DEEP SUBSURFACE MICROBIAL PROCESSES
Derek R. Lovley
Water Resources Division
U.S. Geological Survey
Reston, Virginia
Francis H. Chapelle
Water Resources Division
U.S. Geological Survey
Columbia, South Carolina
Abstract. Information on the microbiology of the
deep subsurface is necessary in order to understand
the factors controlling the rate and extent of the mi-
crobially catalyzed redox reactions that influence the
geophysical properties of these environments. Fur-
thermore, there is an increasing threat that deep aqui-
fers, an important drinking water resource, may be
contaminated by man’s activities, and there is a need
to predict the extent to which microbial activity may
remediate such contamination. Metabolically active
microorganisms can be recovered from a diversity of
deep subsurface environments. The available evidence
suggests that these microorganisms are responsible for
catalyzing the oxidation of organic matter coupled to a
variety of electron acceptors just as microorganisms
do in surface sediments, but at much slower rates. The
technical difficulties in aseptically sampling deep sub-
surface sediments and the fact that microbial pro-
cesses in laboratory incubations of deep subsurface
material often do not mimic in situ processes fre-
quently necessitate that microbial activity in the deep
subsurface be inferred through nonmicrobiological
analyses of ground water. These approaches include
measurements of dissolved H2, which can predict the
predominant microbially catalyzed redox reactions in
aquifers, as well as geochemical and groundwater flow
modeling, which can be used to estimate the rates of
microbial processes. Microorganisms recovered from
the deep subsurface have the potential to affect the
fate of toxic organics and inorganic contaminants in
groundwater. Microbial activity also greatly influences
the chemistry of many pristine groundwaters and con-
tributes to such phenomena as porosity development
in carbonate aquifers, accumulation of undesirably
high concentrations of dissolved iron, and production
of methane and hydrogen sulfide. Although the last
decade has seen a dramatic increase in interest in deep
subsurface microbiology, in comparison with the
study of other habitats, the study of deep subsurface
microbiology is still in its infancy.
INTRODUCTION
Microorganisms are capable of catalyzing reactions
that greatly influence the physical properties of sedi-
ments and waters. As will be detailed below, microbial
metabolism can result in both the dissolution and pre-
cipitation of inorganic compounds, and it is the pri-
mary mechanism for the oxidation of organic matter to
carbon dioxide in low-temperature sedimentary envi-
ronments. In addition to acting upon substances nat-
urally present in sedimentary environments, microbial
activity can also greatly influence the fate and mobility
of toxic compounds introduced through human activ-
ities.
It has long been suspected that microorganisms
living in the deep terrestrial subsurface are responsible
for a number of important geochemical phenomena
(for historical perspectives see Chapelle [1993],
Ghiorse and Wilson [1988] and Hirsch [1992]). How-
ever, only within the last decade has there been irre-
futable documentation that there are diverse commu-
nities of microorganisms living in deep subsurface
environments that have not been introduced from the
Earth’s surface through drilling. At the same time,
new discoveries about the metabolic potential of mi-
croorganisms have increased the known ways in which
microorganisms can influence the geochemistry of sed-
imentary environments. In tandem, these two lines of
investigation have emphasized that the ongoing activ-
ity of microorganisms living in the deep subsurface can
play a major role in controlling the organic and inor-
ganic geochemistry of subsurface environments.
In some aspects, detailed investigation of the mi-
crobiology of deep subsurface environments may
seem superfluous. Geochemical analyses of subsur-
face environments typically treat microorganisms
merely as black boxes that may help facilitate certain
reactions that are thermodynamically favorable. From
this perspective it is unnecessary to have a detailed
understanding of the functioning of the microorgan-
isms because the reactions that the microorganisms
catalyze can be predicted on the basis of purely non-
biological models such as equilibrium thermodynam-
ics.
However, it is becoming increasingly apparent that
even in ancient, relatively nondynamic subsurface en-
Copyright 1995 by the American Geophysical Union.
8755-1209/95/95 RG-01305 $15. O0
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Reviews of Geophysics, 33, 3 / August 1995
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366 Lovley and Chapelle- DEEP SURFACE MICROBIAL PROCESSES 33, 3 / REVIEWS OF GEOPHYSICS
vironments, simplified nonbiological models do not
accurately describe or predict important geochemical
processes. For example, attempts to describe the dis-
tribution of redox reactions in groundwater with equi-
librium thermodynamic models are generally unsuc-
cessful [Fish, 1993; Hostettler, 1984; Lindberg and
Runnells, 1984; Lovley et al., 1994, and references
therein]. This is because most of these redox reactions
do not take place spontaneously but require microor-
ganisms to catalyze them. Microorganisms catalyze
the redox reactions in order to gain energy for main-
tenance and growth. This requirement to conserve
energy places biochemical constraints on the path-
ways by which these redox reactions are carried out
and limits the rate and extent of the microbially cata-
lyzed processes. This is why typical subsurface envi-
ronments often approach steady state conditions but
are generally far removed from redox equilibrium.
