Characterizing the ecophysiologies of uncultured syntrophic associations driving anaerobic methane oxidation: applications of targeted meta'omics and multi-modal analytical imaging of diverse archaeal-bacterial consortia
EMSL Project ID
49956
Abstract
The main objective of this work is to combine the molecular, elemental and cryo-electron imaging and metaproteomics available at EMSL with the single cell genomics pipeline at the JGI in a highly parallelized analysis of individual uncultured methanotrophic consortia. These syntrophic consortia consist of 2 organisms, an anaerobic methanotrophic (ANME) archaea, and a sulfate-reducing bacteria (SRB) which together carry out the anaerobic oxidation of methane (AOM) coupled to sulfate reduction. While each AOM consortia nominally consists of only one ANME and one SRB species, many different ANME and SRB subgroups coexist in the same habitat, resulting in a myriad of partnerships and community structures represented in the environment. A major hurdle remaining in our understanding of the biological underpinnings of AOM is our inability to correlate multiple analytical imaging techniques on individual phylogenetically well-defined aggregates. Previously, our uncoupled observations have led to preliminary generalized models of the syntrophic association for AOM, and how consortia may respond to environmental perturbations, but unfortunately many of the techniques applied to this system are incompatible with each other (e.g. traditional TEM ultrastructure characterization and genomic analysis), which has prevented direct correlation of genomic data with the phenotypic and ultrastructural properties of AOM consortia that are of great value in better understanding their ecology and impact on the methane cycle. Here we propose a targeted sample processing pipeline that builds on the expertise and resources available at the EMSL and the JGI to directly correlate multiple analytical imaging techniques on parallel thin sections of the same AOM consortium, including cryo-EM, ToF-SIMS, nanoSIMS and EDX along with corresponding genomic data. This proposal will leverage our current work with EMSL and the JGI that is developing protocols for activity-based FAC sorting and sequencing of consortia combined with small-scale metaproteomics. The instrumentation available at EMSL through the microscopy and mass spectrometry groups makes this facility uniquely suited to support the analytical imaging and proteomics for this proposal, and the cell isolation and systems analysis (CISA) capability further allows for integration of these samples into the JGI single cell genome pipeline.
Project Details
Project type
FICUS Research
Start Date
2017-10-01
End Date
2019-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members