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Snoeyenbos-West OL, Nevin KP, Anderson RT, Lovley DR.. Enrichment of


Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer
sediments. Microb Ecol 39: 1...

Article  in  Microbial Ecology · March 2000


DOI: 10.1007/s002480000018 · Source: PubMed

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ECOLOGY
Microb Ecol (2000) 39:153-167
DOI: 10.1007/s002480000018
? 2000 Springer-VerlagNew York Inc.

Enrichment of GeobacterSpecies in Response to Stimulation of


Fe(III) Reduction in Sandy Aquifer Sediments

O.L. Snoeyenbos-West,K.P. Nevin, R.T. Anderson, D.R. Lovley


Department of Microbiology,University of Massachusetts,Amherst, MA 01003, USA

Received:19 October 1999; Accepted:28 December 1999; Online Publication:25 April 2000

|A B S T R A CT
Engineeredstimulation of Fe(III) has been proposed as a strategyto enhance the immobilizationof
radioactiveand toxic metals in metal-contaminatedsubsurfaceenvironments.Therefore,laboratory
and field studies were conducted to determine which microbial populations would respond to
stimulation of Fe(III) reduction in the sediments of sandy aquifers. In laboratory studies, the
addition of eithervarious organicelectron donors or electron shuttle compounds stimulatedFe(III)
reductionand resultedin Geobactersequencesbecoming importantconstituentsof the Bacterial16S
rDNA sequences that could be detected with PCR amplificationand denaturinggradientgel elec-
trophoresis (DGGE). Quantification of Geobacteraceaesequences with a PCR most-probable-
number technique indicatedthat the extent to which numbers of Geobacterincreasedwas relatedto
the degreeof stimulationof Fe(III) reduction. Geothrixspecieswere also enrichedin some instances,
but were orders of magnitude less numerous than Geobacterspecies. Shewanellaspecies were not
detected, even when organic compounds known to be electron donors for Shewanellaspecies were
used to stimulate Fe(III) reduction in the sediments. Geobacterspecies were also enriched in two
field experiments in which Fe(III) reduction was stimulated with the addition of benzoate or
aromatichydrocarbons.The apparentgrowth of Geobacterspeciesconcurrentwith increasedFe(III)
reduction suggests that Geobacterspecies were responsiblefor much of the Fe(1II)reduction in all
of the stimulation approachesevaluatedin three geographicallydistinct aquifers.Therefore,strat-
egies for subsurfaceremediationthat involve enhancingthe activityof indigenous Fe(III)-reducing
populations in aquifers should consider the physiologicalproperties of Geobacterspecies in their
treatment design.

Introduction als in subsurfaceenvironments[22]. Severalmetals and met-


alloids, including uranium, technetium, chromium, cobalt,
Engineered stimulation of dissimilatory metal reduction and selenate, are more soluble, and thus mobile, in the oxi-
may be a useful method for immobilizing contaminantmet- dized state and tend to precipitatein the reduced state [22].
For example,many microorganismscapableof dissimilatory
Correspondenceto: D.R. Lovley; Fax: (413) 545-1578; E-mail: dlovley@ metal reductioncan reducesoluble U(VI) to insolubleU(IV)
microbio.umass.edu [25, 36], and stimulation of microbial U(VI) reduction un-

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154 O.L. Snoeyenbos-Westet al.

