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Title: Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO 2 and 13C-Methanol

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 13CO 2 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.

Authors:
 [1];  [2];  [2];  [3];  [2];  [4];  [5];  [3];  [2];  [1];  [6]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Univ. of California, Berkeley, CA (United States)
  4. Naval Research Lab. (NRL), Washington, DC (United States)
  5. Univ. of Tennessee, Knoxville, TN (United States)
  6. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Univ. of Oklahoma, Norman, OK (United States)
Publication Date:
Research Org.:
Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1582222
Alternate Identifier(s):
OSTI ID: 1599789; OSTI ID: 1607201
Grant/Contract Number:  
SC0020356; AC05-00OR22725; SC10010566; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 10; Related Information: Metagenomic sequencing reads associated with this study have been deposited in BioProject under accession PRJNA488251. Mass spectrometry raw files for this study have been deposited in ProteomeXchange under accessions PXD011737, PXD011738, PXD011739, PXD011891, and PXD011892. MAGs recovered in this study can be downloaded from https://figshare.com/s/2a812c513ab14e6c8161.; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; metagenomic analyses; metaproteomic analysis; microbial ecology; rhizosphere; stable isotope probing

Citation Formats

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., and Pan, Chongle. Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol. United States: N. p., 2019. Web. doi:10.3389/fmicb.2019.02706.
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. Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol. United States. doi:10.3389/fmicb.2019.02706.
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., and Pan, Chongle. Fri . "Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol". United States. doi:10.3389/fmicb.2019.02706. https://www.osti.gov/servlets/purl/1582222.
@article{osti_1582222,
title = {Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol},
author = {Li, Zhou and Yao, Qiuming and Guo, Xuan and Crits-Christoph, Alexander and Mayes, Melanie A. and IV, William Judson Hervey and Lebeis, Sarah L. and Banfield, Jillian F. and Hurst, Gregory B. and Hettich, Robert L. and Pan, Chongle},
abstractNote = {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.},
doi = {10.3389/fmicb.2019.02706},
journal = {Frontiers in Microbiology},
issn = {1664-302X},
number = ,
volume = 10,
place = {United States},
year = {2019},
month = {12}
}

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