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DSMZ

DSMZ 1630e . Synthetic Crenarchaeota Medium (SCM)

Official DSMZ medium: This medium was manually curated by experts from the DSMZ.

Culture medium recipe

Vol.
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Medium for Nitrosopumilus zosterae DSM 116344

* Modification: add from sterile filtered stock solution 5 mL/L alpha-ketoglutamate (20 mM)

The modifications for this strain were extracted automatically and have not been curated by experts, yet.
Growth conditions: 7-14 days aerobic 28 °C pH 7.50

Basic salt water medium #

ml
Equipment needed: Autoclave Filter
Compound Amount Unit Conc. [g/L] Conc. [mM]
NaCl 26.0 g 26 444.901
MgSO4 x 7 H2O 5.0 g 5 20.286
MgCl2 x 6 H2O 5.0 g 5 24.594
CaCl2 x 2 H2O 1.5 g 1.5 10.203
KBr 0.1 g 0.1 0.84
NaHCO3 buffer (1M) 2.0 ml - -
HEPES buffer solution 10.0 ml - -
KH2PO4 solution (2.93 nM) 5.0 ml - -
Trace element solution (Nitrososphaera) 1.0 ml - -
FeNaEDTA solution (7.5 mM) 1.0 ml - -
NH4Cl (1 M) 2.0 ml - -
Double distilled water 1000.0 ml - -
alpha-ketoglutamate solution (20mM)* 5.0 ml - -
1 Incubate all used glass ware and magnetic stirring rods in 0.1 M HCl and rinse 3x with double distilled water to remove residual detergents (always check visual for soap bubbles).
2 Autoclave the basic salt water medium and cool to room temperature. This medium should be free of any precipitations!
3 Aseptically, add per L of basic salt water medium the following solutions from sterile stocks (do not store complemented SCM): Trace element solution (Nitrososphaera), FeNaEDTA solution, NaHCO3 solution, HEPES buffer solution, NH4Cl solution, KH2PO4 solution
4 Adjust pH to 7.6.

HEPES buffer solution #

1000
Solution occurs in 3 other media (first defined in Medium 1630).
Compound Amount Unit Conc. [g/L] Conc. [mM]
NaOH
(pellets) 		24.0 g 24 600.045
HEPES
(free acid) 		238.4 g 238.4 1000.42
Distilled water 1000.0 ml - -
1 Fist dissolve NaOH in ca 600 ml water, then add HEPES, adjust pH to 7.5 and fill up to 1000 ml volume.

Trace element solution (Nitrososphaera) #

1000
Solution occurs in 3 other media (first defined in Medium 1630c).
Equipment needed: Filter
Compound Amount Unit Conc. [g/L] Conc. [mM]
HCl
(12.5M) 		8 mL 3.646 100
H3BO3 30 mg 0.03 0.485
MnCl2 x 4 H2O 100 mg 0.1 0.505
CoCl2 x 6 H2O 190 mg 0.19 1.463
NiCl2 x 6 H2O 24 mg 0.024 0.185
CuCl2 x 2 H2O 2 mg 0.002 0.012
ZnSO4 x 7 H2O 144 mg 0.144 0.501
Na2MoO4 x 2 H2O 36 mg 0.036 0.149
Double distilled water 1000 ml - -
1 This solution contains no iron! Sterilise by autoclaving or filtration (0.2 µm) and store in the dark at 4 °C.

FeNaEDTA solution (7.5 mM) #

1000
Solution occurs in 3 other media (first defined in Medium 1630c).
Equipment needed: Filter
Compound Amount Unit Conc. [g/L] Conc. [mM]
FeNa-EDTA 2753 mg 2.753 -
Double distilled water 1000 ml - -
1 Sterilise by filtration (0.2 µm) and store in the dark at 4 °C.

NaHCO3 buffer (1M) #

50
Solution occurs in 2 other media (first defined in Medium 1630c).
Equipment needed: Filter
Compound Amount Unit Conc. [g/L] Conc. [mM]
NaHCO3 4.2 g 84 999.917
Double distilled water 50.0 ml - -
1 Dissolve 4.2 g of NaHCO3 in 50 mL Double distilled water (use a small beaker with stirring rod to dissolve) and sterilize by filtration (0.2 µm) in the laminar flow hood. Store in a sterile 50 mL falcon tube at 4 °C. Avoid high headspace to liquid ratios to ensure stable concentration.

NH4Cl (1 M) #

50
Solution occurs in 3 other media (first defined in Medium 1630c).
Equipment needed: Filter
Compound Amount Unit Conc. [g/L] Conc. [mM]
NH4Cl 2.67 g 53.4 998.317
Double distilled water 50.00 ml - -
1 Dissolve 2.67 g ammonium chloride in 50 mL Double distilled water.
2 Filtrate (0.2 µm).

KH2PO4 solution (2.93 nM) #

1000
Equipment needed: Autoclave
Compound Amount Unit Conc. [g/L] Conc. [mM]
KH2PO4 0.4 g 0.4 2.939
Double distilled water 1000.0 ml - -

alpha-ketoglutamate solution (20mM) #

1000
Compound Amount Unit Conc. [g/L] Conc. [mM]
alpha-ketoglutamate 20 mM - 20
Double distilled water 1000 ml - -

Metadata

Last modified: 17.11.23
Source: MediaDive: DSMZ
Taxonomic range:  Archaea
Medium type: Defined medium
Final pH: 7.6
Equipment needed: Autoclave, Filter
Reference: doi.org/10.1038/nature03911
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Associated strains

All strains for this medium: 1
Strains with modifications: 1
Nitrosopumilus zosterae DSM 116344

+  5 ml alpha-ketoglutamate solution (20mM)

Molecular composition

Compound Conc. [g/L] Conc. [mM]
NaCl 26 444.901
MgCl2 x 6 H2O 5 24.594
MgSO4 x 7 H2O 5 20.286
HEPES 2.384 10.004
CaCl2 x 2 H2O 1.5 10.203
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Cultivation metadata from 1 strains BacDive

phyla 1 1 strain