desulfurococcus_amylolyticus_medium (CultureMech:002548)

Overview

External ontology

mediadive.medium:J187 (source link unavailable) — DESULFUROCOCCUS AMYLOLYTICUS MEDIUM

Applications

Microbial cultivation

pH range

{'min': 6.2, 'max': 6.4}

Notes

Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=187

Composition

flowchart LR
    CultureMech_002548["desulfurococcus_amylolyticus_medium"]
    ing0_NH4Cl["NH4Cl"]
    CultureMech_002548 --> ing0_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing0_NH4Cl -.-> CHEBI_31206
    ing1_KH2PO4["KH2PO4"]
    CultureMech_002548 --> ing1_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing1_KH2PO4 -.-> CHEBI_63036
    ing2_KCl["KCl"]
    CultureMech_002548 --> ing2_KCl
    CHEBI_32588["CHEBI:32588"]
    ing2_KCl -.-> CHEBI_32588
    ing3_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_002548 --> ing3_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing3_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing4_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_002548 --> ing4_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing4_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing5_NaCl["NaCl"]
    CultureMech_002548 --> ing5_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing5_NaCl -.-> CHEBI_26710
    ing6_Sulfur["Sulfur"]
    CultureMech_002548 --> ing6_Sulfur
    CHEBI_26833["CHEBI:26833"]
    ing6_Sulfur -.-> CHEBI_26833
    ing7_Resazurin["Resazurin"]
    CultureMech_002548 --> ing7_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing7_Resazurin -.-> CHEBI_8806
    ing8_Distilled_water["Distilled water"]
    CultureMech_002548 --> ing8_Distilled_water
    ing9_H2SO4["H2SO4"]
    CultureMech_002548 --> ing9_H2SO4

Ingredients (10)

#	Ingredient	Concentration	Ontology	Notes
1	NH4Cl Cl.H4N 53.492 g/mol		CHEBI:31206 ammonium chloride	Source batch input: 0.33 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.
2	KH2PO4 H2O4P.K 136.084 g/mol		CHEBI:63036 potassium dihydrogen phosphate	Source batch input: 0.33 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.
3	KCl Cl.K 74.551 g/mol		CHEBI:32588 potassium chloride	Source batch input: 0.33 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.
4	CaCl2 x 2 H2O Ca.2Cl.2H2O 147.014 g/mol		CHEBI:86158 calcium chloride dihydrate	Source batch input: 0.44 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.
5	MgCl2 x 6 H2O 2Cl.6H2O.Mg 203.301 g/mol		CHEBI:86345 magnesium dichloride hexahydrate	Source batch input: 0.7 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.
6	NaCl Cl.Na 58.443 g/mol		CHEBI:26710 sodium chloride	Source batch input: 0.5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.
7	Sulfur S 32.067 g/mol		CHEBI:26833 sulfur atom	Source batch input: 10 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. Source qualifier: powder.
8	Resazurin C12H7NO4 229.191 g/mol		CHEBI:8806 Resazurin	Source batch input: 1 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.
9	Distilled water	0.99 L		Source water batch input: 990 ml = 0.99 L. This is not a measured final volume. Prior duplicate-collapse notes describe the superseded flattened record.
10	H2SO4			Source-explicit pH adjustment with no fixed dose. Strength, when stated as 1 N, is retained in preparation text; no molarity is inferred.

Preparation

Mix ingredients, except yeast extract, peptone, vitamins, sulfur and Na2S x 9H2O, and autoclave under a N2-CO2 (80:20) atmosphere. Separately autoclave yeast extract and peptone as 10% solutions and Na2S x 9H2O as a 5% solution under a N2 atmosphere. Steam sulfur for 3 hr on each of 3 successive days. Filter-sterilize NaHCO3 as an 8% solution and vitamin solution while gassing with N2. Aseptically and anaerobically add yeast extract, peptone, NaHCO3 and vitamin solutions, and sulfur to the medium under a N2-CO2 (80:20) atmosphere. Prior to inoculation, add the sterile Na2S x 9H2O solution, and adjust pH to 6.2-6.4 with sterile 1 N H2SO4.

Solutions

FeCl2 solution

Dose: 0.001 L

Stock composition
Ingredient	Concentration	Notes
FeCl2 x 4 H2O	1.5 G_PER_L	Source stock batch input: 1.5 g. Retain provider-declared stock g_l=1.5 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Distilled water	0.99 L	Source water batch input: 990 ml = 0.99 L. This is not a measured final volume. Prior duplicate-collapse notes describe the superseded flattened record.

Source stock addition: 1 ml = 0.001 L per receiving batch, not grams per liter or a dose per final liter.

HCl reagent (7.7 M)

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
HCl	7.7 MOLAR	Explicit HCl reagent strength 7.7 M, not a final-medium concentration. The 25% basis is unspecified; the enclosing stock holds the 10 ml batch dose.

Source stock addition: 10 ml = 0.01 L per receiving batch, not grams per liter or a dose per final liter.

