DEEP SUBSURFACE
MICROBIAL
PROCESSES
FrancisH. Chapelle
Derek R. Lovley
Water
Resources
Division
Water
Resources
Division
U.S. GeologicalSurvey
U.S. GeologicalSurvey
Reston, Virginia
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 microbially catalyzed redox reactions that influence the
geophysical properties of these environments. Furthermore, there is an increasingthreat that deep aquifers, 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 subsurfaceenvironments. The available evidence
suggeststhat these microorganismsare responsiblefor
catalyzing the oxidation of organic matter coupled to a
variety of electron acceptorsjust as microorganisms
quently necessitate that microbial activity in the deep
subsurface be inferred through nonmicrobiological
analyses of ground water. These approaches include
INTRODUCTION
It has long been suspected that microorganisms
living in the deep terrestrial subsurfaceare responsible
for a number of important geochemical phenomena
(for historical perspectives see Chapelle [1993],
Ghiorse and Wilson [1988] and Hirsch [1992]). However, only within the last decade has there been irre-
Earth's surface through drilling. At the same time,
new discoveries about the metabolic potential of microorganismshave increased the known ways in which
microorganismscan influence the geochemistry of sedimentary environments. In tandem, these two lines of
investigation have emphasized that the ongoing activity of microorganismsliving in the deep subsurfacecan
play a major role in controlling the organic and inorganic geochemistry of subsurfaceenvironments.
In some aspects, detailed investigation of the microbiology of deep subsurface environments may
seem superfluous. Geochemical analyses of subsurface 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 microorganisms because the reactions that the microorganisms
catalyze can be predicted on the basis of purely nonbiological models such as equilibrium thermodynam-
futable
ics.
measurementsof dissolvedH2, 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 contributes to such phenomena as porosity development
in carbonate aquifers, accumulation of undesirably
high concentrationsof dissolved iron, and production
do in surface sediments, but at much slower rates. The of methane and hydrogen sulfide. Although the last
technical difficulties in aseptically samplingdeep sub- decade has seen a dramatic increase in interest in deep
surface sediments and the fact that microbial pro- subsurface microbiology, in comparison with the
cesses in laboratory incubations of deep subsurface study of other habitats, the study of deep subsurface
material often do not mimic in situ processes fre- microbiology is still in its infancy.
Microorganismsare capableof catalyzing reactions
that greatly influence the physical properties of sediments and waters. As will be detailed below, microbial
metabolismcan result in both the dissolutionand precipitation of inorganic compounds, and it is the primary mechanismfor the oxidation of organic matter to
carbon dioxide in low-temperature sedimentary environments. In addition to acting upon substancesnaturally present in sedimentary environments, microbial
activity can also greatly influence the fate and mobility
of toxic compounds introduced through human activities.
documentation
that there are diverse
commu-
nities of microorganisms living in deep subsurface
environments
that have not been introduced
from the
However, it is becoming increasingly apparent that
even in ancient, relatively nondynamic subsurfaceen-
Copyright1995 by the AmericanGeophysicalUnion.
Reviewsof Geophysics,33, 3 / August 1995
pages 365-381
8755-1209/95/95 RG-01305 $15. O0
Paper number 95RG01305
ß 365 ß
366 ß Lovleyand Chapelle- DEEPSURFACEMICROBIAL PROCESSES
33, 3 / REVIEWSOF GEOPHYSICS
vironments, simplified nonbiological models do not biology of the deep subsurface have focused on proaccurately describe or predict important geochemical cesses in water-saturated environments. For the latter
processes.For example, attempts to describe the dis- type of system it is useful to define "deep" in terms of
tribution of redox reactions in groundwater with equi- the hydrologic environment. For example, a depth of
librium thermodynamic models are generally unsuc- 200 rn in the Tucson basin is a water table aquifer,
cessful [Fish, 1993; Hostettler, 1984; Lindberg and whereas the same depth in the Illinois basin might be
Runnells, 1984; Lovley et al., 1994, and references an oil-producing petroleum reservoir. Clearly, these
therein]. This is because most of these redox reactions environments have little in common hydrologically,
do not take place spontaneouslybut require microor- even though they are at the same depth. For these
ganisms to catalyze them. Microorganisms catalyze reasons, a hydrologic definition of deep subsurface
the redox reactions in order to gain energy for main- environments is more meaningful than trying to estabtenance and growth. This requirement to conserve lish an arbitrary depth as the cutoff between "shalenergy places biochemical constraints on the path- low" and "deep" [Chapelle, 1993].
ways by which these redox reactions are carried out
Groundwater flow systems (Figure 1) can be classiand limits the rate and extent of the microbially cata- fied as local, intermediate, or regional [Toth, 1963].
lyzed processes.This is why typical subsurfaceenvi- Local flow systemsrecharge at a topographichigh and
ronments often approach steady state conditions but discharge in an adjacent topographic low. There is a
are generally far removed from redox equilibrium. high degree of connectednesswith the surface. Local
Therefore
in order to understand the factors controlflow systems typically have high rates of recharge
ling microbially catalyzed reactions in the deep sub- (1-30 cm/yr) and high rates of groundwater flow (1-100
surface, it is necessary to understand the biochemical
m/yr). Rates of recharge and water levels respond
mechanisms of microbial metabolism and the ecologirapidly to individual precipitation events in local flow
cal interactions between various groups of microorsystemsbecausethey are so intimately connected with
ganisms.
the surface. Intermediate flow systems recharge and
The purpose of this review is to illustrate the curdischarge in areas that are separated by one or more
rent understanding of microbially catalyzed processes
topographic highs. Because of this, intermediate flow
in sedimentary environments and to review the evisystemsare much less connected with the surface, and
dence that the microorganisms catalyzing these prorates of recharge (0.01-1 cm/yr) and groundwater flow
cesses are living in the terrestrial deep subsurface.
(0.1-1 m/yr) are proportionally lower. In intermediate
Examples of recent studies that demonstrate how
flow
systems,water levels and rates of recharge do not
these microbially catalyzed processeshave influenced
respond
to individual precipitation events. Regional
important geochemicalphenomenain the deep subsurflow
systems
recharge only at the groundwater divide,
face will be discussed.
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
WHAT
IS THE "DEEP SUBSURFACE"?
between surface environments and regional flow sysRoutine use of the term "deep subsurface" in reference to microbial studies is relatively recent [Sargent 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" sedimentsis probably 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 unsaturated soils in arid regions is beginning to receive
some attention [Brockman et al., 1992; Colwell, 1989;
Kieft et al., 1993], microbial activity in such environments is very limited, and most studies on the micro-
tems.
The depth to which local, intermediate, and regional flow systems penetrate the subsurface is
largely a function of topography [Toth, 1963]. Thus
aquifers in areas of high relief (such as the basinand-range topography of Tucson, Arizona) have local flow systems that penetrate several hundred
meters into the subsurface, whereas flatter-lying areas (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 subsurface" in microbiological studies should be restricted to intermediate and regional flow systems.
