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

Published: 2022-08-13 DOI: 10.17504/protocols.io.14egn7o2yv5d/v1

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