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A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria

Authors: Markus de Raad; Yifan V. Li; Jennifer V. Kuehl; Peter F. Andeer; Suzanne M. Kosina; Andrew Hendrickson; Nicholas R. Saichek; +10 Authors

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria

Abstract

Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.

Country
United States
Keywords

570, Environmental Science and Management, liquid chromatography mass spectrometry, Medical Biochemistry and Metabolomics, Microbiology, 630, 0605 Microbiology (for), 32 Biomedical and Clinical Sciences (for-2020), R2A, defined media, 31 Biological Sciences (for-2020), Biomedical and Clinical Sciences, 3107 Microbiology (for-2020), soil bacteria, 0503 Soil Sciences (for), exometabolomics, Biological Sciences, Medical microbiology, 3205 Medical Biochemistry and Metabolomics (for-2020), 3207 Medical microbiology (for-2020), QR1-502, Infectious Diseases, 0502 Environmental Science and Management (for), Infectious Diseases (rcdc), Soil Sciences

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    Top 10%
    influence
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    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
20
Top 10%
Average
Top 10%
Green
gold