期刊
FRONTIERS IN MICROBIOLOGY
卷 10, 期 -, 页码 -出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fmicb.2019.02706
关键词
stable isotope probing; metagenomic analyses; metaproteomic analysis; microbial ecology; rhizosphere
类别
资金
- U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research
- ORNL Plant-Microbe Interfaces Scientific Focus Area project
- DOE [DOE-SC10010566, DE-SC0020356]
- HASI program
- Naval Research Laboratory
- U.S. Department of Energy (DOE), Office of Science Early Career Award
- U.S. Department of Energy [DE-AC05-00OR22725]
- U.S. Department of Energy (DOE) [DE-SC0020356] Funding Source: U.S. Department of Energy (DOE)
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 (CO2)-C-13 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived C-13 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-13-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-13-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 C-13-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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