alicycliphilus_denitrificans_medium

CultureMech:002942 bacterial DEFINED LIQUID
Original name: ALICYCLIPHILUS DENITRIFICANS MEDIUM

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 100.0 G_PER_L [Collapsed 2 identical 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

  1. 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:
  2. Check the final pH of the medium to be around 7.3.
  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

TimestampCuratorActionNotes
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.
2026-09-02T07:37:55.460438+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.