EBI Personnel Directory Coates, John

Fossil Fuel Bioprocessing

John Coates




Dr. Coates is a Professor of Microbiology at UC Berkeley. He also holds a joint appointment as a Geological Scientist Faculty in the Earth Sciences Division at the Lawrence Berkeley National Laboratory and is co-director of the EBI's Microbially Enhanced Hydrocarbon Recovery (MEHR) program. 

He obtained an Honors B.Sc. in Biotechnology in 1986 from Dublin City University, Ireland and his Ph.D. in Microbiology in 1991 from University College Galway, Ireland.  His major area of interest is geomicrobiology applied to environmental problems.  Specific interests include diverse forms of anaerobic microbial metabolism such as microbial perchlorate reduction, microbial iron oxidation and reduction, and microbial humic substances redox cycles.  Other interests include alternative renewable energies, bioremediation of toxic metals, radionuclides, and organics. 

He has won several awards for research and mentorship, including the 1998 Oak Ridge Ralph E. Powe Young Faculty Enhancement Award, the 2001 DOD SERDP Program Project of the Year award, and the 2002 Southern Illinois University College of Science Researcher of the Year Award. He has authored and co-authored more than 90 peer-reviewed publications and book chapters and has published one book. Nine patent submissions have been based on technologies developed in his lab, several of which are in commercial application.  He sits on the editorial boards of the journals Applied and Environmental Microbiology and Applied Microbiology and Biotechnology.  He is a member of the American Society for Microbiology, the American Chemical Society, the American Geophysical Union, and the International Humic Substances Society.



Souring Systems Biology: Rates and Mechanisms

MEHR -- Microbially Enhanced Hydrocarbon Recovery --  involves a broad diversity of metabolic processes that act either individually or cooperatively to improve hydrocarbon production and energy yields, and reduce the environmental footprint.  An in-depth understanding of these metabolic processes and the controlling parameters comes from focused interdisciplinary research into model organisms or communities known to perform the relevant functions. 

Systems Biology: This work involves a variety of metabolomic, transcriptomic, proteomic, genomic, and biogeochemical approaches.  A focused aspect of these studies is the development of model organisms or microbial assemblies from members of relevant Petroleum Reservoir microbial populations that have been enhanced in specific functional processes(e.g. biosurfactant production, hydrocarbon biotransformation, hydrocarbon viscosity reduction, biosouring control). Overall these studies provide a basic understanding of the microbiology, biochemistry, molecular biology, and biogeochemistry involved in MEHR relevant metabolic processes and will potentially result in the development of novel strategies to control biosouring, enhance hydrocarbon recovery, and reduce the environmental footprint of oil reservoir processes.


Microbial Chlorate Reduction as a Control of Biogenic Hydrogen Sulfide Production in Oil Reservoirs

The generation of hydrogen sulfide (H2S) as a metabolic end product of microbial sulfate respiration results in a variety of oil recovery problems, including oil reservoir souring, contamination of crude oil, and metal corrosion.  It may be possible to control the generation of biogenic H2S through the activity of sulfur-oxidizing bacteria. Coates will determine the ability of chlorate-reducing bacteria to inhibit and reverse microbial sulfate reduction, to identify the environmental and biological parameters under which this occurs, and to demonstrate that suitable chlorate-reducing populations are indigenous to oil reservoirs.

Controlling Fermentation Hygiene via Chlorate Addition and Expression of Chlorate Dismutase in Process Organisms

Our objective is to demonstrate proof-of-concept for a novel bioprocess hygiene strategy. Industrial fermentation facilities are vulnerable to contamination with unwanted eukaryotes, bacteria, and bacteriophage. Growth of contaminating organisms can reduce product yields or lead to bioreactor collapse, entailing financial losses. In Saccharomyces cerevisiae-based fuel ethanol fermentations, lactic acid bacteria and wild yeasts are common contaminants (5, 41). Some facilities use antibiotics to treat or prevent bacterial infections in fuel bioreactors, but antibiotics are not universally effective against bacteria, and they do not prevent contamination by wild yeasts. In the case of bacterial fermentations, antibiotics could be used to selectively inhibit or spare certain species, but they do not protect process organisms from bacteriophage infection. We propose a strategy in which process organisms are engineered to produce the enzyme chlorite dismutase (Cld), which detoxifies the disinfectant compound chlorite by converting it to chloride and molecular oxygen (43). Chlorite added to the fermentation system would then selectively damage non-Cld-expressing contaminants, including eukaryotes, bacteria, and bacteriophage. We will demonstrate that Cld expressed in S. cerevisiae will protect this organism from concentrations of chlorite that kill or inhibit the growth of known contaminants of fuel ethanol fermentations. These studies pave the way for the development of a widely applicable technique to address fermentation hygiene concerns in a variety of industrial fermentations.