Activity-based Protein Capture of Archaeal Enzymes to Constrain Physiological Activity and Their Role in Global Methane Cycling
EMSL Project ID
39918
Abstract
Methane is a potent greenhouse gas, capable of absorbing and releasing 25 times more heat to the atmosphere per molecule than carbon dioxide. A significant fraction of methane on Earth is biologically produced by methanogenic archaea, a diverse assemblage of microorganisms that flourish in a wide variety of anaerobic environments. While microbial methanogenesis is often considered the terminal step in carbon flow of many anaerobic habitats, it is clear that microbially-mediated methane consumption plays a key role in global methane cycling. In anaerobic environments, methane consumption is mediated by methanogen-like archaea that apparently couple the oxidation of methane to the reduction of sulfate and other oxidants. It is likely that archaeal methanotrophs play a major role in minimizing methane release to the atmosphere from the ocean. Of the 70-300 Tg of methane produced in marine sediments, only 5-20 Tg/yr is released to seawater. According to these estimates, at least 70% of marine methane is oxidized within the anoxic sediments. Particularly high rates of methane consumption are found in anoxic basins and sediments associated with methane and hydrocarbon seeps, where methane consumption is accompanied by high rates of sulfate reduction. Notably, recent research (including ongoing efforts in our lab) suggest that the distinction between methanogens and methanotrophs may not be as clear as previously thought. Many studies of lipid carbon isotopic composition imply that archaea may be capable of facultatively producing or consuming methane. However, lipid carbon isotope ratios offer limited phylogenetic resolution, and such these data cannot be used to discern which 'species' (ribotype) are capable of facultative methane metabolism. Our own experiments -in which we were able to enrich particular methanogen-like archaea in a laboratory system- also suggest that canonical methanotrophs are capable of methanogenesis. However, no technology exists that provides sufficient resolution to definitively assess whether particular archaea are making or oxidizing methane in situ. In the absence of this ability, we cannot constrain the role that these ubiquitous and active archaea have on the marine and global methane cycle.
As such, we propose to develop a method for the separation and analysis of the 13C content of proteins from different species of methanogenic archaea, focusing on the abundant methyl-coenzyme reductase protein encoded by the mcr operon. Our objective is to develop an activity-based chemical probing system to enable investigators to distinguish the direction of methane cycling by particular ribotypes in a diverse archaeal community. As mentioned, there are gigatons of methane missing from the marine methane cycle, and existing technologies have not been able to effectively constrain this phenomenon. The research proposed here will provide investigators with the means to characterize the physiological state (methanogenesis or methanotrophy) of key archaeal groups via activity-based chemical probing.
This project falls squarely within the Geochemisty/Biogeochemistry science theme in that it seeks to investigate and quantify the transformation of methane and carbon dioxide - both anthropogenic greenhouse gases - by microbes in natural environments. The proposed research is highly in line with the EMSL's overarching mission to support 'world-class research in the biological, chemical, and environmental sciences to provide innovative solutions to the nation's environmental challenges as well as those related to energy production.' The outcome of this project will enable us to develop a more quantitative understanding of the role of key microbial ribotypes in biogeochemical methane cycling. The application of this tool will provide valuable insight into the formation and destruction of marine gas reservoirs as DoE works to support the development of methane as an energy source for the United States, including methane from marine basins and nontraditional sources such as methane hydrates. The capabilities of EMSL provide a unique opportunity to achieve the goals of this project, by integrating proteomics and stable isotope analysis in an unprecedented way. Finally, we hope these data will form the foundation for future experimental and modeling efforts (ideally in collaboration with the subsurface flow and atmospheric sciences groups at PNNL) that will be aimed at determining the degree to which environmental factors - including anthropogenic factors- influence methane production and consumption (and ultimately methane flux into the atmosphere).
Project Details
Project type
Large-Scale EMSL Research
Start Date
2010-10-06
End Date
2013-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members