This definition is independent of total depth and
instead depends entirely on the hydrologic framework of the system under study. According to this
definition, some environments that have previously
been discussed as belonging to the "deep subsurface" [Ghiorse and Wobber, 1989] would be classi-
fied as local flow systems.
33, 3 / REVIEWSOF GEOPHYSICS
Lovleyand Chapelle- DEEPSURFACEMICROBIAL PROCESSES
ß 367
Local
Flow
System
...
o
Intermediate
Flow
System
o
o
o
Regional
Flow
System
o
o
S = 2000 feet
Local
Flow
System
Intermediate Flow
Regional Flow
System
System
Figure 1. Characterization of local, intermediate, and regional flow systems.
TYPES OF MICROBIAL
SEDIMENTARY
METABOLISM
ENVIRONMENTS
IN
organic matter and other reduced compounds(Mn(II),
Fe(II), ammonia, sulfide) that can be oxidized with the
release of energy. Microorganisms have evolved varMicrdorganisms
are the only life formsthat can ious strategies for conserving energy to support
inhabit most deep subsurfaceenvironments because growth from these oxidations. The primary ways in
the typical pore spacesare too smallfor other typesof which microorganismsgain energy from the oxidation
life [Ghior3eand Wilson, 1988].The types of microbial of organic matter are depicted in Figure 2. Each of
metabolismthat are found in the deep subsurfaceare these types of metabolisminvolves a complex seriesof
likely to be similar to those found in surface sedimen- electron transfer reactions within the microorganisms.
tary environments [Pedersen, 1993]. Thus studies on The environmentally significant electron transfer is the
the microbiology of aquatic sedimentsand soils pro- final electron transfer to an electron acceptor from the
vide a model for the types of microorganisms and environment. This is referred to as the terminal elecmicrobial activities that might be expected in deep tron accepting process (TEAP). The most common
subsurfaceenvironments.This sectionprovidesa brief terminalelectronacceptorsfor organicmatter oxidaoverview of some of the important types of microbial tion are expectedto be 02, nitrate,Mn(IV), Fe(lII),
metabolism that can be found in sedimentary environ- sulfate, and carbon dioxide. Thus the predominant
ments that are most relevant to the deep subsurface. TEAPs in sedimentaryenvironmentsare 02 reduction
For more comprehensive coverage, the reader is re- (aerobic respiration), nitrate reduction (denitrification
ferred to two excellent books on this topic [Ehrlich, and dissimilatory nitrate reduction), Mn(IV) reduc1990; Zehender, 1988].
tion, Fe(III) reduction, sulfate reduction, and carbon
Light is not available in the deep subsurface,so dioxide reduction (methane production).
photosynthesis is not possible. Therefore microbial
For simplicity, the reactions exemplifying each of
life is dependentupon energy sourcesthat have been these TEAPs is illustrated in Figure 2 with acetate as
buried in the sediment or enter as dissolvedcompo- the model organic compound. This is done in part
nents in the recharge water. These energy sourcesare because acetate is one of the simplest organic com-
368ß LovleyandChapelle:DEEPSURFACE
MICROBIAL
PROCESSES
Aerobic
Respiration
Hn(IV)
Reduction
Organic
Platter
Oxidation
202
2H20
4Mn(IV) 4Mn(11)
33, 3 / REVIEWS
OF GEOPHYSICS
Sulfate
Reduction
C2H
0••::•2C•
so•
s:
Relative
I00
87
Predominant
Sulfur
sc•
sc•
sc•,s•
Redox
Fe(111)
Mn(IY)
NO3,N2
Fe(111)
Mn(IY),
Mn(11)
NH;•,N
2
Fe(11)
Mn(11)
NH•,N
2
Energy
6
Yield
Iron
Manganese
Species Nitrogen
Characteristic
Hydrogen
(riM)5
Concentration
NOT
APPLICABLE
Figure2. Properties
ofthepredominant
terminal
electron-accepting
processes
(TEAPs)foundin sedimentary environments.
pounds metabolizedby microorganismscatalyzing gionaiflow systems
are generallydepletedof 02 (aneach TEAP. More importantly, acetate is a Central oxic) owingto their isolationfrom surfacerecharge.
intermediate
in themetabolism
of organic
matterin 02 is expectedto be foundin deepaquifersonly when
many sedimentary environments. However, the or- thereis little or no microbialactivity, suchasis seenin
ganicmatterthat is buriedin sediments
is a complex some sedimentary basins of the American Southwest
mixture of polymericorganicmolecules,and microor- wherethe lack of organiccarbonhasallowedoxygen
ganismsmustusehydrolyticenzymes(oftenextracel- to persist in groundwater that is more than 10,000
lular) to break down the complexorganicmatter to yearsold [Winogradand.Robertson,1982].
monomeric
components
suchas sugars,
arninoacids, Metabolismunderanoxic,or oxygen-depleted,
confatty acids, and monoaromatics
prior to metabolism ditionsis knownasanaerobic.In anaerobicrespiration
(Figure 3). As outlinedbelow, the types of organic componentsother than 02 serve as the oxidant for
compounds that can be oxidized to carbon dioxide are organicmatter and other reduced compounds.The
anaerobic metabolism that is most similar to aerobic
differentfor differentterminalelectronaccept0rs.
The form of microbialmetabolism
that yieldsthe respirationis the reductionof nitrateto N2, whichis
most energy to support microbial growth is oxidation knownas denitrification(see Tiedje[1988]for a review
of organicmatterand otherreducedcompounds
cou- of this metabolism).Most known denitrifyingmicropledto the reductionof 02 (Figure2). Thismetabolism organismswill use 02 preferentiallyif it is available
is knownas aerobicmetabolism,or aerobicrespira- andthengrowby denitrification
when02 is depleted
tion. Aerobic microorganisms
completelyoxidize a [Tiedje, 1988].In someinstances,02 and nitratemay
wide variety of organiccompoundsto carbondioxide be reducedsimultaneously[Tiedje, 1988].Denitrifica(Figure 3). Organics that can be oxidized in this man- tion is muchlike aerobicrespirationin that nitrate can
ner includemostnaturallyproducedorganicmatteras replaceoxygenin most of the reactionswith organic
well as many man-made organics [Gibson, 1984]. andinorganicelectrondonors.However,someimporSome aerobicmicroorganisms
can also catalyzethe tant reactionsthat clearly take place with 02 as the
oxidationof inorganiccompounds
suchasammonium, electron acceptor have not been documented under
Fe(II), Mn(II), and Sø [Ehrlich, 1990].
denitrifyingconditions.For example,the current litBecauseof the lack of photosynthesis,the only eratureindicatesthat benzene,a prevalentgroundwasourceof 02 in the deepsubsurface
is 02 that enters ter contaminant, can not be oxidized with nitrate as
dissolvedin the rechargewater. If organicmatter or the electron acceptor, whereas microorganisms
otherreducedcompounds
are present,aerobicmetab- readilyoxidizeit to carbondioxidewhen02 is availolismgenerallyconsumesthis 02 within a relatively able[Anidet al., 1993;Barbaroet al., 1992;Flyvbjerg
short travel distance. Therefore intermediate and re- et al., 1993;Hutchins et al., 1991].Dissimilatoryni-
33, 3 / REVIEWSOF GEOPHYSICS
Lovleyand Chapelle: DEEPSURFACEMICROBIAL PROCESSES
ß 369
02 Reductionor Denitrification
Hydrolysis
of Complex
Organic Matter
Sugars
'•
'•
Amino Acids
Aerøbes
Denitrifiers
Aromatics
•
'
CO2
LongChainFattyAcids
Fe(111),
Mn(IV),
orSulfate
Reduction
•
Aromatics
•.• •_ .
