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 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C 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. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-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.
Highlights
Plants release a substantial fraction of their photosynthetically fixed carbon from roots into rhizosphere as carbohydrates, amino acids, organic acids, and other compounds (Zhalnina et al, 2018)
The 12 rhizosphere soil samples (3 plant species X 2 timepoints X 2 replicates) and 2 initial soil samples as the controls were measured with metagenomics and metaproteomics (Butterfield et al, 2016; Yao et al, 2018)
The metaproteomics measurements identified an average of 5,287 unlabeled microbial proteins or protein groups per soil sample with protein false discovery rates (FDRs) all less than 2% (Supplementary Table 1)
Summary
Plants release a substantial fraction of their photosynthetically fixed carbon from roots into rhizosphere as carbohydrates, amino acids, organic acids, and other compounds (Zhalnina et al, 2018). These carbon substrates can be consumed by microorganisms in the rhizosphere communities. In previous studies (Lu and Conrad, 2005; Vandenkoornhuyse et al, 2007; el Zahar Haichar et al, 2008; Drigo et al, 2010), 13C-labeled DNAs and RNAs were isolated by density gradient ultracentrifugation and amplicon-sequenced to identify the microbial taxa that assimilated 13C in rhizosphere communities. A genome-resolved metagenomic approach was implemented in a DNA SIP study which recovered a complete genome for Saccharibacteria (TM7) from the rhizosphere of wild oats (Starr et al, 2018)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