der laboratoryconditions has been shown to precipitateura- [30, 31] can also stimulate Fe(III) reduction in sediments
nium from contaminated groundwaters[34]. [46]. These compounds can greatlyaccelerateFe(III) reduc-
Fe(III) is generallythe most abundant possible electron tion by alleviating the need for metal reducers to directly
acceptor for dissimilatory metal-reducing microorganisms contact insoluble metals or metals occluded within pore
in soils and sediments [23, 25]. Most Fe(JII)-reducingmi- spaces too tight for metal reducers to access [30, 31, 46].
croorganisms can also reduce Mn(IV), which is typically Fe(I1I)reduction can also be stimulated in subsurfacesedi-
present at concentrationsabout 10%of those of Fe(III) [23, ments with the addition of Fe(III) chelators that solubilize
25]. Fe(III) and Mn(IV) are abundant in many subsurface Fe(III) and make it more readilyavailablefor Fe(III) reduc-
soils and are likely to be in higher concentrationsthan con- tion [38, 39, 40]. However, this third option is not an ap-
taminant metals, even under conditions of severe contami- propriatestrategyfor stimulatingdissimilatorymetal reduc-
nation. Therefore,stimulation of dissimilatorymetal reduc- tion in metal-contaminated subsurface environments be-
tion to immobilize metal contaminantsalso involves micro- cause the chelators that solubilize Fe(III) may also chelate
bial reduction of the Fe(III) and Mn(IV) in the soils. The contaminant metals and enhance their mobility.
reduction of Fe(III) and Mn(IV) along with contaminant Highly transmissivesandy aquifers are likely subsurface
metals may be beneficialbecause the Fe(II) and Mn(II) pro- environmentsin which contaminantmetal mobility may be
duced can serveas a redox bufferto help preventreoxidation of concern. Such highly porous sediments are also among
of the reducedcontaminantmetals. Furthermore,since most the most amenable for in situ treatment strategiesthat in-
of the dissimilatoryFe(III)- and Mn(IV)-reducingmicroor- volve the addition of soluble stimulants. Therefore,a com-
ganisms that have been evaluated are capable of reducing bination of laboratoryand field studies was conducted in
contaminant metals [24, 25, 29], stimulation of Fe(III) and order to determine which microbial populations are stimu-
Mn(IV) reduction may increase the population size of mi- lated when Fe(III)reductionis acceleratedin sandy aquifers.
croorganismsthat can also reduce contaminantmetals. Such The results from both field and laboratorystudies demon-
stimulation may thus enhance rates of contaminant metal stratethat stimulation of dissimilatorymetal reductionwith
reduction. a variety of electron donors and/or electron shuttling com-
In order to understandhow to most effectivelyaccelerate pounds results in the specific enrichment of Geobacterspe-
dissimilatorymetal reduction in subsurfaceenvironments,it cies.
is important to know which microbialpopulations are pro-
moted when dissimilatory metal reduction is artificially
stimulated. A wide phylogenetic diversity of Bacteria [24] Materials and Methods
and Archaea [53] are capableof dissimilatoryFe(III) reduc- Incubations
Laboratory
tion. It is conceivablethat the growth and activityof any of
these known Fe(III) reducers,or as yet undescribedspecies, Sediments for laboratory studies were collected from an aquifer
locatedin Bemidji,Minnesota.Portionsof the aquiferat this site
might be enhanced when Fe(III) reduction is stimulated in
have been contaminatedwith crude oil, and the petroleum-
contaminated subsurface environments. Which dissimila- contaminatedportionof the aquifercontainsan extensivezone of
tory metal reducersbecome predominant might be affected Fe(III)reduction [4, 5, 50]. For this study, sedimentswere collected
by such factorsas the physiologicalpropertiesof the Fe(III)- from a nearbyuncontaminated,aerobicportion of the aquiferwith
reducing microorganisms,the geochemistryof the environ- a truck-mounted drill rig and sterilizedcore barrels,as previously
ment, the composition of the microbialcommunity prior to described [5]. The cores were sectioned, immediately capped,
wrappedin plasticwrap, sealedwith duct tape, and placedin plastic
stimulation, and the method used to stimulatemetal reduc-
bags under an N2 atmosphere prior to shipment in coolers via
tion. overnightcarrierto the laboratory.In the laboratory,sediments (40
Three mechanisms for stimulating Fe(III) reduction in g) were transferredinto serum bottles (5 ml) under N2 in a glove
sedimentary environments have been identified. Previous bag. The bottles were sealed with thick butyl rubber stoppers and
studies have demonstratedthat addition of known electron removed from the glove bag, and the headspacewas flushed with
donors for Fe(III) reducers can stimulate Fe(III) reduction N2-CO2 (93:7). Acetate(10 mM), lactate(5 mM), formate (5 mM),
benzoate (2 mM), or glucose (3.3 mM) were added as electron
in aquaticsediments [33], and this is also a likely strategyfor
donors at the stated final concentrations from anaerobic stocks.
stimulatingFe(III)reduction in organic-poorsubsurfaceen- Triplicatebottles of each treatmentwere incubated in the dark at
vironments. The addition of electron shuttlingorganic com- 20?C. The sediments were subsampled over time, and HCl-
pounds such as humic acids or other extracellularquinones extractableFe(II) and Fe(III) were determined as previously de-