Hydrolysis
Suga,/•'••m
,• •e•enters>
aHn2'2•
Chain
Fatty
Acids
SCFA
Oxiclizers•
ofComplex
Organic
Matter
CO2
ß
ß
LongChain FattyAcids
Methane
Production
Aromatics
?ce•toO;•
Hydrolysis
ofComplex
• SugarsFarmenters
'• H2,
Acetate
•ethano•ens)
CO•,
CH4
Organic
Matter Amino
Acids
:.,o••"v• tPr
iA
oton-Reduc
Long
Chain•l••'•e•
$
Other
Short-Chain
cx"•
FattyAcids
cetogens
FattyAcids
Figure 3. Pathways of organic matter decompositionby various microbial processesin sedimentary
environments.
trate reducers that can oxidize organic compounds organics. In some instances, H 2 and carbon dioxide
with the reductionof nitrate to ammoniamay compete are also produced. For example, in aquatic sediments
with denitrifiers
for nitrate under some instances
a common sugar such as glucose may be fermented
[Tiedje, 1988]. Like aerobic respiration, nitrate reduc- primarily to acetate, carbon dioxide, and H 2 [Lovley
tion is expected to be a minor process for organic and Phillips, 1989]'
matter oxidation in most deep subsurface environments because nitrate inputs from groundwater are 1 glucose + 2 waters --• 2 acetates + 4 H 2
low and there are no significant mineral sources of
nitrate.
The pathways for organic matter oxidation by most
anaerobic microbial processesare much different than
those for aerobic respiration and denitrification.
Whereas single organisms can, by themselves, completely oxidize a wide variety of organiccompoundsto
carbon dioxide during aerobic respiration and denitrification, in most types of anaerobic respiration the
microorganisms are very limited in the types of organic compounds they can completely oxidize. For
example, microorganisms that use Fe(III) as an electron acceptor can only oxidize simple organic acids,
long chain fatty acids, and monoaromaticcompounds
to carbondioxide [Lovley, 1991, 1994].Thus in nitratedepleted, anoxic environments a significantamount of
the organic matter released from hydrolysis of complex organic matter is first metabolized by fermentative microorganisms(Figure 3). Fermentative microorganismsconvert large organiccompoundsto smaller
+ 2 carbon dioxides + 2 protons
or benzoate, a model for the degradation of many
monoaromatic compounds, may be fermented as follows [Ferry and Wolfe, 1976]:
1 benzoate + 6 waters--• 3 acetates + 3 H2
carbon dioxide + 2 protons
In sedimentaryenvironmentsthe predominant fermen-
tation productsare acetate and H2, but other simple
fatty acids such as propionate and butyrate are also
produced [Lovley and Klug, 1986;Lovley and Phillips,
1989; SOrensen et al., 1981]. Because fermentative
microorganisms do not completely oxidize organic
matter to carbon dioxide, other types of microorganisms operate in conjunction with the fermentative microorganismsin order to bring about a complete oxidation of organic matter in anoxic, nitrate-depleted
sediments (Figure 3).
370 ß LovleyandChapelle-DEEPSURFACE
MICROBIALPROCESSES
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33, 3 / REVIEWS
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;':..'.:..",,....'-:..'.T..",,...
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" •AND MN(IV)-
• ........................
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REDUCING
.........
FE(!!i)-REDUCING
METHANOGENIC
Figure4. Typicaldistribution
of majorterminalelectron-accepting
processes
(TEAPs)in deepaquifers.
When Fe(III) is available in the sediments, microorganismsthat can couplethe oxidationsimpleorganic
acids and H2 to the reduction of Fe(III) to Fe(II)
(Figures2 and 3) are active and Fe(III) reductionis the
TEAP [Lovley, 1991]. Fe(III)-reducing microorganisms can also directly oxidize monoaromatic compounds and long-chain fatty acids that are released
from complex organic matter (Figure 3). When manganeseoxidesare available,thesemicroorganisms
can
carry out similar reactions, substitutingthe reduction
of Mn(IV) to Mn(II) for Fe(III) reduction. In addition
to Fe(III) and Mn(IV), some bacteria may use other
metals or metalloids as electron acceptors in their
metabolism [Lovley, 1993]. The reduction of metals
other than Fe(III) and Mn(IV) is generally not signifi-
tabolize[Ordmland,1988].The principaltypesof
cant in termsof organicmatteroxidationbecauseof
SEGREGATION
the relatively low concentrations of these electron
acceptors.However, the reductionof thesemetalshas
DISTINCT
the potentialto greatlyinfluencemetalgeochemistry.
The various TEAPs are generally segregatedinto
distinct zones in aquatic sediments [Ponnamperuma,
Metal and metalloid reductions carried out by micro-
methaneproductionare the dismutationof acetate to
methane and carbon dioxide and the reduction of car-
bon dioxideto methanewith H2 servingas the electron
donor. Methane-producing microorganisms cannot
usefatty acidswith more than two carbonsand cannot
metabolize aromatic compounds. Therefore under
methanogenicconditions,anothergroupof organisms,
the proton-reducingacetogenicbacteria, are also required(Figure 3). They convertthe organicacidsand
aromatic compoundsto acetate and H2, which can
then be consumedby the methane-producingmicroorganisms.
OF MICROBIAL
PROCESSES INTO
ZONES
1972; Reeburgh, 1983], and a similar successionof
TEAPs (Figure 4) is expected along the flow path of
many aquifers [Champ et al., 1979; Jackson.and
Sulfatemay alsobe usedas an electronacceptorfor Patterson, 1982; Lovley and Goodwin, 1988]. This
the oxidation of organic compounds in sedimentary segregationof TEAPs is important becausethe preenvironments (see Widdel [1988] for a detailed review dominant form of many elements is different for difof this metabolism). The reactions carried out by sul- ferent processes(Figure2), and this in turn affectsthe
fate reducers(Figures2 and 3) are similar to thosefor propertiesof both the groundwaterandthe sediments.
organismsinclude U(VI) to U(IV); Se(VI) to Seø,
Cr(VI) to Cr(III),
Au(O).