Trace element solution

Dose: 0.001 L

Stock composition
Ingredient	Concentration	Notes
ZnCl2	0.07 G_PER_L	Source stock batch input: 70 mg. Retain provider-declared stock g_l=0.07 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
MnCl2 x 4 H2O	0.1 G_PER_L	Source stock batch input: 100 mg. Retain provider-declared stock g_l=0.1 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
H3BO3	0.006 G_PER_L	Source stock batch input: 6 mg. Retain provider-declared stock g_l=0.006 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
CoCl2 x 6 H2O	0.19 G_PER_L	Source stock batch input: 190 mg. Retain provider-declared stock g_l=0.19 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
CuCl2 x 2 H2O	0.002 G_PER_L	Source stock batch input: 2 mg. Retain provider-declared stock g_l=0.002 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
NiCl2 x 6 H2O	0.024 G_PER_L	Source stock batch input: 24 mg. Retain provider-declared stock g_l=0.024 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Na2MoO4 x 2 H2O	0.036 G_PER_L	Source stock batch input: 36 mg. Retain provider-declared stock g_l=0.036 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Distilled water	1 L	Source water batch input: 1000 ml = 1 L. This is not a measured final volume. Prior duplicate-collapse notes describe the superseded flattened record.

Source stock addition: 1 ml = 0.001 L per receiving batch, not grams per liter or a dose per final liter.

Trace vitamins

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
Biotin	0.002 G_PER_L	Source stock batch input: 2 mg. Retain provider-declared stock g_l=0.002 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Folic acid	0.002 G_PER_L	Source stock batch input: 2 mg. Retain provider-declared stock g_l=0.002 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Pyridoxine hydrochloride	0.01 G_PER_L	Source stock batch input: 10 mg. Retain provider-declared stock g_l=0.01 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Thiamine HCl	0.005 G_PER_L	Source stock batch input: 5 mg. Retain provider-declared stock g_l=0.005 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Riboflavin	0.005 G_PER_L	Source stock batch input: 5 mg. Retain provider-declared stock g_l=0.005 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Nicotinic acid	0.005 G_PER_L	Source stock batch input: 5 mg. Retain provider-declared stock g_l=0.005 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Calcium pantothenate	0.005 G_PER_L	Source stock batch input: 5 mg. Retain provider-declared stock g_l=0.005 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Vitamin B12	0.0001 G_PER_L	Source stock batch input: 0.1 mg. Retain provider-declared stock g_l=0.0001 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
p-Aminobenzoic acid	0.005 G_PER_L	Source stock batch input: 5 mg. Retain provider-declared stock g_l=0.005 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Lipoic acid	0.005 G_PER_L	Source stock batch input: 5 mg. Retain provider-declared stock g_l=0.005 only, not a final-medium concentration or an independently verified final stock volume. Prior duplicate-merge notes describe the superseded flattened record.
Distilled water	1 L	Source water batch input: 1000 ml = 1 L. This is not a measured final volume. Prior duplicate-collapse notes describe the superseded flattened record.

Source stock addition: 10 ml = 0.01 L per receiving batch, not grams per liter or a dose per final liter.

NaHCO3 separately prepared solution

Stock composition
Ingredient	Concentration	Notes
NaHCO3		Source batch input: 0.8 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. This is the contribution specified for the receiving medium batch, not the mass for preparing an unspecified volume of stock.

The source specifies a separate percentage-labelled preparation but does not establish percentage basis or its addition volume. No numeric stock strength or dose is asserted. Composition notes record the receiving-batch contribution only.

Yeast extract separately prepared solution

Stock composition
Ingredient	Concentration	Notes
Yeast extract		Source batch input: 0.2 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. This is the contribution specified for the receiving medium batch, not the mass for preparing an unspecified volume of stock. Source qualifier: BD-Difco.

Bacto peptone separately prepared solution

Stock composition
Ingredient	Concentration	Notes
Bacto peptone		Source batch input: 5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. This is the contribution specified for the receiving medium batch, not the mass for preparing an unspecified volume of stock. Source qualifier: BD-Difco.

Na2S x 9 H2O separately prepared solution

Stock composition
Ingredient	Concentration	Notes
Na2S x 9 H2O		Source batch input: 0.5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. This is the contribution specified for the receiving medium batch, not the mass for preparing an unspecified volume of stock.

Target organisms

No target organisms are recorded.

Provenance

Timestamp	Curator	Action	Notes
2026-01-26T17:53:15.907871Z	mediadive-import	Imported from MediaDive	Source: JCM, ID: J187
2026-03-13T06:19:14.083603Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:002548
2026-03-17T06:30:23.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:27.282172+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "DESULFUROCOCCUS AMYLOLYTICUS MEDIUM" to "desulfurococcus_amylolyticus_medium" for consistent matching
2026-06-05T07:40:58.344702+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 29 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:46:56.243904+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.
2026-10-08T13:52:57.998884+00:00	codex	RESTORED_JCM_STOCK_PREPARATION_BOUNDARIES_WITH_EVIDENCE	Restored preparation boundaries and explicit stock-dose bases. Preserved source-specific conflicts, chemical annotations and earlier history. Batch-mass notes do not assert final concentrations; provider-declared stock rates remain qualified. No growth or identity equivalence claim inferred.