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BuG ReMeDEE project seeks to use extremophile bacteria to convert methane to biofuels, biopolymers and electricity

Researchers from South Dakota School of Mines & Technology (SDSMT) are heading a project to to investigate methane cycling in deep and extreme environments and to develop new biological routes using previously unexplored and novel microorganisms from extreme environments for converting methane into value-added products such as liquid biofuels, biopolymers, and direct current electricity.

The project—Building Genome-to-Phenome Infrastructure for Regulating Methane in Deep and Extreme Environments (BuG ReMeDEE)—was awarded a $6-million grant by the National Science Foundation in October 2017. BuG ReMeDEE, which runs through July 2021, intends to accomplish its goals via a set of integrated objectives:

  1. Characterize extreme methane oxidizing microbial communities;

  2. Investigate the metabolic activities of novel methanotrophs and their roles in methane flux;

  3. Model critical interactions of select members of these communities;

  4. Edit genomes of select methanotrophs for phenotypic improvement in methane uptake and oxidation; and

  5. Establish a consortium for sustained collaborations among university partners in South Dakota, Montana, and Oklahoma in the field of methane regulation in extreme environments.

The research will include:

  1. Analysis of methane flux among novel methanotrophs individually as well as in interacting microbial communities;

  2. Molecular investigations in genome editing to overexpress methane related synthetic gene cassettes and protein profiling;

  3. Computational biofilm modeling, in-silico characterization of active sites of regulatory proteins responsible for methane oxidation to determine underlying molecular mechanisms; and

  4. Bioelectrochemical investigations to elucidate electrogenic activity of new, extremophilic, methanotrophs and evaluate their potential for controllable, catalytic methane oxidation.

The project involves a collaborative consortium of three institutions (South Dakota School of Mines and Technology, Montana State University and University of Oklahoma). The Sanford Underground Research Facility (SURF) and Yellowstone National Park will be used as testbeds for extreme environments in deep biosphere and thermal systems, respectively.

The BuG ReMeDEE consortium includes industrial partners LanzaTech (US) and Bijson Innovations Pvt. Ltd. (India).

As an example of the type of work, SDSMT researchers just published a study, supported in part by the BuG ReMeDEE initiative, on the production of methane methanol and electricity from organic waste. Among the highlights were the oxidation of mixed methane gas to liquid biofuel by Methyloferula sp, an obligately methanotrophic bacterium.

SURF is located in Lead, South Dakota at the former site of the Homestake Gold Mine. This, the deepest mine in North America, began filling with water following its closure in 2002. As momentum built to turn the mine into an underground lab, pumps were installed to dewater the flooded shafts and tunnels.

As the water receded, Rajesh Sani, Ph.D., an associate professor in the Department of Chemical and Biological Engineering at SD Mines and the Principal Investigator for BuG ReMeDEE, was among the first researchers to enter the deeper sections of the mine. Sani and his team were looking for microbes.

Extremophiles are microorganisms that live in harsh environments such as geothermal vents of the mid-Atlantic rift, the frigid waters of Antarctic lakes, or the veins of hot water found in tiny cracks deep underground.

This BuG ReMeDEE consortium will garner the world’s attention on the significance of analyzing the methane regulation in deep subsurface and extreme environments.

—Rajesh Sani


  • Saurabh Sudha Dhiman, Namita Shrestha, Aditi David, Neha Basotra, Glenn R. Johnson, Bhupinder S. Chadha, Venkataramana Gadhamshetty, Rajesh K. Sani (2018) “Producing methane, methanol and electricity from organic waste of fermentation reaction using novel microbes,” Bioresource Technology, Volume 258, Pages 270-278 doi: 10.1016/j.biortech.2018.02.128


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