Mo(VI) to Mo(V), and Au(III) to
Fe(III) reduction,with the exceptionthat sulfatere-
The succession
of TEAPsalongthe groundwater
flow path in deep aquifersfollows the potential therreduced to sulfide.
modynamicyield from the various processes(Figure
Microorganismsmay also convert organicmatter to 2). Aerobic respiration, which yields the most energy
a mixture of carbon dioxide and methane. However,
of the variousmetabolicprocesses,is the predominant
the methane-producingmicroorganismsare strictly TEAP when O2 is available.After O2 is depletedfrom
limitedin the typesof compoundsthat they can me- the groundwater, aerobic respiration is followed by
ducers substitute sulfate for Fe(III).
The sulfate is
33, 3 / REVIEWSOF GEOPHYSICS
Lovleyand Chapelle: DEEPSURFACEMICROBIAL PROCESSES
ß 371
nitrate reduction, which is the next most energetically
favorable TEAP, etc. Thus the segregation of processesis often simply explained with the thermodynamic rationale that the redox reaction that provides
the most potential energy predominates [Stumm and
Morgan, 1981]. However, this is an inadequateexplanation. On a purely thermodynamic basis, reactions
yielding less energy should also take place as long as
they are energetically favorable [McCarty, 1972]. The
segregation of TEAPs can be more accurately explained on the basis of physiological controls on microbial metabolism and the competition between different types of microorganismsfor electron donors.
The lack of anaerobic respiration in the presenceof
02 is due to the fact that microorganismsthat can
respire both aerobically and anaerobically typically
regulate their metabolism to use only 02 when it is
available [Tiedje, 1988]. Anaerobic organisms that
cannot use 02 as an electron acceptor are generally
inhibited in the presenceof 02.
A key factor in the segregationof Fe(III) reduction,
sulfate reduction, and methane production into distinct zones is the competition between Fe(III) reducers, sulfate reducers, and methane producers for acetate and H2, which are, as was discussedabove, the
central intermediates in much of the organic matter
metabolism in anaerobic sedimentary environments.
Comparison of H2 concentrations in sediments in
which Fe(III) reduction, sulfate reduction, or methane
production is the TEAP (Figure 2) have demonstrated
that H2 concentrationsare lowest in sediments in
which Fe(III) reduction is the TEAP, intermediate in
sulfate-reducing sediments, and highest in sediments
in which methane production is the TEAP [Lovley et
al., 1994; Lovley and Goodwin, 1988]. Acetate concentrationsfollow a similarpattern [Chapelle and Lovley, 1992; Lovley and Phillips, 1987]. This pattern of
H2 and acetate concentrationscan be ascribed to the
physiological capabilities of the microorganismsinvolved in H 2 and acetateconsumption.Organismsthat
use Fe(III) for acetate and H2 oxidation can metabolize H2 and acetateto concentrationslower than those
that can be utilized by sulfate reducers, and sulfate
reducerscan metabolize H2 and acetateto concentrations below what can be used by methane-producing
microorganisms [Caccavo et al., 1992; Chapelle and
Lovley, 1992; Cord-Ruwisch et al., 1988;Lovley, 1985;
Lovley et al., 1982, 1989; Lovley and Goodwin, 1988;
Lovley and Phillips, 1987]. Thus when the availability
of Fe(III) does not limit the rates of microbial Fe(III)
reduction, sulfate reduction and methane production
from H2 and acetate are inhibited because Fe(III)
reducers maintain the concentrationsof H2 and acetate too low for sulfate reducers or methane producers
to metabolize [Caccavo et al., 1992; Chapelle and
Lovley, 1992; Lovley and Phillips, 1987; Lovley et al.,
1989]. In a similar manner, when sulfate is not limiting,
sulfate reducers can prevent methane production from
H 2 and acetate [Lovley, 1985; Lovley et al., 1982;
Lovley and Goodwin, 1988]. Another mechanismfor
inhibition of sulfate reduction in the presence of
Fe(III) is that some sulfate reducers can also use
Fe(III) as an electron acceptor and may preferentially
reduce Fe(III)
1993].
[Coleman et al., 1993; Lovley et al.,
The lack of methane production, sulfate reduction,
and Fe(III) reduction in the presence of nitrate and
Mn(IV) may be explainedin part by the findingthat H 2
[Lovley and Goodwin, 1988] and presumably acetate
concentrations are even lower in nitrate- and Mn(IV)reducing sedimentary environments than they are in
Fe(III)-reducing environments. Many Fe(III) reducers
and somesulfatereducersare capable of nitrate reduction and may preferentially reduce nitrate when it is
available. Although Fe(III) reducers can simultaneously reduce Fe(III) and Mn(IV), Mn(IV) chemically reoxidizes Fe(II) produced during Fe(III) reduction back to Fe(III) [Lovley, 1991] so that there can be
no net Fe(III) reduction until Mn(IV) is depleted.
Thus regulation of metabolism within some microorganisms and the competition for electron donors
between various communities of microorganisms are
the major factors responsiblefor the segregationof the
TEAPs into distinct zones. It is important to recognize
that the segregationof TEAPs is not absolute. For
example, when perturbations to the environment result in a major shift from steady state conditions, two
or more TEAPs may coexist and compete until conditions that permit one microbial community to dominate over another are established [Lovley and Goodwin, 1988]. Furthermore, when the supply of an
electron acceptor limits the metabolism of one community (for example, low Fe(III) availability permitting only slow rates of Fe(III) reduction), this can
permit the coexistenceof another community (sulfate
reducers in this example) that would otherwise be
excluded.
DIVERSITY
AND
MICROORGANISMS
DISTRIBUTION
OF
IN THE DEEP SUBSURFACE
Within the last decade it has become apparent that
most, if not all, of the physiological types of microorganisms that are thought to be important in sedimentary environments as was discussed above can be
recovered from the deep subsurface (Table 1). These
studieshave relied on the ability of the investigators to
culture the organisms. However, in some instances,
standard cultural techniques do not yield any microorganismsin samplesin which the microorganismscan
be observed microscopically [Ekendahl et al., 1994].
In such instances the identity of the microorganisms
may be revealed by analyzing the gene sequencesin
DNA extracted from the water or sediments [Ekendahl
et al., 1994].
