Resolving carbon fluxes within microbial communities inhabiting full-scale bioenergy facilities
EMSL Project ID
51515
Abstract
Elucidating the physiology and metabolic function of uncultivated microorganisms in their in situ environment remains a critical challenge in microbial ecology. This knowledge gap obfuscates attempts to model inter-organismal interactions and metabolic network topology to predict fluxes of carbon and nutrients through microbiomes important to bioenergy production and biogeochemical cycling. Methanogenic environments are excellent ecosystems with which to examine the importance of inter-organismal interactions to metabolic functioning, due to known thermodynamic constraints and obligate interdependencies (e.g. syntrophy) associated with many forms of anaerobic metabolisms. Methanogenic microbiomes also play a central role in the engineered anaerobic digestion (AD) process, a biotechnology with the potential to convert biomass feedstocks into renewable natural gas (RNG) that can be distributed into the existing energy grid. In many full-scale AD microbiomes, the majority of carbon flows through uncharacterized communities of syntrophic acetate oxidizing bacteria that provide electrons to hydrogenotrophic archaea. Here, we propose to utilize a suite of multi-omic approaches that expand our quantitative understanding of the inter-organismal carbon fluxes involved in syntrophic acetate oxidation within full-scale AD bioenergy facilities. We will leverage an existing research partnership with the Surrey Biofuel Facility (British Columbia), a full-scale AD bioenergy plant, to answer three driving questions: (1.) What organisms are responsible for SAO in full-scale anaerobic digestion systems? (2.) What metabolic pathways or novel enzymes are associated with SAO activity? (3.) Is the carbon flux through the SAO pathway limited by the growth kinetics of syntrophic bacteria, or rather methanogenic archaea? We will answer these questions by collaborating with scientists at the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI) to develop new applications of molecular biology tools that leverage stable isotope probing and amino acid tagging to enable quantitative measurements of carbon flux through uncharacterized microbial populations. Metagenomic sequencing, fluorescence activated cell sorting of active microbial cells, and gene synthesis requested at the JGI will be paired with amino-acid tagging based stable isotope measurements of peptides at the single-cell and community levels at EMSL. The quantitative multi-omic isotope labeling data will be coupled with metabolomics and activity measurements to calibrate a community-scale metabolic model for carbon flow through discrete taxa within the methanogenic consortia. The concerted resources requested from the JGI and EMSL will expand our predictive toolkit for uncovering in situ physiologies and modelling a variety of microbiomes that are central to biofuel production and biogeochemical cycling.
Project Details
Project type
FICUS Research
Start Date
2020-10-01
End Date
N/A
Status
Active
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Team Members