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SubsurfaceFe(III)-ReducingCommunity Structure 155

scribed [4]. Subsamples(2 g) of sediment were frozen at -80?C for ing an argonheadspace.Samplesfor molecularanalysiswere frozen
the molecular analysesdescribedbelow. at -80?C.
The effect of humics and anthraquinone 2,6-disulfonate Concentrationsof dissolved hydrogen at the gate 2 and gate 3
(AQDS) on the rate of Fe(III) reduction in the sedimentswere also sampling sites were determined in October 1997 using the bubble
determinedin a relatedstudy [46], where all of the sedimentswere strip method as previously described [28]. HCl-extractableFe(III)
amended with acetate (5 mM) as the electron donor and various and Fe(II) on the same sediments used for molecularanalysiswere
concentrationsof humics or AQDS. Subsamplesthat were frozen at determined as describedabove.
-800C for molecularanalysisduringthat study were analyzedin the
study reported here.
PCR-DGGE
Analysisof SedimentMicrobialCommunities

The phylogeneticdiversityof the microbialcommunity in the sedi-


Columbus Field Site
ments was evaluatedwith PCR amplificationof 16S rDNA genes
and denaturinggradientgel electrophoresis(DGGE) [44, 45]. PCR-
A field study was conducted to determinethe effect of the addition
DGGE methods employed were as previously described [50], but
of petroleum hydrocarbonson the microbiologyand geochemistry
included the following modifications: PCR was performed using
of a sand and gravel aquifer at the Columbus Air Force Base,
bacterialprimers 338F-GC (the complement of EUB338) [2] and
Columbus, Mississippi [6, 41]. This is the site of a groundwater
907R [20] with touchdown primer annealing from 65 to 55?C
researchfacilityfor the U.S. Air Force.A syntheticjet fuel mixture
(decreasing0.5?C per cycle), followed by 10 cycles at 55?C. This
was placed within the aquifer in order to simulate the effect of a
prevents amplification of nonspecific PCR products. In addition,
hydrocarbonspill in an aquifer.The development of the hydrocar-
archaealdiversitywas accessed in the sampled sediments with Ar-
bon plume and its effects on the subsurfacemicrobialecology were
chaea-specific primers ARC344 (5'-ACGGGGAGCAGCAGGC-
monitored over time. Sedimentswere cored and samplesprocessed
GCGA-3') [48] and 0915Ra Reverse (5'-GTGCTCCCCCGC-
as described above. The predominant terminal electron-accepting
CAATTCCT-3')[1]. 16S rDNA ampliconswere resolvedby DGGE
process in the sediments was determined with the [2-'4C]acetate
with a 40 to 80% denaturinggradient(where 100%is equivalentto
technique [26]. Samples from a portion of the Fe(III)-reducing
7 M urea and 40% formamide) [45] on a 7% acrylamidegel in lx
zone that developed in the aquiferas well as a nearby,uncontami-
TAE (40mM Tris-acetate(pH 7.4), 20 mM sodium acetate, 1 mM
nated site were frozen at -800C for molecular analysis.
EDTA). Standardsof referenceDNA, extractedfrom various pure
cultures as previouslydescribed [50], were run along with the en-
vironmental samples for ease of comparison among the different
Borden Field Site
gels. DGGEgels were run for 15 h at 65 V and 60?C.PCRproducts
from excised DGGEbands were purified using the QlAquick PCR
Sedimentsfrom a field study in which benzoate was injected into a
Purificationkit (Qiagen Inc., Valencia, CA), and sequenced using
sandy aquifer in order to promote anaerobic respiration were
Dye Deoxy Terminator Cycle Sequencing (Perkin-ElmerCetus)
kindly provided by B.J.Butler,Universityof Waterloo. Portions of
and an ABI 377 automated sequencer (Applied Biosystems,Foster
the Borden aquiferwere divided with sheet piling to fashion three
City, CA) at the University of MassachusettsSequencingFacility.
treatmentgates parallelto groundwaterflow. A contaminant solu-
tion containing perchloroethylene(6 MtM),carbon tetrachloride(6
riM), and toluene (12 1iM)was added to the groundwaterin the Phylogenetic
Analysisof SequenceData
gates. Gate 2 receivedthis contaminantsolution only and no other
additions. However, gate 3, in addition to the contaminants, also The Ribosomal DatabaseProject (RDP) [42] CHECK_CHIMERA
received during the treatment period a solution of benzoate (2.1 programand secondarystructuredeterminationwere used to check
mM), which was injected into the groundwaterat gate 3 approxi- the partial16S rRNAgene sequencesfor potentialchimericartifacts
mately every 14 days. This was done in order to promote anaerobic [18]. Sequenceswere analyzedusing BLAST(National Center for
respirationin the gate. In this study, sediments of gate 2 and gate Biotechnology Information) and SIMILARITY_RANK (RDP) in
3 were analyzed,as well as sedimentsfrom a nearbysite that did not order to find the most similar available database sequences. Se-
receive any additions. Sediment cores were collected from gates 2 quences were then manuallyaligned with closely related 16S rRNA
and 3 and the backgroundsite over an intervalof 1.5 to 3 m below sequencesfrom RDP and GenBank,using the graphicaluser inter-
ground surface on 4 July and 4 November 1997, after severalpe- face SeqLab (Wisconsin Package version 10; Genetics Computer
riodic injections of benzoate into the gate 3 site. Sediment cores Group (GCG), Madison, WI). Only those sequence regions that
were collected in aluminum core barrels, capped and sealed with could be alignedwith confidencewere included in the analyses,and
duct tape, then returned to the lab where each 1.5-m core sample gaps were treated as missing nucleotides. Phylogenetictrees were
was cut into 0.3-m sections. Each section was then placed into an inferredfrom unambiguouslyaligned sequence data, using the dis-
N2-filled anaerobicbag. About 1 cm of materialfrom the ends of tance, maximum-likelihood, and maximum-parsimony tools of
each section was discardedand the center portion of each section PAUP* [51].
was sampled, homogenized in sterilizedaluminum pans, and allo- Distance and maximum likelihood analyseswere performedus-
cated into sterile Whirlpakbags inside sterile canningjars contain- ing heuristic tree searchingvia simple stepwise addition with tree

