freshwater_iron_gel_medium

CultureMech:003011 bacterial DEFINED LIQUID
Original name: FRESHWATER IRON GEL MEDIUM

Overview

External ontology
mediadive.medium:J665 (source link unavailable) — FRESHWATER IRON GEL MEDIUM
Applications
  • Microbial cultivation
pH
7.0
Notes
Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=665

Composition

flowchart LR
    CultureMech_003011["freshwater_iron_gel_medium"]
    ing0_NaHCO3["NaHCO3"]
    CultureMech_003011 --> ing0_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing0_NaHCO3 -.-> CHEBI_32139
    ing1_NH4Cl["NH4Cl"]
    CultureMech_003011 --> ing1_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing1_NH4Cl -.-> CHEBI_31206
    ing2_NaH2PO4_x_H2O["NaH2PO4 x H2O"]
    CultureMech_003011 --> ing2_NaH2PO4_x_H2O
    CHEBI_37585["CHEBI:37585"]
    ing2_NaH2PO4_x_H2O -.-> CHEBI_37585
    ing3_KCl["KCl"]
    CultureMech_003011 --> ing3_KCl
    CHEBI_32588["CHEBI:32588"]
    ing3_KCl -.-> CHEBI_32588
    ing4_Na2SeO4["Na2SeO4"]
    CultureMech_003011 --> ing4_Na2SeO4
    CHEBI_77775["CHEBI:77775"]
    ing4_Na2SeO4 -.-> CHEBI_77775
    ing5_FeCl2["FeCl2"]
    CultureMech_003011 --> ing5_FeCl2
    CHEBI_30812["CHEBI:30812"]
    ing5_FeCl2 -.-> CHEBI_30812
    ing6_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_003011 --> ing6_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing6_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing7_Sodium_acetate["Sodium acetate"]
    CultureMech_003011 --> ing7_Sodium_acetate
    CHEBI_32954["CHEBI:32954"]
    ing7_Sodium_acetate -.-> CHEBI_32954
    ing8_Biotin["Biotin"]
    CultureMech_003011 --> ing8_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing8_Biotin -.-> CHEBI_15956
    ing9_Folic_acid["Folic acid"]
    CultureMech_003011 --> ing9_Folic_acid
    CHEBI_27470["CHEBI:27470"]
    ing9_Folic_acid -.-> CHEBI_27470
    ing10_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
    CultureMech_003011 --> ing10_Pyridoxine_hydrochloride
    CHEBI_30961["CHEBI:30961"]
    ing10_Pyridoxine_hydrochloride -.-> CHEBI_30961
    ing11_Thiamine_HCl["Thiamine HCl"]
    CultureMech_003011 --> ing11_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing11_Thiamine_HCl -.-> CHEBI_49105
    ing12_Riboflavin["Riboflavin"]
    CultureMech_003011 --> ing12_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing12_Riboflavin -.-> CHEBI_17015
    ing13_Nicotinic_acid["Nicotinic acid"]
    CultureMech_003011 --> ing13_Nicotinic_acid
    CHEBI_15940["CHEBI:15940"]
    ing13_Nicotinic_acid -.-> CHEBI_15940
    ing14_DL_Calcium_pantothenate["DL-Calcium pantothenate"]
    CultureMech_003011 --> ing14_DL_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing14_DL_Calcium_pantothenate -.-> CHEBI_31345
    ing15_Vitamin_B12["Vitamin B12"]
    CultureMech_003011 --> ing15_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing15_Vitamin_B12 -.-> CHEBI_176843
    ing16_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
    CultureMech_003011 --> ing16_p_Aminobenzoic_acid
    CHEBI_30753["CHEBI:30753"]
    ing16_p_Aminobenzoic_acid -.-> CHEBI_30753
    ing17_Lipoic_acid["Lipoic acid"]
    CultureMech_003011 --> ing17_Lipoic_acid
    CHEBI_16494["CHEBI:16494"]
    ing17_Lipoic_acid -.-> CHEBI_16494

Ingredients (18)

