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Front. Microbiol. | doi: 10.3389/fmicb.2019.02706

Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities using 13CO2 and 13C-methanol

Zhou Li1, 2,  Quiming Yao1,  Xuan Guo2, Alexander Crits-Christoph3,  Melanie A. Mayes1,  William J. Hervey IV4, Sarah L. Lebeis2,  Jillian F. Banfield3, Gregory B. Hurst1,  Robert L. Hettich1 and  Chongle Pan5*
  • 1Oak Ridge National Laboratory (DOE), United States
  • 2The University of Tennessee, Knoxville, United States
  • 3University of California, Berkeley, United States
  • 4United States Naval Research Laboratory, United States
  • 5University of Oklahoma, United States

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 we show the integration of proteomic SIP with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This new approach, called Genome-REsolved Proteomic Stable Isotope Probing (GREP SIP), 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 GREP 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 GREP SIP for functional characterization of active microorganisms in complex microbial communities.

Keywords: Stable isotope probing (SIP), Metagenomic analyses, Metaproteomic analysis, microbial ecology, rhizosphere

Received: 16 Jul 2019; Accepted: 08 Nov 2019.

Copyright: © 2019 Li, Yao, Guo, Crits-Christoph, Mayes, Hervey IV, Lebeis, Banfield, Hurst, Hettich and Pan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Chongle Pan, University of Oklahoma, Norman, United States, cpan@ou.edu