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156 O.L. Snoeyenbos-Westet al.

bisection reconnection rearrangement. Unweighted parsimony


analysis used the branch-and-bound algorithm. In addition, 80
the distance tools (neighbor joining of Kimura distances) of
TREECONfor Windows 1.3b [52] were employed. Three different 70
methods of phylogenetictree constructionwere used with the same
data set in order to test the robustness of the generatedtree topo- 60
logy. One thousand bootstrap replicates were performed on the
data set. Phylogenetictrees inferredusing the two differentsoftware 50
packagesdescribedabove showed the same topologies.
uL 40

MPN-PCR
Analysisof Sediments 3 -0 0 Cont-ol
30 -U-- ~~~~~~~~Acetate
// Benzoate
The relative numbers of Geobacteraceae, Geothrix,and Shewanella
20 -v- Formate
species were determined in sediment samples using an MPN-PCR Glucose
-4-
technique [5, 47]. DNA was extracted from triplicate sediment
10 Lactate
---~~~~~~~~~
samplesas describedabove. Serial10-fold dilutions of the sediment
10
DNA were made in sterile water, and 3-[dlaliquots of the diluted
DNA were used as template in the PCR.PartialGeobacteraceae 16S
0 10 20 30 40 50
rDNA sequences were amplified with bacterialforwardprimer 8F
(5' -AGAGTTTGATCCTGGCTCAG-3') and Geobacteraceae- Days
specific reverse primer Geo825R (5'-TACCCGCRACACCTAGT-
3') in the first round of a semi-nested PCR protocol, followed by Fig. 1. Rates of Fe(IIL)reduction shown as an increase of Fe(II)
338F [2] and Geo825R in the second round. The PCR conditions over time in sediments from the Bemidji aquifer incubated under
were as previouslydescribed [5] except that 1 [l of the first-round anaerobic conditions and amended with various electron donors.
reaction product served as template in second-round reactions. The resultsare the means of triplicatedeterminations,and standard
Geothrixspecies were also enumeratedwith a semi-nested MPN- deviations are shown on the graph as error bars.
PCR protocol. The primersfor the first round of PCRwere 8F and
the Geothrix-specific reverse primer Gx.472R (5' -AGGT-
ACCGTCAAGTAACASS-3'). The Geothrix-specificforwardprimer
Gx. 182F (5' -AGACCTTCGGCTGGGATGCT-3')and Gx.472R
were analyzedafter49 days of incubation.Samplesamplified
were the primers for the second round. Both the Geobacteraceae with primers designed to amplify the 16S rDNA from Ar-
and Geothrix-specificprimers were designed and tested for speci- chaea did not yield detectablePCRproduct. However,prim-
ficity in our lab prior to use in lab and field experiments (manu- ers which amplify the 16S rDNA of most Bacteriadid yield
script in preparation). In addition, partial Shewanella16S rDNA PCRproductswhich could be resolvedvia DGGE(Fig. 2). In
sequencesin sediment from the stimulationexperimentswere enu-
accordancewith previous analysesof the Bemidji sediments
merated using the Shewanella-specificprimer set Sw.783-F (5'-
AAAGACTGACGCTCAKGCA-3')and Sw. 1245-R (5' -TTYG- [50], a low diversityof bandswas recoveredfrom the control
CAACCCTCTGTACT-3')(manuscriptin preparation). sediments. Sequenceanalysisof excised bands demonstrated
that the control sediments contained a 16S rDNA sequence
closely relatedto known Geobacterspecies. Other sequences
Results recoveredfrom the control sedimentswere closely relatedto
Effectof ElectronDonorAmendmentsto BemidjiAquifer Thiobacillusaquaesulisand several unidentified ,B-Proteo-
Sediments bacteria. Thiobacillusaquaesulis is not known to reduce
Fe(III), but we do not rule out the possibility that some of
Each of the electron donors evaluated produced an increase these as yet unidentified13-Proteobacteriamay be able to do
in the rate of Fe(III) reduction in Bemidji sediment relative so. This question awaits further study.
to unamended controls (Fig. 1). The addition of acetate, DGGE bands with mobilities similar to that of the Geo-
glucose, and lactate resulted in the fastest rates of Fe(III) bacterband observed in the control sediments were recov-
reduction; rates were intermediate with benzoate. Formate ered from sedimentsamendedwith the electrondonors (Fig.
additions resulted in the lowest rates of Fe(III) reduction. 2). The sequences of these bands were 99.8-100% similar
Each sediment type was subsampled for analysis of 16S and could be assignedto the genus Geobacter(Fig. 3). Band
rDNA sequences when approximately 60% of the Fe(LII)had intensitywas muchgreaterin the sediments amended with
been reduced, with the exception of control sediments which electron donors than' in the control. Sediments in which

