Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol

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

doi:10.3389/fmicb.2019.02706

Title: Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using ¹³CO₂ and ¹³C-Methanol

Journal Article · Fri Dec 06 00:00:00 EST 2019 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2019.02706· OSTI ID:1582222

Li, Zhou ^[1]; Yao, Qiuming ^[2]; Guo, Xuan ^[2]; Crits-Christoph, Alexander ^[3]; Mayes, Melanie A. ^[2]; IV, William Judson Hervey ^[4]; Lebeis, Sarah L. ^[5]; Banfield, Jillian F. ^[3]; Hurst, Gregory B. ^[2]; Hettich, Robert L. ^[1]; Pan, Chongle ^[6]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of California, Berkeley, CA (United States)
Naval Research Lab. (NRL), Washington, DC (United States)
Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Univ. of Oklahoma, Norman, OK (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, 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.

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Research Organization:: Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: SC0020356; AC05-00OR22725; SC10010566; AC02-05CH11231

OSTI ID:: 1582222

Alternate ID(s):: OSTI ID: 1599789; OSTI ID: 1607201

Journal Information:: Frontiers in Microbiology, Vol. 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.; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 16 works

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Title: Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol

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Title: Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using ¹³CO₂ and ¹³C-Methanol