372 ß Lovleyand Chapelle: DEEPSURFACEMICROBIAL PROCESSES
33, 3 / REVIEWSOF GEOPHYSICS
TABLE 1. Recent Examples of Recovery of MicroorganismsFrom the Deep Subsurface
Environment
Reference
Aerobic Microorganisms
Deep aquifers in Atlantic coastalplain
Balkwill [1989], Balkwill et al. [1989], Chapelle et al. [1987,
1988], Fredrickson et al. [1989, 1991a], Sinclair and
Ghiorse [ 1989]
Buried-valley aquifer system, northeasternKansas
Groundwaters from granite bedrock, Sweden
Ashfall tuff at Rainer Mesa, Nevada Test Site
Deep aquifers in Atlantic coastal plain
Alkaline, basaltic aquifers, Washington
Sinclair et al. [1990]
Pedersen and Ekendahl [1990]
Amy et al. [1992] Haldeman et al. [1993]
Fe(III) and Mn(IV) Reducers
Lovley et al. [1990] Chapelle and Lovley [1992]
Stevens et al. [1993]
Sulfate Reducers
Olson et al. [1981]
Groundwaters from Madison Formation (dolomitic
limestone)
Jones et al. [1989] Chapelle and Lovley [1992]
Deep aquifers in Atlantic coastal plain
Groundwaters from granite bedrock, Sweden
Alkaline, basaltic aquifers, Washington
Pedersen and Ekendahl [ 1990]
Stevens et al. [1993]
Methane
Groundwater from deep aquifer in Florida
Alkaline, basaltic aquifers, Washington
Formation waters of oil fields thermophilic
Producers
Godsy [1980]
Stevens et al. [1993]
Belyaev et al. [1983], Davydova-Charakhch'yan et al. [1992]
Until recently there were seriousquestionswhether sulfate reducers, and methane producers have also
the microorganisms that had been previously recov- been isolated (Table 1).
Microorganisms have been recovered from the
ered from the deep subsurfacemight be contaminants
that had been introduced from the surface either dursandy sediments comprising deep aquifers and from
ing drilling or from the subsequentexposure of deep clayey aquitards [Balkwill, 1989; Chapelle et al., 1987,
aquifers to the surface. Now, rigorous samplingtech- 1988; Fredrickson et al., 1989; Sinclair and Ghiorse,
niques have been developed to prevent contamination 1989] as well as within deeply buried rock [Amy et al.,
of the deep subsurfaceduring drilling operations. Cur- 1992; Haldeman et al., 1993; Pedersen and Ekendahl,
rent techniques for minimizing contamination of deep 1990]. Microbial numbers and activity are generally
subsurfacesamplesinclude (1) the use of various trac- lower in the clayey layers than in the sandy sediments
ers (microspheres, bromide, rhodamine dye, and per- [Balkwill, 1989; Chapelle and Lovley, 1990; Fredrickfluorocarbons)in drilling fluids to monitor drilling fluid son et al., 1989; Hicks and Fredrickson, 1989; Phelps
contamination of cores, (2) steam cleaning of bore et al., 1989; Sinclair and Ghiorse, 1989]. This might be
equipment and the use of chlorinated water in drilling the result of lower pH [Sinclair and Ghiorse, 1989],
muds, and (3) paring away of the external surfacesof hydraulic conductivity [Fredrickson et al., 1989], or
the sediment core prior to sampling [Chapelle, 1993; water potential [Fredrickson et al., 1989] in the clayey
Russell et al., 1992]. With the use of these techniques sediments.Alternatively, it has been proposedthat the
there is a high level of confidencethat the microorgan- very small pore throat diameters in the clays restrict
isms recovered from deep subsurface cores represent the mobility of microorganismsand that the low interindigenouspopulations. Further indication of the lack connectedness of the pores in the clays limits the
of surface contamination is the finding that the micro- movement of nutrients relative to the sandy aquifer
organisms recovered from the deep subsurface are sediments [Chapelle and Lovley, 1990]. Recent expergenerally different strains from those that inhabit the imental evidence suggeststhat small pore throats do in
surface [Balkwill et al., 1989; Olson et al., 1981; Bee- fact restrict microbial activity [Sharma and Mclnerman and $ufiita, 1989; Jones et al., 1989].
ney, 1994].
The source of microorganisms living in the deep
Of the various types of microorganisms, aerobic
ones have been studied most intensively (Table 1) subsurface is a current area of intense investigation.
becauseof the ease in culturing these organisms.Stud- Indirect evidence for microorganisms living on reies of deep aquifers in the Atlantic coastal plain have duced gases emanating from the Earth's core raises
indicated that there is a wide diversity of aerobic the possibility that life may have actually evolved in
microorganisms, mostly living attached to the sedi- deep subsurface environments [Gold, 1992]. The
ment surface [Balkwill et al., 1989; Fredrickson et al.,
aquatic sedimentsthat were buried to form many deep
1991a;Hazen et al., 1991]. However, other physiolog- aquifers undoubtedly contained high numbers of a
ical types of microorganisms such as Fe(III) reducers, wide diversity of microorganisms. The aquifer envi-
33, 3 / REVIEWSOF GEOPHYSICS
Lovleyand Chapelle: DEEPSURFACEMICROBIAL PROCESSESß 373
ronment is much different from the original aquatic
sediments,especially with regard to the availability of
easily degradedorganicmatter. Thus present-daydeep
subsurfacemicroorganismsmay be a relic community
consistingof the microorganismsthat had the appropriate characteristics to metabolize and grow, or at
least survive, for long periods of time during continued
sediment burial and aquifer formation. Some microorganisms may also be introduced into deep aquifers
along with recharge water. However, because of the
slow flow of water through deep aquifers beyond the
recharge area, such introduced microorganismsmust
be well adapted to the aquifer environment or they will
not survive to reach the interior portions of the aquifer. Thus regardless of the original source of the microorganisms, the current microbial community is the
result of a host of environmental pressuresthat over
long periods of time have selectedfor the present-day
composition. Therefore the source of the organismsis
likely to be less significantthan the present environmental conditions as a factor controlling the types of
microbial activity in deep aquifers.
As long as appropriate energy sourcesare available,
the primary factors limiting the distribution of microbial life in the deep subsurfaceare likely to be temperature and water activity [Pedersen, 1993]. The generally acceptedupper temperaturelimit for microbial life
is approximately 110øC[Stetter et al., 1990], but some
microbiologists speculate that the actual upper limit
may be closer to 150øC[Demirig and Baross, 1993]. A
variety of thermophilic microorganismshave been recovered from the deep subsurface(Table 1). The recovery of ultrafine-grainedmagnetite, presumablydue
to the activity of Fe(III)-reducing microorganisms,has
been suggestedas evidence of life as deep as 6.7 km
[Gold, 1992].