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Subsurface Fe(III)-Reducing Community Structure 157

Standard Standard
.. Fotn 3azaormate

Clostridium
_

Clostridium
redeubacterium
f1-Proteobacten

_ ~~~~ M 1i#t r .
_ ~~~~~~Formats Goo2
f3-Proteobacteri' Denftrobancterium
aq
Thiobaoillus

Fig. 2. DGGE profile of bacterial 16S rDNA fragmentsretrievedfrom Bemidji sediments. Individualbands that yielded useful sequence
data are labeled with the microorganismsto which the sequenceswere most similar. Other unlabeledbands were not separatedenough to
be cut from the gel, were chimeras, or did not yield good-quality sequence data. DGGE bands labeled in bold were sequenced, and the
phylogenetic placement of these sequences is shown in Fig. 3.

Fe(III) reductionwas greatlystimulated (acetateand glucose the control sediments. These results indicate that the stimu-
amended) had the most intense bands (Fig. 2). The intensity lation of Fe(III) reduction with electron donors resulted in
of an analogous band in the formate-amended sediments increasednumbers of Geobacteraceae. This is in accordance
was notably less, correspondingto the lower rates of Fe(III) with the qualitativeresults from the DGGE analysis.
reduction (Fig. 1). Dominant and intense DGGEbands may Another notable result from the DGGE analysiswas the
be consideredthe most abundantbacterialspecies [13], and detection of 16S rDNA sequences closely related to Clos-
based on their intensity, the Geobacterbands can be consid- tridiumspecies in the sediments amended with glucose, but
ered to represent the predominant species in the amended not in the other electron donor amendments (Fig. 2). This is
sediments. The formate- and lactate-amended sediments consistent with the concept that fermentative microorgan-
also contained a second Geobacterband, Formate Geo-2 isms metabolize glucose in sediments in which Fe(III) re-
(Fig. 2), that differed in mobility, but was closely related to duction is the terminal electron-acceptingprocess with sub-
the other Geobactersequences in the sediments (Fig. 3). sequent metabolismof the fermentationproductsby Fe(III)-
These resultssuggestedthat, regardlessof the electron donor reducing microorganisms [23, 35].
added, stimulation of Fe(III) reduction with the electron Sequences for other extensively studied Fe(III)-reducing
donors enriched for Geobacterspecies that were very closely microorganismssuch as Shewanellaspecies or Geothrixfer-
related. mentanswere not detectedwith the DGGEanalysis.In order
In order to further evaluate the effect of the added elec- to furtherevaluatethe potential role of these organisms,they
tron donors on the size of the Geobacterpopulation, num- were enumeratedwith the MPN-PCRtechnique, with prim-
bers of Geobacteraceae16S rDNA sequences from donor- ers that were specific for these organisms. No Shewanella
amended sediments were enumerated with MPN-PCR [5, sequences could be detected, even in sediments amended
47]. The sediments that initially had the highest rates of with known electron donors for Shewanellaspecies, such as
Fe(III)reductionhad severalordersof magnitudemore Geo- lactate and formate.No Geothrixsequenceswere detected in
bacteraceaesequences than the control sediments or sedi- unamendedcontrol sediments,but Geothrixsequencescould
ments amended with formate (Fig. 4). Formate-amended be enumeratedin sediments amended with electron donors
sediments had slightly more Geobacteraceae sequences than (Fig. 4). The highest number of Geothrixsequences were

