1 Introduction

Geomicrobiology deals with the role that microbes play at present on Earth in a number of fundamental geologic processes and have played in the past since the beginning of life. These processes
include the cycling of organic and some forms of inorganic matter at the surface and in the subsurface of Earth, the weathering of rocks, soil and sediment formation and transformation, and the
genesis and degradation of various minerals and fossil fuels.
Geomicrobiology should not be equated with microbial ecology or microbial biogeochemistry.
Microbial ecology is the study of interrelationships between different microorganisms; among microorganisms, plants, and animals; and between microorganisms and their environment. Microbial biogeochemistry is the study of microbially influenced geochemical reactions, enzymatically catalyzed
or not, and their kinetics. These reactions are often studied in the context of cycling of inorganic and
organic matter with an emphasis on environmental mass transfer and energy flow. These subjects
overlap to some degree, as shown in Figure 1.1.
It is unclear as to when the term geomicrobiology was first introduced into the scientific vocabulary. This term is obviously derived from the term geological microbiology. Beerstecher (1954)
defined geomicrobiology as the study of the relationship between the history of the Earth and
microbial life upon it. Kuznetsov et al. (1963) defined it as the study of microbial processes currently taking place in the modern sediments of various bodies of water, in ground waters circulating
through sedimentary and igneous rocks, and in weathered Earth crust [and also] the physiology
of specific microorganisms taking part in presently occurring geochemical processes. Neither
author traced the history of the term, but they pointed to the important roles that scientists such as
S. Winogradsky, S. A. Waksman, and C. E. ZoBell played in the development of the field.
Geomicrobiology is not a new scientific discipline, although until the 1980s it did not receive
much specialized attention. A unified concept of geomicrobiology and the biosphere can be said
to have been pioneered in Russia under the leadership of V. I. Vernadsky (18631945) (see Ivanov,
1967; Lapo, 1987; Bailes, 1990; Vernadsky, 1998, for insights and discussions of early Russian
geomicrobiology and its practitioners).
Certain early investigators in soil and aquatic microbiology may not have thought of themselves
as geomicrobiologists, but they nevertheless exerted an important influence on the subject. One of the
first contributors to geomicrobiology was Ehrenberg (1836, 1838), who discovered the association
of Gallionella ferruginea with ochreous deposits of bog iron in the second quarter of the nineteenth
century. He believed that this organism, which he classified as an infusorian (protozoan), but which
we now recognize as a stalked bacterium (see Chapter 16), played a role in the formation of such
deposits. Another important early contributor to geomicrobiology was S. Winogradsky, who discovered that Beggiatoa, a filamentous bacterium (see Chapter 19), could oxidize H2 S to elemental sulfur
(Winogradsky, 1887) and that Leptothrix ochracea, a sheathed bacterium (see Chapter 16), promoted
oxidation of FeCO3 to ferric oxide (Winogradsky, 1888). He believed that each of these organisms
gained energy from the corresponding processes. Still other important early contributors to geomicrobiology were Harder (1919), a researcher trained as a geologist and microbiologist, who studied the
significance of microbial iron oxidation and precipitation in relation to the formation of sedimentary
iron deposits, and Stutzer (1912) and others, whose studies led to the recognition of the significance
of microbial oxidation of H2S to elemental sulfur in the formation of sedimentary sulfur deposits. Our
early understanding of the role of bacteria in sulfur deposition in nature received a further boost from
the discovery of bacterial sulfate reduction by Beijerinck (1895) and van Delden (1903).

1
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Geomicrobiology

Geomicrobiology
Biogeochemistry

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Microbial
ecology

Microbial
biogeochemistry

FIGURE 1.1 Interrelationships between geomicrobiology, microbial ecology, microbial biogeochemistry,

and biogeochemistry.