MONITORING
THE ACTIVITY
MICROORGANISMS
OF
IN THE DEEP
SUBSURFACE
Several studies have indicated that not only are
microorganismspresent in the deep subsurface, but
they have the potential to be active under the environmental conditionsin the deep subsurface.Incubations
of deep subsurfacesedimentmaterial have resulted in
the production of carbon dioxide or methane over time
[Chapelle et al., 1988; Jones et al., 1989; Kieft and
Rosacker, 1991; McMahon et al., 1990; Morris et al.,
1988], suggestingthat microorganismshave the potential to metabolize the organic matter present in these
samples.Furthermore,low concentrations
of •4C-labeled organic compounds added to deep subsurface
samples are often rapidly metabolized [Chapelle and
Lovley, 1990; Hicks and Fredrickson, 1989; Madsen
and Bollag, 1989; McMahon and Chapelle, 1991b;
Phelps et al., 1989]. Laboratory incubations have also
demonstrated that microorganismswith the potential
to reduce nitrate to N2 [Francis and Dodge, 1989;
Morris et al., 1988] and Fe(III) to Fe(II) [Lovley et al.,
1990] are present in the deep subsurface.
The limitation of such laboratory incubations is that
they may not reflect the in situ activity of deep subsurface microorganisms. The rates of microbial activity in such laboratory incubations can be orders of
magnitude faster than what actually takes place in
deep aquifers [Chapelle and Lovley, 1990]. Thus laboratory incubations demonstrate the potential for microbial activity in such environments but do not give
quantitative information on the processesactually taking place.
The potential limitations of laboratory incubations
and the technical difficulties and expense in sampling
deep subsurfacesedimentshave led to approachesin
which microbial activity in aquifers is inferred through
the analysis of groundwater chemistry. The newest of
these techniquesis the measurementof dissolved H2
[Lovley et al., 1994]. This technique was developed
becauseit is not often possible to determine the TEAP
in a given groundwater through standard analysis of
groundwater chemistry [Fish, 1993; Hostettler, 1984;
Lindberg and RunnelIs, 1984] The H2 technique is
basedon the concept that as was outlined above, H2 is
constantlyproduced and consumedin anoxic sedimentary environments. It has been demonstrated both
theoretically and experimentally that under the steady
state conditions typical of such environments, the H2
concentrationis dependent solely upon the physiological properties of the microorganisms consuming the
H2 and is independentof other factors suchas the rate
of organicmatter decomposition(e.g., rate of H 2 production) [Lovley et al., 1994; Lovley and Goodwin,
1988]. Thus there are specific H2 concentrationsthat
are characteristic for each type of anaerobic microbial
process(Figure 2), and measurementof H2 concentrations in groundwater can be used to identify which
TEAPs are taking place in a particular anoxic zone of
an aquifer.
The usefulnessof the H2 technique was evidenced
in a study of the microbial metabolism of the Black
Creek aquifer in South Carolina [Chapelle and McMahon, 1991; McMahon and Chapelle, 1991a]. It could
be demonstrated that organic matter was being oxidized to carbon dioxide in the aquifer from the accumulation of dissolved inorganic carbon along the
groundwater flow path. However, there was not sufficient loss of potential electron acceptors or accumulation of reduced products to account for the carbon
dioxide production. H2 measurementsindicated that
the organic matter was being oxidized to carbon dioxide with the reduction
of sulfate.
This conclusion
was
later corroborated by analysis of sediment cores,
which indicated that sulfide was being produced but
was precipitating as iron sulfide. The reason that sul-
374 ß Lovleyand Chapelle: DEEPSURFACEMICROBIALPROCESSES
33, 3 / REVIEWSOF GEOPHYSICS
Figure5. Ratesfor oxidationof organicmatterto carbondioxidein deep seawater,deepoceansediments,
and deep aquifer systems.
fate was not being depleted from the groundwater was
that sulfate was diffusing in from the confining beds.
The H2 technique is limited in that it can only
specify which TEAP predominates in a given section
of an aquifer and cannot be used to estimate the rates
of microbial processes.However, through geochemical modeling it is often possibleto estimate the rate of
microbial processesin aquifers solely on the basis of
changes in water chemistry along groundwater flow
paths. For example, the rates of organic matter oxidation in several deep aquifers in the Atlantic coastal
plain were estimated from the accumulation of dissolved inorganic carbon in the groundwater along
groundwaterflow paths of the aquifers [Chapelle and
Lovley, 1990]. Data on other mineral constitutentsand
basic geochemical principles were used to estimate
how much of the increase in dissolved inorganic carbon was the result
of the dissolution
of carbonate
minerals, and the estimates of the amount of dissolved
inot--gaaic
ca•bo•!••ifing••m
organicmaer ox• a-
tion were corrected accordingly. The rates of organic
carbon oxidation estimated from geochemical modeling were consistent with the known age of the sediments and the probable availability of organic matter
in the aquifers. These studies demonstrated that the
rates of microbial metabolism in the deep aquifers
examined are at least 103-105 times slower than those
in modern surface sedimentary environments and are
comparableto the rates of organic matter oxidation in
highly oligotrophic deep ocean waters (Figure 5).
SOURCES
OF ORGANIC
MICROBIAL
MATTER
FOR
METABOLISM
The organic matter that supports microbial metabolism in deep subsurfaceenvironmentsprobably originates within the deep subsurface. Recharge to local
flow systems is generally low in dissolved organic
carbon [Thurman,
1985]. Furthermore,
studies on
deep aquifers in the Atlantic coastal plain demonstrated that there was no net decrease
in dissolved
organic carbon as water moved through the aquifers
[Lee, 1984].
The amount of particulate organic matter in deep
subsurface environments can be extremely variable.
aaqun
y
• er se •mentsconta•n•relativelylittle metabolizable organiccarbon (---0.1%) comparedwith the
clayey confining beds (1-50%) [Johnson and Wood,
1993; McMahon et al., 1990]. Yet as was discussed
above, rates of microbial oxidation of organic compounds to carbon dioxide and the numbers and diversity of microorganisms are generally highest in the
sandy aquifer sediments. These observations raise
33, 3 / REVIEWSOF GEOPHYSICS
Lovleyand Chapelle: DEEPSURFACEMICROBIAL PROCESSESß 375
Figure 6. Model for organic matter metabolism in some deep aquifers in the Atlantic coastal plain in which
organic matter is fermented within the clayey confining beds and the fermentation acids diffuse into the
sandy aquifer sediments,where they are consumedby respiratory processessuch as Fe(III) reduction and
sulfate reduction.
fundamental questionsas to sourcesof organic carbon
supportingmicrobial activity in the sandy aquifer sediments.
reduction of protons to H 2 with reduced minerals in
the basalt may provide H 2 as an electron donor to
support microbial activity [Stevens and McKinley,
A potential explanation for the apparent higher 1994].