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158 O.L. Snoeyenbos-Westet al.

Borden Geo-1
_ Borden Geo-2
Borden Geo-3
70 Borden Geo-4
Borden Geo-5
Borden Geo-6
Borden Geo-7
62
Borden Geo-8
Borden Geo-9
Borden Geo-1 0
LBorden Geo-1I
Humics Geo-82
Humics Geo-24
ControlGeo-1
AQDS Geo-i
Humics Geo-1
Humics Geo-2 ma
94. Humics Geo-3 Z L
Formate Geo-2 co
Glucose Geo-1
Acetate Geo-1
Benzoate Geo-1
Formats Geo-1 0
Lactate Geo-1
BemidjiGeo-60
BemidjiGeo-83 O
Borden Geo-101 0 0
Bemidjibenzene enrichment(Benz-76) @ Fig. 3. Phylogenetic tree inferred
Columbus Geo-1 0 from 16S rRNA sequences showing
Columbus Geo-2 the phylogeneticplacementof Geo-
"Geobacterbemidjiensis"
Geobacter arculus bacter sequences amplified from
82 o
Geobactersulfureducens Q sediments in three different aqui-
Geobacter metallireducens 0 fers, and from environmental iso-
Geobacter hydrogenophilus lates. Phylogenetic relationships
L Pelobacterpropionicus shown here were inferredby using
Geobacter chapellei
GeobacterALA6 neighbor joining and Kimuratwo-
Geobacter humireducens parameter genetic distances in
GeobacterALA5 TREECON[52]. A total of 400 base
Geobacter akaganeitreducens positions were considered in the
84 100 Desulfuromrusa bakii
100 LDesulfuromusakysingii analysis.Bootstrapvalues above 60
Desulfuromnusasuccinoxidans are shown adjacentto branchnodes
Pelobacter carbinolicus and were calculatedfrom 1,000 re-
r Pelobacter acetylenicus sampled data sets using neighbor
Desulfuromonasacetoxidans joining. The scale bar shows ex-
Desulfuromonasacetexigens
pected nucleotide substitutionsper
Pelobacter venetanus
100 Humics Dsf-1 site per unit of branch length. Op-
100 FColumbus Dsfi1 erationalTaxonomic Units (OTUs)
BemidjiGeo-144 0 shown on the tree in bold are the
62 1 Borden Dsf-1o 0
same sequences obtained using
LI BemidjiGeo-47
uE DGGE from amended sediments
BemidjiGeo-52 0
100 BemidjiGeo-48 and fields sites in this study. Those
61 r 1Bemidji Geo-58 shown in plain text are from a pre-
c Ua
00 BemidjiGeo-43 q vious study of the Bemidji aquifer
BemidjiGeo-3 [50], and from GenBank and the
BemidjiGeo-2 RDP databases.A similar tree to-
Desulfovibriovulgaris
Escherichiacoli pology was generatedfor trees con-
structed using maximum-likeli-
0.1 substitutions/site
hood and maximum-parsimony
methods (data not shown).

