geobacter_medium

CultureMech:003256 bacterial DEFINED LIQUID
Original name: GEOBACTER MEDIUM

Overview

External ontology
mediadive.medium:J907 (source link unavailable) — GEOBACTER MEDIUM
Applications
  • Microbial cultivation
pH
7.0
Notes
Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=907

Composition

flowchart LR
    CultureMech_003256["geobacter_medium"]
    ing0_KH2PO4["KH2PO4"]
    CultureMech_003256 --> ing0_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing0_KH2PO4 -.-> CHEBI_63036
    ing1_NH4Cl["NH4Cl"]
    CultureMech_003256 --> ing1_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing1_NH4Cl -.-> CHEBI_31206
    ing2_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_003256 --> ing2_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing2_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing3_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_003256 --> ing3_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing3_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing4_Sodium_acetate["Sodium acetate"]
    CultureMech_003256 --> ing4_Sodium_acetate
    CHEBI_32954["CHEBI:32954"]
    ing4_Sodium_acetate -.-> CHEBI_32954
    ing5_Na2SO4["Na2SO4"]
    CultureMech_003256 --> ing5_Na2SO4
    CHEBI_32149["CHEBI:32149"]
    ing5_Na2SO4 -.-> CHEBI_32149
    ing6_NaHCO3["NaHCO3"]
    CultureMech_003256 --> ing6_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing6_NaHCO3 -.-> CHEBI_32139
    ing7_Nitrilotriacetic_acid_trisodium_salt_monohydrate["Nitrilotriacetic acid trisodium salt monohydrate"]
    CultureMech_003256 --> ing7_Nitrilotriacetic_acid_trisodium_salt_monohydrate
    ing8_FeCl3_x_6_H2O["FeCl3 x 6 H2O"]
    CultureMech_003256 --> ing8_FeCl3_x_6_H2O
    CHEBI_86254["CHEBI:86254"]
    ing8_FeCl3_x_6_H2O -.-> CHEBI_86254
    ing9_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
    CultureMech_003256 --> ing9_Nitrilotriacetic_acid
    CHEBI_44557["CHEBI:44557"]
    ing9_Nitrilotriacetic_acid -.-> CHEBI_44557
    ing10_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
    CultureMech_003256 --> ing10_MnCl2_x_4_H2O
    CHEBI_86368["CHEBI:86368"]
    ing10_MnCl2_x_4_H2O -.-> CHEBI_86368
    ing11_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
    CultureMech_003256 --> ing11_CoCl2_x_6_H2O
    CHEBI_53503["CHEBI:53503"]
    ing11_CoCl2_x_6_H2O -.-> CHEBI_53503
    ing12_ZnCl2["ZnCl2"]
    CultureMech_003256 --> ing12_ZnCl2
    CHEBI_49976["CHEBI:49976"]
    ing12_ZnCl2 -.-> CHEBI_49976
    ing13_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
