Printed on recycled paper U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2012–3109

May 2013

Microbial Production of Natural Gas from Coal 

and Organic-Rich Shale

Natural gas is an important component of the energy mix 

in the United States, producing greater energy yield per unit 

weight and less pollution compared to coal and oil. Most of the 

world’s natural gas resource is thermogenic, produced in the 

geologic environment over time by high temperature and pressure within deposits of oil, coal, and shale. About 20 percent of 

the natural gas resource, however, is produced by microorganisms (microbes). Microbes potentially could be used to generate 

economic quantities of natural gas from otherwise unexploitable 

coal and shale deposits, from coal and shale from which natural 

gas has already been recovered, and from waste material such 

as coal slurry. Little is known, however, about the microbial 

production of natural gas from coal and shale. 

Since 2006, the U.S. Geological Survey Energy Resources 

Program has supported studies of microbial natural gas production from coal and shale. Major goals of this work are to:

1. Examine environmental and geologic conditions (water 

chemistry, coal type, geologic framework) that promote 

microbial natural gas production in the field. 

2. Determine, by use of laboratory bioreactors, the most 

effective types of microorganism combinations and the 

mechanisms they use to convert complex organic molecules 

in coal and shale to natural gas (fig. 1); the project will 

develop approaches to increase the rate and yield of microbial natural gas production. 

3. Develop a microbiological test (bioassay) to assess 

the potential of coal and shale for microbial natural 

gas production.

4. Develop and test, based on laboratory and field results, a 

field protocol or process that is practical and can be used 

to stimulate microbes to produce economic quantities of 

natural gas from coal and shale.

Figure 1. Drill core of coal from Texas (top) used 

in laboratory bioreactors (bottom) to examine 

microbial natural gas production.

Microbial Natural Gas Production 

The principal component in microbial natural gas is 

methane gas (CH4 ), and the overall biodegradation process 

is referred to as methanogenesis. Biodegradation pathways 

in methanogenesis are complex (fig. 2) and involve different 

microorganisms acting as a team or consortium. Certain bacteria 

initiate biodegradation by hydrolytic fermentation, releasing 

enzymes that break chemical bonds in the geopolymers and 

release smaller organic molecules into the fluid medium. These 

smaller organic molecules (alkanes, fatty acids, aromatics) are 

then utilized by many other types of microorganisms, including 

syntrophic bacteria that use the byproducts produced by each 

other. The organisms that produce methane gas in the final step 

using acetate (C2H3O2

–

 ) or carbon dioxide (CO2 ) and hydrogen 

(H2 ) are the methanogens.

Enzymatic

hydrolysis

depolymerization 

Long-chain 

alkanes 

Single-ring 

aromatics 

Long-chain 

fatty acids 

Phenols 

benzoate 

Non-aromatic 

rings 

Midchain 

fatty acids 

Degradation

of soluble

coal-derived

 organic

compounds 

Butyrate, propionate 

Acetate 

Methanogenesis

–Acetoclastic (acetate) 

–Hydrogenotrophic (H2+CO2)

–Methylotrophic (methanol,

 methylamines (not shown)) 

Methane 

gas 

H2

H2

H2

H2

H2+CO2

Microbial methane 

production from coal:

A three-step process 

Geopolymeric 

structure of coal 

OH OH OH

OH OH COOH NH2

O

O

S

S

S

O

O O

O

OH H

N

Figure 2. Microbial biodegradation pathway of coal 

geopolymers to methane gas. 
0 100 200 300 400 500 MILES

0 250 500 KILOMETERS

38°

48°

124° 114° 104° 94° 84° 74°

28°

Anthracite

Lignite

Low-volatile bituminous

Medium- and high-volatile bituminous

Subbituminous

<1

Shale core <1

1 to 5

Coal mine Coal core

1 to 5 5 to 10

EXPLANATION

Predominant coal rank

Sample type and gas yield, in SCF/T

5 to 50

>50

Base modified from U.S. Geological Survey digital files

Albers equal-area projection, central meridian 96°W

Reference latitude 37.5°N; standard parallels: 29.5°N, 45.5°N

LA

ID

NH

OR

NV

CA

NM

TX

UT

AZ

NE

ND

MT

WY

CO

OK

KS

SD

AR

MO

GA

IA

AL

TN

MS

NC

WI MI

MN

IL IN

KY

SC

OH

WV

VA

MD

DE

MA

ME

NY

PA NJ

CT

RI

VT

WA

FL

Figure 3. Coal map of the United States showing the location of samples used in the bioassay experiment (modified from East, 2013). 

SCF/T, standard cubic feet per ton. 

Methanogenesis Bioassay

A bioassay (called WBC–2) was developed to examine the 

potential of different coals for natural gas production (Jones and 

others, 2008). The bioassay is a microbial consortium isolated 

from industrially contaminated wetland sediments; cultured in 

the laboratory, the bioassay has the capacity to degrade coal 

to methane gas. This bioassay can be used to evaluate various 

coals for their potential to produce microbial natural gas, with 

the Wilcox coal in Texas and the Upper Wyodak coal in the 

Powder River Basin, Wyoming, having the highest potential 

(fig. 3). 

Enhancement of Biomethanogenesis 

Laboratory investigations are exploring methods for 

enhancing microbial methane production from coal and shale. 

Approaches being investigated include (1) adding nutrients to 

enhance the activity of native populations of microorganisms 

in coal and shale deposits (biostimulation), (2) adding microorganisms to enhance methane production (bioaugmentation), 

(3) altering the chemical and physical properties of the coal and 

shale to increase its availability for microbial degradation, and 

(4) using various combinations of these approaches. Laboratory 

protocols that show promising results will be tested in a selected 

coal bed in the Powder River Basin, Wyoming or Montana, 

where microbial coal-bed methane has already been identified. 

A successful outcome could result in enhanced quantities of 

microbial natural gas being produced as biomethanogenic 

approaches are repeated over several cycles. 

References Cited

Jones, E.J.P., Voytek, M.A., Warwick, P.D., Corum, M.D., Cohn, 

Alexander, Bunnell, J.E., Clark, A.C., and Orem, W.H., 2008, 

Bioassay for estimating the biogenic methane-generating 

potential of coal samples: International Journal of Coal Geology, 

v. 76, p. 138–150.

East, J.A., 2013, Coal fields of the conterminous United States—

National Coal Resource Assessment updated version: U.S. Geological Survey Open-File Report 2012–1205, one sheet, scale 

1:5,000,000, available at http://pubs.usgs.gov/of/2012/1205/.

For additional information, contact:

William Orem 

U.S. Geological Survey 

956 National Center

Reston, VA 20192

Email: borem@usgs.gov

or visit the USGS Energy Resources Program 

homepage: http://energy.usgs.gov/