# Ingredient Concentration Ontology Notes
1 NaHCO3
CHO3.Na 84.006 g/mol
119.048 G_PER_L CHEBI:32139
sodium hydrogencarbonate
2 NH4Cl
Cl.H4N 53.492 g/mol
11.9048 G_PER_L CHEBI:31206
ammonium chloride
3 NaH2PO4 x H2O
H2O4P.Na 119.976 g/mol
28.5714 G_PER_L CHEBI:37585
sodium dihydrogenphosphate
4 KCl
Cl.K 74.551 g/mol
4.7619 G_PER_L CHEBI:32588
potassium chloride
5 Na2SeO4
2Na.O4Se 188.936 g/mol
1 G_PER_L CHEBI:77775
sodium selenate
6 FeCl2
Cl2Fe 126.751 g/mol
0.1 G_PER_L CHEBI:30812
iron dichloride
7 CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
0.1 G_PER_L CHEBI:86158
calcium chloride dihydrate
8 Sodium acetate
C2H3O2.Na 82.034 g/mol
0.1 G_PER_L CHEBI:32954
sodium acetate
9 Biotin
C10H16N2O3S 244.316 g/mol
0.02 G_PER_L CHEBI:15956
biotin
10 Folic acid
C19H19N7O6 441.404 g/mol
0.002 G_PER_L CHEBI:27470
folic acid
11 Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
0.01 G_PER_L CHEBI:30961
pyridoxine hydrochloride
12 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.005 G_PER_L CHEBI:49105
thiamine hydrochloride
13 Riboflavin
C17H20N4O6 376.369 g/mol
0.005 G_PER_L CHEBI:17015
riboflavin
14 Nicotinic acid
C6H5NO2 123.111 g/mol
0.005 G_PER_L CHEBI:15940
nicotinic acid
15 DL-Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.005 G_PER_L CHEBI:31345
Calcium pantothenate
16 Vitamin B12 0.0001 G_PER_L CHEBI:176843
vitamin B12
17 p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
0.005 G_PER_L CHEBI:30753
4-aminobenzoic acid
18 Lipoic acid
C8H14O2S2 206.332 g/mol
0.005 G_PER_L CHEBI:16494
lipoic acid

Preparation

  1. Add components to distilled water, bring volume to 1.0 L and adjust pH to 7.0. Distribute the medium into culture vessels under a N2-CO2 (4:1, v/v) gas mixture, sparge with the same gas mixture for 10 - 15 min, seal with butyl rubber stoppers and autoclave. Before inoculation, add the following sterile solutions (autoclaved and stored under a N2 gas atmosphere) to the medium (per 10 ml of medium):
  2. Dissolve 108 g FeCl3 in 1.0 L distilled water. Adjust pH to 7.0 with 10 N NaOH. Allow the suspension to sit for 30 min, then readjust pH to 7.0. Centrifuge the suspension at 5,000 x g for 20 min and pour off supernatant. Wash the precipitate with distilled water by resuspending in distilled water followed by the centrifugation. Repeat the washing at least 5 times, then, resuspend in 1.0 L distilled water. Use the Fe(III) suspension as 0.67 M solution. More precisely, check the concentration of Cl- to be less than 1 mM and determine the concentration of Fe(III) by using hydroxylamine as described by Lovley and Phillips (Appl. Environ. Microbiol. 54, 751-757, 1986).
  3. Use Trace minerals of Medium No. 151 supplemented with 0.025 g (final) Na2MoO4 x 2H2O, 0.024 g NiCl2 x 6H2O and 0.025 g Na2WO4 x 2H2O (per liter).
  4. Comment: For strain JCM 12378, inoculate with a 10% inoculum.

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-26T17:53:17.224181Z mediadive-import Imported from MediaDive Source: JCM, ID: J665
2026-03-13T06:19:17.130271Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:003011
2026-03-17T06:30:55.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:30.781146+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "FRESHWATER IRON GEL MEDIUM" to "freshwater_iron_gel_medium" for consistent matching
2026-06-05T07:41:05.451105+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 17 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:37:34.889618+00:00 primary-term-regrounding-v1.0 Re-grounded wrong primary term id (OAK-verified) 1 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.
2026-06-10T07:46:58.793712+00:00 primary-term-label-canonicalization-v1.0 Canonicalized primary term label to OBO canonical (OAK) 2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.