Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using CO and C-Methanol.

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ID: 73013
2019
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Abstract
Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from CO to the rhizosphere communities of , , and . Rhizosphere microorganisms that assimilated plant-derived C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.
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li2019genomeresolvedfrontiers Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Li, Zhou;Yao, Qiuming;Guo, Xuan;Crits-Christoph, Alexander;Mayes, Melanie A;Iv, William Judson Hervey;Lebeis, Sarah L;Banfield, Jillian F;Hurst, Gregory B;Hettich, Robert L;Pan, Chongle;
Journal Frontiers in microbiology
Year 2019
DOI
10.3389/fmicb.2019.02706
URL
Keywords
rhizosphere microbial ecology stable isotope probing metagenomic analyses metaproteomic analysis

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