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Tracking carbon flow through syntrophic interspecies interactions in methanogenic microbiomes


EMSL Project ID
51366

Abstract

Determining in situ metabolic processes and interactions among diverse assemblages of microorganisms remains a critical challenge in microbial ecology. Consequently, identifying novel genes and metabolic pathways among poorly-characterized and candidate division microorganisms remains difficult, but is an essential component to unravel nutrient and carbon fluxes impacting global biogeochemical cycles and engineered bioprocesses. Methanogenic environments are excellent ecosystems to explore microbial interactions due to the thermodynamic constraints and obligate interdependencies (e.g., syntrophy) associated with many forms of anaerobic metabolism. Metaproteomics is a promising technique that can elucidate the ecophysiology and in situ metabolic capabilities of uncultivated microorganisms by sequencing the bulk protein pool of microbiomes. The combination of stable isotope probing (SIP) with metaproteomics using labelled (i.e. 13C) substrates further allows for the identification of isotope incorporation into individual microbiome members, and thus provides additional evidence for novel functional protein identification. Here, we seek to collaborate with EMSL to develop a new approach for SIP-based metaproteomics that utilizes click-chemistry with non-canonical amino acids to enrich for newly translated proteins, and thus improves labeled peptide detection by minimizing background proteins that interfere with the desired biological signal. We will apply this new approach to examine novel genomic mechanisms of syntrophic interspecies carbon processing involved in methane production in a full-scale engineered anaerobic digester bioreactor, as well as in a hypersaline meromictic lake. By coupling time-series peptide labeling measurements with metabolomic profiling and deep metagenomic sequencing, we will incorporate these datasets into community-level models that predict carbon fluxes through uncultivated taxa within anaerobic environments. The datasets resulting from this project will help to elucidate genome-resolved metabolic responses of syntrophic bacteria-archaea partnerships in diverse anaerobic ecosystems, ultimately identifying novel genes involved in metabolic adaptation and interspecies cooperation. This work will also benefit other DOE research programs focusing on microbial community interactions by developing a new targeted proteomics technique that improves our resolution of currently uncharacterized metabolic networks involved in bioenergy production and biogeochemical cycling.

Project Details

Project type
Large-Scale EMSL Research
Start Date
2020-10-01
End Date
2022-09-30
Status
Closed

Team

Principal Investigator

Ryan Ziels
Institution
The University of British Columbia

Co-Investigator(s)

Steven Hallam
Institution
The University of British Columbia

Team Members

Elizabeth McDaniel
Institution
The University of British Columbia

Brandon Kieft
Institution
The University of British Columbia

Daniel Mulat
Institution
The University of British Columbia

Hugh Mitchell
Institution
Pacific Northwest National Laboratory