    CultureMech_003256 --> ing13_CuCl2_x_2_H2O
    CHEBI_86318["CHEBI:86318"]
    ing13_CuCl2_x_2_H2O -.-> CHEBI_86318
    ing14_H3BO3["H3BO3"]
    CultureMech_003256 --> ing14_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing14_H3BO3 -.-> CHEBI_33118
    ing15_NaCl["NaCl"]
    CultureMech_003256 --> ing15_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing15_NaCl -.-> CHEBI_26710
    ing16_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
    CultureMech_003256 --> ing16_NiCl2_x_6_H2O
    CHEBI_34887["CHEBI:34887"]
    ing16_NiCl2_x_6_H2O -.-> CHEBI_34887
    ing17_Na2SeO3_x_5_H2O["Na2SeO3 x 5 H2O"]
    CultureMech_003256 --> ing17_Na2SeO3_x_5_H2O
    CHEBI_131361["CHEBI:131361"]
    ing17_Na2SeO3_x_5_H2O -.-> CHEBI_131361
    ing18_Biotin["Biotin"]
    CultureMech_003256 --> ing18_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing18_Biotin -.-> CHEBI_15956
    ing19_Folic_acid["Folic acid"]
    CultureMech_003256 --> ing19_Folic_acid
    CHEBI_27470["CHEBI:27470"]
    ing19_Folic_acid -.-> CHEBI_27470
    ing20_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
    CultureMech_003256 --> ing20_Pyridoxine_hydrochloride
    CHEBI_30961["CHEBI:30961"]
    ing20_Pyridoxine_hydrochloride -.-> CHEBI_30961
    ing21_Thiamine_HCl["Thiamine HCl"]
    CultureMech_003256 --> ing21_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing21_Thiamine_HCl -.-> CHEBI_49105
    ing22_Riboflavin["Riboflavin"]
    CultureMech_003256 --> ing22_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing22_Riboflavin -.-> CHEBI_17015
    ing23_Nicotinic_acid["Nicotinic acid"]
    CultureMech_003256 --> ing23_Nicotinic_acid
    CHEBI_15940["CHEBI:15940"]
    ing23_Nicotinic_acid -.-> CHEBI_15940
    ing24_Calcium_pantothenate["Calcium pantothenate"]
    CultureMech_003256 --> ing24_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing24_Calcium_pantothenate -.-> CHEBI_31345
    ing25_Vitamin_B12["Vitamin B12"]
    CultureMech_003256 --> ing25_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing25_Vitamin_B12 -.-> CHEBI_176843
    ing26_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
    CultureMech_003256 --> ing26_p_Aminobenzoic_acid
    CHEBI_30753["CHEBI:30753"]
    ing26_p_Aminobenzoic_acid -.-> CHEBI_30753
    ing27_Lipoic_acid["Lipoic acid"]
    CultureMech_003256 --> ing27_Lipoic_acid
    CHEBI_16494["CHEBI:16494"]
    ing27_Lipoic_acid -.-> CHEBI_16494
    ing28_Na2WO4_x_2_H2O["Na2WO4 x 2 H2O"]
    CultureMech_003256 --> ing28_Na2WO4_x_2_H2O
    CHEBI_63939["CHEBI:63939"]
    ing28_Na2WO4_x_2_H2O -.-> CHEBI_63939

