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

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2019 Dec 24

PMID 31866955

Citations 17

Authors

Zhou Li

Qiuming Yao

Xuan Guo

Alexander Crits-Christoph

Melanie A Mayes

William Judson Hervey IV

Sarah L Lebeis

Jillian F Banfield

Gregory B Hurst

Robert L Hettich

Chongle Pan

Affiliations

Soon will be listed here.

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 CO to the rhizosphere communities of , , and . Rhizosphere microorganisms that assimilated plant-derived C 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-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-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 C-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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