rates of organic matter oxidation in the sandy aquifer
material despite lower supplies of organic carbon is
EFFECTS OF MICROBIAL
ACTIVITY
that the processesof fermentation and respiration are GEOCHEMICAL
segregated into distinct zones [McMahon and IN THE DEEP SUBSURFACE
Chapelle, 1991b]. This hypothesisis based, in part, on
There have been only a few microbiological studies
the finding that production and consumption of fermentation products are not necessarilycoupled in lab- that have directly examined the geochemical effects of
oratory incubations of deep subsurface sediments microbial activity in the deep subsurface. As is de[Johnson and Wood, 1992; Jones et al., 1989; McMatailed below, much of the information on geomicrobial
hon and Chapelle, 1991b]. In this model (Figure 6), processes in the deep subsurface must be inferred
organic acids produced in the confining beds diffuse from the geochemistry of groundwater. Most microbiinto the sandy aquifer sediments,where they are con- ologically oriented studies have focused on the potensumed by respiratory microorganisms which oxidize tial metabolic capabilities of microorganisms recovthe organic acids to carbon dioxide. Gradients of or- ered from the deep subsurfacewith little investigation
ganic acids between confining beds and aquifer sedi- into whether that metabolic potential could be exments sufficient to support microbial metabolism pressed in situ.
through diffusive flux of organic acids from confining
beds to aquifer sedimentshave been documented [Mc- ContaminantMobility
Much of the recent interest in the microbiology of
Mahon and Chapelle, 1991b]. In this way, large pools
of organic carbon in the confining beds may support the deep subsurfacehas been stimulated by a concern
microbial activity in the sandy aquifers. However, it about potential contamination of these important
has yet to be explained why respiration is inhibited in drinking water resources. Microbial degradation or
the confiningbedsbut fermentation
is not.
immobilization of contaminantsmay naturally mitigate
Another potential source of electron donors in the the effect of some groundwater pollution, and it might
deep subsurfaceis reduced compoundsproduced abi- be possibleto stimulate the activity of microorganisms
ologically within the deep subsurface.For example, it capable of removing contaminantsfrom groundwater.
has been speculatedthat reducedgasessuchas H 2 and Several studies have demonstrated that aerobic micromethane emanating from great depth in the Earth may organismscapable of degrading contaminants such as
support microbial activity in the deep subsurface phenol [Hicks and Fredrickson, 1989], indole [Madsen
[Gold, 1992]. In deep basalt aquifers the abiological and Bollag, 1989], quinoline [Brockman et al., 1989],
376 ß Lovleyand Chapelle: DEEPSURFACEMICROBIAL PROCESSES
33, 3 / REVIEWSOF GEOPHYSICS
carbonate as the result of organic matter oxidation can
also drive the above equation from right to left with a
the rate and extent to which these contaminants would
net precipitation of carbonate matehal [Dimitrakopoube degraded in situ cannot readily be predicted from a los and Muehlenbachs, 1987; McMahon and Chapelle,
mere demonstration of the presence of such organ- 1991a]. In many deep subsurface environments the
isms.
history of porosity enhancement via carbon dioxide
At present it is difficult to envision how reliable production and porosity destruction via carbonate prepredictions of the rates of contaminant degradation in cipitation is very complex. In most ancient carbonates
the deep subsurface will be made. As was noted these processeshave led to the complete cementation
above, attempts to measure the rates of degradation of of the original material and the production of fully
naturally occurring organic matter in the deep subsur- lithified limestones and dolomites. However, the presface with laboratory incubations of deep subsurface ervation of small zones characterized by porosity enmaterial have been found to grossly overestimate the hancementare extremely important becausethis availrates of in situ degradation. The concern is that similar able porosity can store petroleum and natural gas
types of incubations examining the degradation of or- [Moore and Druckman, 1981]. The production of secganic contaminantswill yield equally spuriousresults ondary porosity in deep subsurfaceenvironments is
and predict faster rates of contaminant degradation one of the most important processes leading to the
accumulationof economic hydrocarbon deposits.
than are likely to take place in situ.
The potential for introduction of radioactive waste
Organic acids produced by fermentation of organic
into deep subsurfaceenvironments through accidental matter in anoxic deep subsurface environments may
spills or the potential deep subsurfacedisposal of ra- also have an important influence on the diagenesisof
dioactive material has also been a major motivating deep sediments.However, the role of these fermentafactor in the study of deep subsurface microbiology tion productshas only recently been investigated[Mc[Pedersen, 1993]. Microorganisms attached to parti- Mahon and Chapelle, 1991b] and reflects the difficulty
cles in the deep subsurface may adsorb radioactive of accounting for observed secondary porosity based
contaminants from groundwater. Deep subsurfacemi- solely on abiological processes [Lundergard et al.,
croorganismscapable of Fe(III) reduction may also be 1984]. Studies with shallow subsurface sediments concapable of reducing U(VI) to U(IV) (unpublished taminated with petroleum hydrocarbons [Hiebert and
data), and this can precipitate uranium in anoxic envi- Bennett, 1992] indicate that organic acid production
ronments [Lovley and Phillips, 1992; Lovley et al., can significantlyenhancethe porosity of silicate aqui1991a]. Microorganisms may also enhance the mobil- fer materials. It is possiblethat similar processesmay
ity of radioactive contaminants through transport of be importantin deep subsurfaceenvironmentsas well,
contaminants adsorbed onto unattached bacteria, cor- particularly in organic-rich or hydrocarbon-bearing
rosion of waste disposal containers, or production of horizons.
chelating agents which might solubilize contaminants
Microbial Processes Associated With Fossil Fuels
[Pedersen and Ekendahl, 1990].
Microbial processes in the deep subsurface may
and aromatic hydrocarbons [Fredrickson et al., 1991b]
can be recovered from the deep subsurface.However,
PorosityDevelopment
Although much of the recent work on microbial
processesin the deep subsurfacehas focused on the
effect of microorganisms on contaminant mobility,
other phenomena are more common and of more general importance, since most deep subsurfaceenvironments are relatively contaminant-free. For example,
the progressive accumulation of dissolved inorganic
carbon along the groundwater flow path is one of the
most universally observed features of intermediate
and regional flow systems [Back, 1966; Chapelle and
Lovley, 1990; Murphy et al., 1992; Plummer et al.,
1990;Thorstensonet al., 1979].CO2is a weak acid and
contribute
to the formation
or alteration
of fossil fuels.
Although some investigators have suggestedthat petroleum can form by purely microbial processes
[Levorsen, 1967], it is more generally acceptedthat the
microbial contribution to petroleum and coal formation is the selective removal of labile organic compounds from the organic matter that is subsequently
transformed into fossil fuels by abiotic processes
[Hatcher et al., 1983; Pettijohn, 1975]. Thus the initial
formation of petroleum and coal deposits is actually
the result of a lack of microbial degradation of the bulk
of the organic matter.
