NLDM: A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria
Markus De Raad, Yifan V. Li, Jennifer V. Kuehl, Peter F. Andeer, Suzanne M. Kosina, Andrew Hendrickson, Nicholas R. Saichek, Amber N. Golini, La Zhen Han, Ying Wang, Benjamin P. Bowen, Adam M. Deutschbauer, Adam Arkin, Romy Chakraborty, Trent R. Northen
Defined medium
defined media
exometabolomics
liquid chromatography mass spectrometry
soil bacteria
R2A
Disclaimer
Abstract
This is the protocol for the preparation of NLDM medium as described in de Raad et al., 2022 - A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria.
The Northen Lab Defined Medium (NLDM) is a defined medium and thus suited for exometabolomic experiments. It is based on the metabolite composition of R2A and soil, metabolite usage by microbes, and biologically relevant elemental stoichiometry of these compounds. NLDM supports the growth of a wide range of phylogenetically diverse soil bacterial isolates and all of its metabolites are trackable through LC–MS/MS analysis. This demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities. We anticipate that the NLDM medium will enable the examination of microbial substrate utilization for a broad range of isolates both directly and through dilution and amendments. We speculate that this media may have additional value in supporting microbial isolations and additional types of microbial characterization.
Please cite NLDM as follows : de Raad M, Li YV, Kuehl JV, Andeer PF, Kosina SM, Hendrickson A, Saichek NR, Golini AN, Han LZ, Wang Y, Bowen BP, Deutschbauer AM, Arkin AP, Chakraborty R and Northen TR (2022) A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria. Front. Microbiol. 13:855331. DOI:10.3389/fmicb.2022.855331
Steps
NLDM Components
NLDM stock solutions
- See Materials section on how to prepare stock solutions
| A |
|---|
| Medium components |
| NLDM Solution 1 - 'Sugars' - 10X |
| NLDM Solution 2 - 'Organic_Acids' - 10X |
| NLDM Solution 3 - 'Amino_Acids' - 10X |
| NLDM Solution 4 - 'Nucleobases/Nucleosides' - 50X |
| NLDM Solution 5 - 'Other_Cpds' - 50X |
| NLDM Salt solution 1 - 'MgSO4' - 50X |
| NLDM Salt solution 2 - 'NH4Cl' - 50X |
| NLDM Salt solution 3 - 'CaCl2' - 50X |
| NLDM Salt solution 4 - 'PO4' - 50X |
| Vitamin solution - 100X |
| Trace Mineral solution - 100X |
NLDM PREPARATION
For the preparation of 500 mL NLDM medium mix the following stock solutions:
| A | B |
|---|---|
| Volume (mL) | |
| NLDM Solution 1 - 'Sugars' - 10X | 50 |
| NLDM Solution 2 - 'Organic_Acids' - 10X | 50 |
| NLDM Solution 3 - 'Amino_Acids' - 10X | 50 |
| NLDM Solution 4 - 'Nucleobases/Nucleosides' - 50X | 10 |
| NLDM Solution 5 - 'Other_Cpds' - 50X | 10 |
| NLDM Salt solution 1 - 'MgSO4' - 50X | 10 |
| NLDM Salt solution 2 - 'NH4Cl' - 50X | 10 |
| NLDM Salt solution 3 - 'CaCl2' - 50X | 10 |
| NLDM Salt solution 4 - 'PO4' - 50X | 10 |
| Vitamin solution - 100X | 5 |
| Trace Mineral solution - 100X | 5 |
| Milli-Q Water | 280 |
| TOTAL | 500 |
NLDM pH
Adjust the pH of the NLDM medium 7.0 - 7.2 if needed
STERILIZATION
Filter sterilize the NLDM medium using a 0.22 um filter
STORAGE
Store the NLDM medium at 4ºC in the dark