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SubsurfaceFe(III)-ReducingCommunity Structure 159

109 Fe(III)had been reducedin all of the humics-amendedsedi-


1 At8
-
lE Geobacter ments [46]. The Geobacterband was also intensified in the
Fig.4 Geothrix control sediments after 82 days of incubation,which is con-
106- sistent with significantFe(III) reduction in those sediments
fee)n dn10 r
by that time [46].
Other bands that comprised Geobactersequences were
1- 104
E also recoveredfrom some of the humics-amendedsediments
z 0
" 100 V (Fig. 5A). These Geobactersequences were very closely re-
lated to the Geobactersequence that predominatedin all the
humics-amended sediments. However, one Geobacteraceae
sequence, which yielded a faint DGGE band (Dsf-1), fell
within the Desulfuromonascluster of the Geobacteraceae
[21]. A sequence closely relatedto the thermophilicFe(III)-
reducing microorganismBacillusinfernus[7] was recovered
from the sediments amendedwith the highest concentration
of humics, but not from the other sediments. Also, some
recoveredfrom sediments amendedwith acetateand lactate. other unique bands emergedin the sedimentsamendedwith
This is in accordance with the physiological properties of high concentrations of humics (Fig. 5A and Fig. 5B), but
known Geothrix species, which oxidize acetate and lactate none of these are known humics- or Fe(III)-reducingmi-
with Fe(III) as the electron acceptor,but do not metabolize croorganisms.
glucose, benzoate, or formate [10]. In results similar to those observed with the humics
In all of the sedimentsamendedwith electron donors, the amendments, the addition of 10, 50, or 100 iM AQDS
numbers of Geothrixsequenceswere severalorders of mag- stimulatedFe(IIJ)reduction [46] and resultedin an enrich-
nitude lower than the number of Geobactersequences (Fig. ment of a Geobacterspecies (Fig. 6) whose sequence was
4). This is consistent with the predominance of Geobacter 99.6% similar to the sequences that predominated in the
sequences and lack of Geothrix sequences in the DGGE humics- and donor-amended sediments (Fig. 3). This band
analysis. These results further indicate that stimulation of associatedwith Geobacterwas not observedin the sediments
Fe(III) reduction by addition of electron donors primarily amendedwith 500 [tMAQDS, which correspondsto the fact
resulted in an increase in Geobacterspecies. that the addition of 500 [M AQDS did not stimulateFe(III)
reduction in these sediments [46].
MPN-PCR analysis indicated that the humics-amended
Effectof Stimulationof Fe(lll)Reductionwith
sediments contained up to three orders of magnitude more
Extracellular
Quinones
Geobacteraceaethan the control sediment after 24 days of
The addition of humics or the humics analog AQDS stimu- incubation (Fig. 7). The number of Geobacteraceaese-
lated Fe(III) reductionrinBemidji sediments [46]. Humics- quences increasedin the control sediments between 24 and
amended sediments from that study were analyzedafter 24 82 days of incubation (Fig. 7), correspondingto increased
days of incubation,at which point the following percentages Fe(III) reduction in the control sediments over this period
of the HCl-extractableiron had been reduced: no humics [46]. However,the number of Geobactersequencesremained
added, 3.7%;0.1 g humics added, 8.2%;0.5 g humics added, significantlyhigher in the humics-amended sediments. The
54.4%; 1 g humics added, 58%; 2 g humics added, 82.1% AQDS-amendedsediments had a similar trend, but with an
[46]. PCR,DGGE,and sequence analysisindicateda specific even wider disparitybetween the number of sequencesin the
enrichment of a Geobacterspecies in the humics-amended control sediments versus the sediments in which Fe(III) re-
sediments (Fig. 5A). The dominant Geobactersequence ob- duction was stimulated.Therewere five ordersof magnitude
servedwas 99% similarto the Geobactersequencesthat pre- more Geobactersequencesin the sediment amendedwith 10
dominated in the electron-donor amended sediments (Fig. and 100 MMAQDS than in the control (Fig. 8). The sedi-
3). The enrichment of this Geobactersequence continued ments that were amendedwith 500 [MM AQDS had numbers
through 82 days of incubation (Fig. SB) when most of the of Geobactersequences similar to those in the control sedi-

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160 O.L. Snoeyenbos-Westet al.