Starting with the Russian investigator Nadson (1903, 1928) at the end of the nineteenth century,
and continuing with such investigators as Bavendamm (1932), the important role of microbes in
some forms of CaCO3 precipitation began to be noted. Microbial participation in manganese oxidation and precipitation in nature was first recognized by Beijerinck (1913), Soehngen (1914), Lieske
(1919), and Thiel (1925). Zappfe (1931) later related this activity to the formation of sedimentary
manganese ore (see Chapter 17). A microbial role in methane formation (methanogenesis) became
apparent through the observations and studies of Bchamp (1868), Tappeiner (1882), Popoff(187 5),
Hoppe-Seyler (1886), Omeliansky (1906), Soehngen (1906), and Barker (1956). The role of bacteria in rock weathering was first suggested by Muentz (1890) and Merrill (1895). Later, the involvement of acid-producing microorganisms, such as nitrifiers, and crustose lichens and fungi in such
weathering was suggested (see Waksman, 1932). Thus by the beginning of the twentieth century,
many important areas of study of geomicrobial processes had begun to receive serious attention
from microbiologists. In general it may be said that most of the early geomicrobially important
discoveries were made through physiological studies in the laboratory, which revealed the capacity
of specific organisms to promote geomicrobially important transformations, causing later workers
to study the extent of the occurrence of such processes in nature.
In the United States, geomicrobiology can be said to have begun with the work on iron-depositing
bacteria by Harder (1919). Other early American investigators of geomicrobial phenomena include
J. Lipman, S. A. Waksman, R. L. Starkey, and H. O. Halvorson, all prominent in soil microbiology,
and G. A. Thiel, C. Zappfe, and C. E. ZoBell, all prominent in aquatic microbiology. ZoBell was a
pioneer in marine microbiology (see Ehrlich, 2000).
Very fundamental discoveries in geomicrobiology continue to be made, some having been made
as the twentieth century progressed and others very recently. For instance, the concept of environmental limits of pH and Eh for microbes in natural habitats was first introduced by Baas-Becking
et al. (1960) (see Chapter 6). The pH limits as these authors defined them have since been extended
at both the acidic and alkaline ends of the pH range (pH 0 and 13) as a result of new observations.
Life at high temperature was systematically studied for the first time in the 1970s by Brock
(1978) and associates in Yellowstone National Park in the United States. A specific acidophilic, ironoxidizing bacterium, originally named Thiobacillus ferrooxidans and later renamed Acidithiobacillus
ferrooxidans, was discovered by Colmer et al. (1950) in acid coal mine drainage in the late 1940s
and thought by these investigators and others to be directly involved in its formation by promoting
oxidation of pyrite occurring as inclusions in bituminous coal seams (see also Chapters 16 and 20).

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Introduction

The subsequent demonstration of the presence of A. ferrooxidans in acid mine drainage from
an ore body with sulfidic copper as chief constituent, located in Utah, United States (Bingham
Canyon open pit mine), and the experimental finding that A. ferrooxidans can promote the
leaching (mobilization by dissolution) of metals from various metal sulfide ores (Bryner et al.,
1954) led to the first industrial application of a geomicrobially active organism to ore extraction (Zimmerley et al., 1958; Ehrlich, 2001, 2004). After these pioneering studies on microbial
participation of A. ferrooxidans in the formation of acid mine drainage, other organisms with
iron-oxidizing capacity have been discovered in acid mine drainage from different sources and
implicated in its formation, as have other microorganisms associated in consortia with the iron
oxidizers (see review by Ehrlich, 2004).
The first attempt at visual detection of Precambrian prokaryotic fossils in sedimentary rocks
was made by Tyler and Barghoorn (1954), Schopf et al. (1965), and Barghoorn and Schopf (1965)
(see Chapter 3). These paleontological discoveries have had a profound influence on current theories about the origin and evolution of life on Earth (Schopf, 1983). The discovery of geomicrobially active microorganisms around submarine hydrothermal vents (Jannasch and Mottl, 1985;
Tunnicliffe, 1992) and the demonstration of a significant viable microflora with a potential for geomicrobially important activity in the deep subsurface of the Earths continents at depths of hundreds
and thousands of meters below the surface (Ghiorse and Wilson, 1988; Sinclair and Ghiorse, 1989;
Fredrickson et al., 1989; Pedersen, 1993) and deep beneath the surface of the ocean floor (Parkes
et al., 1994) have revealed previously unsuspected regions of Earth where microbes are geomicrobiologically active. These discoveries have also had a major impact on the development of the field
of astrobiology.
As this book will show, many areas of geomicrobiology remain to be fully explored or developed
further.

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