
|
| 14 |
MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
|
0.1 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
|
| 15 |
H3BO3
H3BO3 61.833 g/mol
|
0.006 G_PER_L |
CHEBI:33118
boric acid
|
|
| 16 |
CoCl2 x 6 H2O
2Cl.Co.6H2O 237.929 g/mol
|
0.19 G_PER_L |
CHEBI:53503
cobalt chloride hexahydrate
|
|
| 17 |
CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
|
0.002 G_PER_L |
CHEBI:86318
copper(II) chloride dihydrate
|
|
| 18 |
NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
|
0.024 G_PER_L |
CHEBI:34887
nickel dichloride
|
|
| 19 |
Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.036 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
|
| 20 |
NaOH
HO.Na 39.997 g/mol
|
0.4 G_PER_L |
CHEBI:32145
sodium hydroxide
|
|
| 21 |
Na2SeO3 x 5 H2O
5H2O.2Na.O3Se 263.012 g/mol
|
0.006 G_PER_L |
CHEBI:131361
disodium selenite pentahydrate
|
|
| 22 |
Na2WO4 x 2 H2O
2H2O.2Na.O4W 329.846 g/mol
|
0.008 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
|
| 23 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
0.04 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
|
| 24 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.01 G_PER_L |
CHEBI:15956
biotin
|
|
| 25 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
0.1 G_PER_L |
CHEBI:15940
nicotinic acid
|
|
| 26 |
DL-Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.05 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
|
| 27 |
Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
|
0.1 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
|
| 28 | Sodium phosphate buffer | 200.0 G_PER_L | [Merged 2 duplicates: 100.0, 100.0] | |
| 29 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.1 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
|
| 30 | Vitamin B12 | 0.05 G_PER_L |
CHEBI:176843
vitamin B12
|
Preparation
- Prepare all solutions and autoclave under a N2 atmosphere. After cooling, combine the solutions and replace the gas phase with a N2-CO2 (4:1, v/v) gas mixture. Then, aseptically and anaerobically add the following autoclaved or *filter-sterilized solutions to the medium:
- Check the final pH of the medium to be around 7.3.
- Comment: JCM 14587 grows also in a modified medium with benzene and chlorate. For preparation of the modified medium, replace NaNO3 with 1.06 g NaClO3(in 900 ml solution A). After combining all solutions (A, B and C), add 1.0 ml/L of 1.0 M sodium acetate solution (autoclaved), 25 ml/L of 20 mM benzene (water-saturated, autoclaved), and 1 ml/L of each of vitamin solution (see Medium No. 403, filter-sterilized), thiamine solution (see Medium No. 403, filter-sterilized) and vitamin B12 solution (see Medium No. 403, filter-sterilized) to the medium. Otherwise, prepare the modified medium as described above.
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- alicycliphilus_denitrificans_medium (CultureMech:002942)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-26T17:53:17.033222Z | mediadive-import | Imported from MediaDive | Source: JCM, ID: J594 |
| 2026-01-28T19:48:11.785467Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-03-13T03:08:47.230305Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:19:16.719494Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:002942 |
| 2026-03-17T06:29:50.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:45:30.312395+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "ALICYCLIPHILUS DENITRIFICANS MEDIUM" to "alicycliphilus_denitrificans_medium" for consistent matching |
| 2026-06-05T07:40:47.742966+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 27 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:46:52.745448+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. |
| 2026-08-06T03:05:22.279192+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint b7e62cdde42c959f2ec2c36700a14a9af5da254b57647da12b3399f612cd1f55 |