Ingredients (29)

# Ingredient Concentration Ontology Notes
1 KH2PO4
H2O4P.K 136.084 g/mol
0.133203 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
2 NH4Cl
Cl.H4N 53.492 g/mol
0.523996 G_PER_L CHEBI:31206
ammonium chloride
3 MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
0.199804 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
4 CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
0.243976 G_PER_L CHEBI:86158
calcium chloride dihydrate
 [Merged 2 duplicates: 0.143976, 0.1]
5 Sodium acetate
C2H3O2.Na 82.034 g/mol
0.803134 G_PER_L CHEBI:32954
sodium acetate
6 Na2SO4
2Na.O4S 142.043 g/mol
0.139079 G_PER_L CHEBI:32149
sodium sulfate
7 NaHCO3
CHO3.Na 84.006 g/mol
31.64 G_PER_L CHEBI:32139
sodium hydrogencarbonate
 [Merged 2 duplicates: 30.0, 1.64]
8 Nitrilotriacetic acid trisodium salt monohydrate 2.75 G_PER_L
9 FeCl3 x 6 H2O
Cl3Fe.6H2O 270.294 g/mol
4.050000000000001 G_PER_L CHEBI:86254
iron trichloride hexahydrate
 [Merged 2 duplicates: 2.7, 1.35]
10 Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
12.8 G_PER_L CHEBI:44557
nitrilotriacetic acid
11 MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
0.1 G_PER_L CHEBI:86368
manganese(II) chloride tetrahydrate
12 CoCl2 x 6 H2O
2Cl.Co.6H2O 237.929 g/mol
0.024 G_PER_L CHEBI:53503
cobalt chloride hexahydrate
13 ZnCl2
2Cl.Zn 136.296 g/mol
0.1 G_PER_L CHEBI:49976
zinc dichloride
14 CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
0.025 G_PER_L CHEBI:86318
copper(II) chloride dihydrate
15 H3BO3
H3BO3 61.833 g/mol
0.01 G_PER_L CHEBI:33118
boric acid
16 NaCl
Cl.Na 58.443 g/mol
1 G_PER_L CHEBI:26710
sodium chloride
17 NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
0.12 G_PER_L CHEBI:34887
nickel dichloride
18 Na2SeO3 x 5 H2O
5H2O.2Na.O3Se 263.012 g/mol
0.03 G_PER_L CHEBI:131361
disodium selenite pentahydrate
 [Merged 2 duplicates: 0.026, 0.004]
19 Biotin
C10H16N2O3S 244.316 g/mol
0.002 G_PER_L CHEBI:15956
biotin
20 Folic acid
C19H19N7O6 441.404 g/mol
0.002 G_PER_L CHEBI:27470
folic acid
21 Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
0.01 G_PER_L CHEBI:30961
pyridoxine hydrochloride
22 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.005 G_PER_L CHEBI:49105
thiamine hydrochloride
23 Riboflavin
C17H20N4O6 376.369 g/mol
0.005 G_PER_L CHEBI:17015
riboflavin
24 Nicotinic acid
C6H5NO2 123.111 g/mol
0.005 G_PER_L CHEBI:15940
nicotinic acid
25 Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.005 G_PER_L CHEBI:31345
Calcium pantothenate
26 Vitamin B12 0.0001 G_PER_L CHEBI:176843
vitamin B12
27 p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
0.005 G_PER_L CHEBI:30753
4-aminobenzoic acid
28 Lipoic acid
C8H14O2S2 206.332 g/mol
0.005 G_PER_L CHEBI:16494
lipoic acid
29 Na2WO4 x 2 H2O
2H2O.2Na.O4W 329.846 g/mol
0.004 G_PER_L CHEBI:63939
sodium tungstate dihydrate

Preparation

  1. Mix components thoroughly and autoclave under a N2-CO2 (80:20, v/v) gas mixture. After cooling, add aseptically and anaerobically the following solutions to the medium:
  2. Adjust pH to 7.0 - 7.2, if necessary.
  3. Firstly, dissolve NaHCO3 in 80 ml distilled water. Then, add NTA and FeCl3 x 6H2O to the solution and bring volume to 100 ml with distilled water. Adjust pH to 7.0 with NaOH. Filter-sterilize and store under a N2 atmosphere.
  4. Comment:
  5. 100 mM Fe NTA solution can be replaced with Iron(III)citrate solution (see Medium No. 1014, autoclaved and stored under N2).
  6. Dissolve nitrilotriacetic acid first in 200 ml of distilled water, and adjust pH to 6.5 with KOH. Then add the remaining salts and adjust volume to 1.0 L. Readjust pH to 7.0 with KOH.
  7. Comment: For strain JCM 10134, incubate with a 10-20% inoculum.

Target organisms

No target organisms are recorded.

Provenance

Merged from 1 source record.

TimestampCuratorActionNotes
2026-01-26T17:53:17.965976Z mediadive-import Imported from MediaDive Source: JCM, ID: J907
2026-03-13T03:09:44.195898Z data-quality-cleanup-v1.0 Data quality fixes Merged 4 duplicate ingredient(s)
2026-03-13T06:19:18.975025Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:003256
2026-03-17T06:30:57.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:32.872909+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "GEOBACTER MEDIUM" to "geobacter_medium" for consistent matching
2026-06-05T07:40:17.870403+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 28 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:46:43.161531+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.
2026-08-06T03:04:37.488290+00:00 merge_recipes.py MERGED_RECIPES merged 1 source recipe(s) on fingerprint 4a3a503821a36bcbf415f7fbff985e4adfc3b70aa2697bd929e586f69a2b40e7