Identification and ecophysiological understanding of new microbial players, processes, and multi-scale interactions in the global methane cycle 

Victoria J. Orphan, California Institute of Technology (Principal Investigator) 

Gene Tyson, University of Queensland (Co-Investigator)

Chris Kempes, Santa Fe Institute (Co-Investigator)

Mark Ellisman, University of California, San Diego (Co-Investigator)

Christof Meile, University of Georgia (Co-Investigator)

Robert Hettich, Oak Ridge National Laboratory (Co-Investigator)

Members of the Domain Archaea are key biological catalysts driving the global methane cycle. Methanogens produce an estimated 1 Gt of CH4 annually, with up to 80% of that methane oxidized by methanotrophic archaea in some environments. A remarkable number of recent paradigm-altering discoveries have dramatically changed our view of major phylogenetic players and syntrophic processes driving the methane cycle. These include the discovery of intact methanogenic pathways in reconstructed genomes of uncultured Bathyarchaeota from deep coal seams- a unique metabolic capability that has been exclusively ascribed to members of the Euryarchaeota- as well as new forms of cooperation and interactions between methane-oxidizing archaea and co-associated bacterial partners (for example, archaeal members of the Methanoperedenaceae (ANME-2d), gaining energy by coupling methane oxidation with nitrate reduction and the recent finding of interspecies extracellular electron transfer (EET) between diverse methanotrophic ANME archaea and physically associated sulfate-respiring bacterial partners.

The overarching scientific goal of this multi-disciplinary research proposal is to build on these recent discoveries and expand our understanding of the key microorganisms (players), metabolic strategies (processes), and interspecies relationships (interactions) involved in formation and oxidation of methane in the environment. Our four specific objectives are to 1) identify novel archaea and syntrophic microorganisms involved in methane cycling and examine their genomic characteristics and inferred metabolic potential; 2) explore potential new metabolisms of methane-oxidizing archaea (e.g. methanogenic/methanotrophic potential of Bathyarchaeota) using ‘omics and single-cell and subcellular resolved microscopy and analytical imaging techniques and test our recent hypothesis of energy conservation in anaerobic methane oxidation through extracellular electron transfer between ANME archaea and associated bacteria; 3) examine and model spatial patterns of cellular activity in structured archaeal-bacterial consortia (at the micron scale), to determine whether these patterns change depending on the nature of the specific metabolic interchange; and 4) empirically measure microorganism/microbial aggregate distribution and anabolic activity in the context of the surrounding environmental matrix (e.g. sediment particles) and model the relationship between the distribution of active methanotrophic consortia in sediment with predicted geochemical gradients and biogeochemical reactions occurring on the mm/cm-scale. 

These research goals will be accomplished through the optimization and application of novel metagenomic, transcriptomic, and proteomic techniques, state-of-the-art analytical imaging (ion, electron, light, and X-ray based), high-resolution stable isotope geochemistry, and reaction-transport modeling that spans spatial scales of nanometers to many millimeters. Our research plan is scalable and designed to elucidate processes and interactions within and between individual methane-metabolizing environmental microorganisms, while also building towards increasing levels of understanding of the collective processes in microbial communities, including the spatial complexity inherent in sedimentary ecosystems. Applied in tandem, these complementary multi-disciplinary approaches have the potential to provide a new and more holistic ‘eco-systems level’ understanding of factors which regulate methane cycling in anoxic sedimentary ecosystems.