Therefore in order to understand the factors control-
ling microbially catalyzed reactions in the deep sub-
surface, it is necessary to understand the biochemical
mechanisms of microbial metabolism and the ecologi-
cal interactions between various groups of microor-
ganisms.
The purpose of this review is to illustrate the cur-
rent understanding of microbially catalyzed processes
in sedimentary environments and to review the evi-
dence that the microorganisms catalyzing these pro-
cesses are living in the terrestrial deep subsurface.
Examples of recent studies that demonstrate how
these microbially catalyzed processes have influenced
important geochemical phenomena in the deep subsur-
face will be discussed.
WHAT IS THE \"DEEP SUBSURFACE\"?
Routine use of the term \"deep subsurface\" in ref-
erence to microbial studies is relatively recent [Sar-
gent and Fliermans, 1989], and this term has generally
been only vaguely defined. Ghiorse and Wobber[1989,
p. 1] defined deep aquifer systems as \"those that are
hundreds to thousands of meters below land surface.\"
Many investigators, however, have applied the term to
sediments buried to depths greater than about 10 rn
[Fredrickson et al., 1989]. The use of arbitrary depths
to separate \"deep\" from \"shallow\" sediments is prob-
ably inappropriate because \"deep\" has different
meanings in different disciplines. In soil science, for
example, \"deep\" might refer to anything deeper than
2 or 3 m. In petroleum geology, on the other hand,
\"deep\" is seldom used to describe sediments that are
shallower than 3000 rn below land surface.
Although the microbiology of deeply buried unsat-
urated soils in arid regions is beginning to receive
some attention [Brockman et al., 1992; Colwell, 1989;
Kieft et al., 1993], microbial activity in such environ-
ments is very limited, and most studies on the micro-
biology of the deep subsurface have focused on pro-
cesses in water-saturated environments. For the latter
type of system it is useful to define \"deep\" in terms of
the hydrologic environment. For example, a depth of
200 rn in the Tucson basin is a water table aquifer,
whereas the same depth in the Illinois basin might be
an oil-producing petroleum reservoir. Clearly, these
environments have little in common hydrologically,
even though they are at the same depth. For these
reasons, a hydrologic definition of deep subsurface
environments is more meaningful than trying to estab-
lish an arbitrary depth as the cutoff between \"shal-
low\" and \"deep\" [Chapelle, 1993].
Groundwater flow systems (Figure 1) can be classi-
fied as local, intermediate, or regional [Toth, 1963].
Local flow systems recharge at a topographic high and
discharge in an adjacent topographic low. There is a
high degree of connectedness with the surface. Local
flow systems typically have high rates of recharge
(1-30 cm/yr) and high rates of groundwater flow (1-100
m/yr). Rates of recharge and water levels respond
rapidly to individual precipitation events in local flow
systems because they are so intimately connected with
the surface. Intermediate flow systems recharge and
discharge in areas that are separated by one or more
topographic highs. Because of this, intermediate flow
systems are much less connected with the surface, and
rates of recharge (0.01-1 cm/yr) and groundwater flow
(0.1-1 m/yr) are proportionally lower. In intermediate
flow systems, water levels and rates of recharge do not
respond to individual precipitation events. Regional
flow systems recharge only at the groundwater divide,
and they discharge only at the bottom of the basin.
Recharge rates in regional flow systems are very low,
and flow is often sluggish. There is little connection
between surface environments and regional flow sys-
tems.
The depth to which local, intermediate, and re-
gional flow systems penetrate the subsurface is
largely a function of topography [Toth, 1963]. Thus
aquifers in areas of high relief (such as the basin-
and-range topography of Tucson, Arizona) have lo-
cal flow systems that penetrate several hundred
meters into the subsurface, whereas flatter-lying ar-
eas (such as the Illinois basin) have regional flow
systems that are within a few hundred meters of land
surface.
We suggest that the use of the term \"deep sub-
surface\" in microbiological studies should be re-
stricted to intermediate and regional flow systems.
This definition is independent of total depth and
instead depends entirely on the hydrologic frame-
work of the system under study. According to this
definition, some environments that have previously
been discussed as belonging to the \"deep subsur-
face\" [Ghiorse and Wobber, 1989] would be classi-
fied as local flow systems.