Hydrogen-oxidizing bacteria medium

CultureMech:007506 bacterial DEFINED LIQUID

Overview

External ontology
nbrc.medium:936 (source link unavailable) — NBRC Medium 936
Notes
Source: NBRC Medium 936 | Link: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=936 NBRC lists Hydrogen-oxidizing bacteria medium with KP buffer, MgCl2·6H2O, CaCl2·2H2O, NH4Cl, Na2S2O3, trace element and vitamin stocks, Na2CO3, and distilled water. The basal medium is dispensed under H2/CO2/O2, KP buffer is autoclaved separately under N2, vitamin solution is filter-sterilized, and inoculated vessels are pressurized to 150 kPa with H2/CO2/O2. NBRC does not list a final medium pH.

Composition

flowchart LR
    CultureMech_007506["Hydrogen-oxidizing bacteria medium"]
    ing0_KP_buffer_["KP buffer*"]
    CultureMech_007506 --> ing0_KP_buffer_
    ing1_MgCl2_6H2O["MgCl2·6H2O"]
    CultureMech_007506 --> ing1_MgCl2_6H2O
    CHEBI_86345["CHEBI:86345"]
    ing1_MgCl2_6H2O -.-> CHEBI_86345
    ing2_CaCl2_2H2O["CaCl2·2H2O"]
    CultureMech_007506 --> ing2_CaCl2_2H2O
    CHEBI_86158["CHEBI:86158"]
    ing2_CaCl2_2H2O -.-> CHEBI_86158
    ing3_NH4Cl["NH4Cl"]
    CultureMech_007506 --> ing3_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing3_NH4Cl -.-> CHEBI_31206
    ing4_Na2S2O3["Na2S2O3"]
    CultureMech_007506 --> ing4_Na2S2O3
    CHEBI_132112["CHEBI:132112"]
    ing4_Na2S2O3 -.-> CHEBI_132112
    ing5_Trace_elements_solution__["Trace elements solution**"]
    CultureMech_007506 --> ing5_Trace_elements_solution__
    ing6_Vitamin_solution___["Vitamin solution***"]
    CultureMech_007506 --> ing6_Vitamin_solution___
    ing7_Na2CO3["Na2CO3"]
    CultureMech_007506 --> ing7_Na2CO3
    CHEBI_29377["CHEBI:29377"]
    ing7_Na2CO3 -.-> CHEBI_29377
    ing8_Distilled_water["Distilled water"]
    CultureMech_007506 --> ing8_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing8_Distilled_water -.-> CHEBI_15377

Ingredients (9)

# Ingredient Concentration Ontology Notes
1 KP buffer* 10 ML_PER_L
2 MgCl2·6H2O
2Cl.6H2O.Mg 203.301 g/mol
0.75 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
3 CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
0.15 G_PER_L CHEBI:86158
calcium chloride dihydrate
4 NH4Cl
Cl.H4N 53.492 g/mol
0.54 G_PER_L CHEBI:31206
ammonium chloride
5 Na2S2O3
2Na.O3S2 158.111 g/mol
1.6 G_PER_L CHEBI:132112
sodium thiosulfate
6 Trace elements solution** 2 ML_PER_L
7 Vitamin solution*** 2 ML_PER_L
8 Na2CO3
CO3.2Na 105.988 g/mol
0.5 G_PER_L CHEBI:29377
sodium carbonate
9 Distilled water
H2O 18.015 g/mol
1 L CHEBI:15377
water

Preparation

  1. Mix ingredients except KP buffer and vitamin solution.
  2. Dispense the medium into suitable culture vessels under a stream of H2/CO2/O2 (75/20/5) and seal with butyl rubber stoppers.
  3. Separately autoclave KP buffer under an N2 atmosphere.
  4. Sterilize vitamin solution by filtration.
  5. Prior to inoculation, aseptically add KP buffer and vitamin solution.
  6. Pressurize inoculated vessels to 150 kPa with H2/CO2/O2 (75/20/5).
  7. For the trace elements solution, first dissolve NTA, adjust pH to 6.5 with NaOH, then add minerals; final pH is 7.0.

Solutions

KP buffer

Stock composition
IngredientConcentrationNotes
KH2PO4 119 G_PER_L
K2HPO4 21 G_PER_L
Distilled water 1 L

Trace elements solution

Stock composition
IngredientConcentrationNotes
Nitrilotriacetic acid (NTA) 12.8 G_PER_L
FeCl3·6H2O 1.35 G_PER_L
MnCl2·4H2O 0.1 G_PER_L
CoCl2·6H2O 0.024 G_PER_L
CaCl2·2H2O 0.1 G_PER_L
ZnCl2 0.1 G_PER_L
CuCl2·2H2O 0.025 G_PER_L
H3BO3 0.01 G_PER_L
Na2MoO4·2H2O 0.024 G_PER_L
NaCl 1 G_PER_L
NiCl2·6H2O 0.12 G_PER_L
Na2SeO4 0.004 G_PER_L
Na2WO4 0.004 G_PER_L
KAl(SO4)2·12H2O 0.02 G_PER_L
Distilled water 1 L
NaOH variable VARIABLE NBRC Medium 936 uses NaOH to adjust the trace elements solution to pH 6.5 before mineral addition.

Vitamin solution

Stock composition
IngredientConcentrationNotes
Biotin 2 MG_PER_L
Folic acid 2 MG_PER_L
Pyridoxine-HCl 10 MG_PER_L
Thiamine-HCl 5 MG_PER_L
Riboflavin 5 MG_PER_L
Nicotinic acid 5 MG_PER_L
Ca-pantothenate 5 MG_PER_L
p-Aminobenzoic acid 1 MG_PER_L
Vitamin B12 0.01 MG_PER_L
Distilled water 1 L

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-02-20T00:22:35.993417Z nbrc-import Imported from NBRC Source: NBRC, Media No. 936, URL: http://www.nbrc.nite.go.jp/NBRC2/NBRCMediumDetailServlet?NO=936. Imported via ethical web scraping.
2026-03-09T08:04:43.134031+00:00 solution-migrator-v1.0 Migrated solutions from ingredients to solutions array Moved 1 solution(s) from ingredients
2026-03-13T03:09:13.229494Z data-quality-cleanup-v1.0 Data quality fixes Merged 90 duplicate ingredient(s)
2026-03-13T06:19:49.288100Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007506
2026-03-14T00:00:00+00:00 schema-defaulter-v1.0 Applied schema defaults and normalizations Added default solution name
2026-05-16T09:03:06.751204+00:00 migrate_legacy_fields.py MIGRATED_LEGACY_FIELDS curation_history.date->timestamp=1
2026-08-19T21:54:23.081793+00:00 recover_nbrc_composition.py Recovered composition from source HTML Re-parsed the NBRC medium 936 composition table from the preserved scrape; 9 ingredient(s) restored, 3 stock solution(s) nested rather than flattened, 1 unparsed solution blob(s) removed (#299).
2026-08-20T19:01:16.166599+00:00 apply_mim_groundings.py Adopted MIM published grounding Grounded 18 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308).
2026-08-26T02:12:33.141574+00:00 apply_mim_groundings.py Adopted MIM published grounding Grounded 1 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308).
2026-09-11T00:00:00-07:00 repair_nbrc_937_score15.py RESOLVED_NBRC_937_SCORE15 Added the NBRC Medium 936 source term and official title, grounded the recovered formula and stocks, added the source-defined NaOH trace-stock adjuster, converted preparation instructions into ordered steps, and added the official NBRC reference.