Microbiological processes in the deep subsurface
can
ir•y
genera e me ane. sotop•c an m•cro •can ••ve
carbonates in sediments:
ologicalevidence suggeststhat microbial methane production is an important mechanism for methane forCO2+ CaCO3+ H20--> Ca2+ + 2HCO•mation in some hydrocarbon-bearing deposits
Carbonate dissolution can result in the development of [Belyaev and Ivanov, 1983;Belyaev et al., 1983;Davysecondary porosity and permeability in deep subsur- dova-Charakhch'yan et al., 1992]. Biogenic methane
face environments [McMahon et al., 1992; Moore and can be distinguishedfrom thermogenic methane by its
Druckman, 1981]. However, the accumulation of bi- characteristically light carbon isotopic signature and
33, 3 / REVIEWSOF GEOPHYSICS
Lovleyand Chapelle: DEEPSURFACEMICROBIAL PROCESSESß 377
its lack of associated C2 and C3 hydrocarbons ganismswas responsible for the accumulation of Fe(II)
[Schoell, 1983]. Biogenic methane is often encoun- in the groundwater.
tered in shallow (<2000 m), immature reservoirs
[Sohoell, 1983]. Microbial methane production has
also been reported in intermediate and regional aquifer
systems, where it can significantly affect the major ion
and carbon isotopic composition of the groundwater
[Grossman and Coffman, 1989; Thorstenson et al.,
1979]. Active methane production in the deep subsurface has been reported only in the absence of alternative electron acceptors such as sulfate or Fe(III)
[Thorstenson et al., 1979]. Deep aquifer systems that
have extensive
mineral
sources of sulfate
were found
to lack significant methane production [Plumruer et
al., 1990]. These observations are in accordance with
the ability of Fe(III) reducers and sulfate reducers to
outcompete methane producers, as discussedabove.
Fe(111)Reduction
Microbial Fe(III) reduction is one of the dominant
microbially catalyzed redox processesin many subsurface environments [Chapelle, 1993]. Although Fe(III)
reduction in sedimentary environments is frequently
regarded as an nonenzymatic process, recent studies
have demonstrated that most of the organic matter
oxidation coupled to Fe(III) reduction is enzymatically
catalyzed [Lovley, 1991; Lovley et al., 1991b].
Fe(III) reduction in the deep subsurfaceis of interest because in addition to serving as an important
mechanism for organic matter oxidation, it can cause
serious water quality problems. This is because the
Fe(III) reduction converts highly insoluble Fe(III) oxides to Fe(II), which is much more soluble. Undesirably high concentrations of soluble Fe(II) cause problems because when the groundwater is pumped to the
surfaceand contacts02, the Fe(II) is oxidized back to
Fe(III) oxides, which will either clog wells or, if they
make it through the plumbing system, discolor the
water and cause staining problems.
In zones of Atlantic coastal plain aquifers with high
concentrations of dissolved Fe(II), geochemical evidence indicated that organic matter was being oxidized
Sulfate Reduction
Sulfate reduction has been one of the most intensely
studied deep subsurface microbial processes [Bastin,
1926; Davis, 1967; Dockins et al., 1980; Jones et al.,
1989; Olson et al., 1981; Rosnes et al., 1991; Rozanova
and Khudyakova, 1974; Rozanova and Nazina, 1979].
In fact, one of the classic debates in deep subsurface
microbiology was whether or not there was microbial
sulfate reduction in clastic aquifers lacking mineral
sources of sulfate (such as gypsum). Cedarstrom
[1946] proposed that sulfate reduction was the principal bicarbonate-producing mechanism in the clastic
aquifers of the Atlantic and Gulf coastal plains. However, no direct evidence for sulfate reduction in these
sediments was provided. Foster [1950] argued that
sulfate reduction could not be important because increases in bicarbonate concentrations along aquifer
flow paths were not balanced by decreases in sulfate
concentrations. She suggested that the accumulation
of bicarbonate in the groundwater was the result of
abiological decarboxylation reactions. Evidence for
the potential importance of microbial sulfate reduction
in these aquifers was provided by the recovery of
sulfate reducers from these sediments [Chapelle et al.,
1987]. Furthermore, the lack of sulfate depletion noted
by Foster has been reconciled by the finding that there
are high concentrations of sulfate in the confining beds
and that diffusive flux from the confining beds to the
aquifers can support the sulfate reduction [Chapelle
and McMahon, 1991].
One of the best examples of sulfate reduction in a
sulfate mineral-bearing carbonate aquifer was given in
a study of the Madison aquifer system [Plummet et al.,
1990]. The Madison aquifer was one of the first regional aquifer systems shown to harbor active sulfatereducing bacteria [Olson et al., 1981]. Sulfate concentrations continually increase along flow paths because
the progressive dissolution of gypsum and anhydrite
exceeds the rate of sulfate reduction. However, sulfate
to carbon dioxide and the concentrations
of dissolved
reduction is indicated by the accumulation of bicarH 2 were characteristicof sedimentsin which organic bonate associated with the generation of dissolved
matter was being oxidized with the reduction of Fe(III)
sulfides and by the relatively light isotopic composi[Chapelle and Lovley, 1992]. Fe(III) reducers could be tion of the dissolved sulfides.
recovered only from portions of the aquifers with
undesirably high Fe(II) [Lovley et al., 1990]. Furthermore, a Fe(III) reducer isolated from these sediments CONCLUSIONS
could couple the oxidation of organic matter to the
Studies to date have demonstrated
that a wide direduction of the Fe(III) oxides in the aquifer sediments
[Lovley et al., 1990]. There was no Fe(III) reduction in versity of microorganisms can be recovered from the
incubated sediments in the absence of the Fe(III)deep subsurface and that their activity can greatly
reducing microorganism. These findings, and the fact influence the geochemistry of deep subsurface envithat there is no known mechanism
other than microronments. However, in comparison to the study of
bial Fe(III) reduction that can significantlycouple the surface aquatic habitats, the study of biogeochemistry
oxidation of organic matter to the reduction of Fe(III),
of the deep subsurface is still in its infancy.
indicated that the activity of Fe(III)-reducing microorMore detailed investigations into the physiology
378 ß Lovleyand Chapelle' DEEPSURFACEMICROBIAL PROCESSES
33, 3 / REVIEWSOF GEOPHYSICS
surface sampling procedures using serendipitous microand ecology of deep subsurface microorganisms are
bial contaminants as tracer organisms, Geomicrobiol. J.,
likely to give further insight into the factors controlling
7, 223-233, 1989.
the rate and extent of important geologicalphenomena
Belyaev, S.S., and M. V. Ivanov, Bacterial methanogenesis
in the deep subsurface. A relatively small number of
in undergroundwaters, in Environmental Biogeochemisstudieshave recovered microorganismsfrom the deep
try and Ecology Bulletin, edited by R. Hallberg, pp.
subsurface,and those studieshave focuseddispropor273-280, Ecological Bulletins Publishings House, Stockholm, 1983.
tionately on aerobic microorganisms. More study on
anaerobic microorganisms is necessary, given that Belyaev, S.S., R. Wolkin, W. R. Kenealy, M. J. DeNiro, S.
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D. R. Lovley,Water ResourcesDivision,U.S. Geological
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