I
.e~~~~~~~~~~~~~~~~~1

G
Humics
Humics
Humics
Humics
Humics
GA *

ControlGo trII le

| ~~~~~~~~~~infemus
tLFS

A Increasing of humics(gramsperl_fer)
concentration
Stndr
Humics mct Standard2
DenitrffyingFe
(d)-oxidizing
aedum
Abateou
j~~~~~~~~~~ _

A (Grams concentration
Increasing of humics perler)
Standard Standard
-postbaduum
Bac-tq dirostasonisum
* -t!t w _ w -. + ~~~~Erysipelothnx

~~~~~~~~~~~~~~~~~~~~~~Unidentified e-e-

u_ Cysprotoobacter
:s:.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
....X_X
..........
s-s.s
..

B of humics(gramsperliter)um
Increasingconcentration
2 .^;.: ;rffl ^ ^ w --Cyst ystbacter
Fi. .Deaurn gadet 0.0
e eetroporsi (G 0.1 E)prfl of0.5 1.0 t1 2-o
>obacteria6rDAfgmnsetivdroh umic-mne eij

sediment after24 (A) and 82 (B) days of incubation. Individualbands that yielded useful sequence data are labeledwith the microorganisms
to which the sequenceswere most similar.DGGEbands labeled in bold were sequenced,and the phylogeneticplacement of these sequences
is shown in Fig. 3.

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Subsurface Fe(III)-Reducing Community Structure 161

Stadard Standard

Dechiorimonas
aiau
PDsudnmonas

Pseudomonas

Go-
AQDS Itr_MIcans10-Protob
terIum
subgroup)

Increasingco raton of AQDS(pM)

Fig. 6. Denaturinggradientgel electrophoresis(DGGE) profile of bacterial16S rDNA fragmentsretrievedfrom AQDS-amendedBemidji


sediment after 82 days of incubation. DGGEbands labeled in bold were sequenced, and the phylogeneticplacement of these sequences is
shown in Fig. 3.

ments, which is consistent with the fact that rates of Fe(III)


in these sedimentswere similarto those in control sediments
[46]. c 107
Since Geothrixfermentansis known to oxidize acetateand E
.5 fl~~24
Days
reduce humics [10], the number of Geothrixsequences was '106
dyof incuban82.Days
also estimatedwith MPN-PCR.However,analysisof selected E
humics- and AQDS-amended sediments indicated that
numbers of Geothrixwere always at least four orders of
aL
CD) 104
magnitudelower than Geobacteraceae(unpublished data).
103
CO)
CD

In SituEnrichment
of Geobactersat a
CIS
Petroleum-Contaminated
Aquifer 0; 101
0) 10
In order to determine whether the stimulation of Fe(III)
reductionin the Columbus aquiferwith the addition of hy-
z
drocarbonsresultedin an enrichmentof Geobacteraceae, the 0 0.1 0.5 1 2
numberof Geobacteraceae sequences in the Fe(III)-reducing
Humics Added (grams/liter)
sedimentswere enumeratedwith MPN-PCR. Sedimentsad-
jacent to the hydrocarbonemplacement were anaerobic as
Fig. 7. MPN-PCRfor Geobacteraceaein Bemidjiaquifersediment
demonstratedby the accumulationof Fe(II) (44-394 iiM) in amended with humics. Sediments were sampled after 24 and 82
the groundwaterand the fact that 50% of the iron in the days of incubation.

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162 O.L. Snoeyenbos-Westet al.

CD
MPN-PCRanalysisindicated that there were 3.7 x 1 +
E 7.8 x 102 (mean ? standard deviation) Geobacteraceaese-
a) 108.-
quences in these Fe(III)-reducingsediments.In comparison,
nearbybackgroundsediments that were not affectedby the
0 hydrocarbonemplacementcontained only 7.7 x 102 ? 2.7 x
107 -
CY 106 lI1Geobacteraceaesequences. Thus, the development of
L)
CL Fe(III)-reducingconditions was associatedwith an increase
105
U"
in the number of Geobacteraceae.
2' The Geobacteraceaepopulations in the hydrocarbon-
0102
impacted sediments were further evaluated by amplifying
a) 101
aI) Geobacteraceae16S rDNA from the sediments with primers
338F-GC and Geo 825R, separatingthe PCR products with
DGGE, and excising and sequencing the resultant bands.
This procedureyielded four distinctbands,which comprised
three different sequences. Two of these sequences (Colum-
bus Geo-1 and Columbus Geo-2) were closely related Geo-
bactersequences (Fig. 3). The other sequence (Columbus
Dsf-1), which came from a faint DGGE band, was in the
ment after 82 days. Desulfuromonascluster of the Geobacteraceae[21].

sediments extractablein 0.5 N HCl was in the form of Fe(II). In SituEnrichment


of Geobacter in a
When [2-'4C]acetatewas added to the sediments it was oxi- Benzoate-AmendedAquifer
co

dized
0 to0 '4C02 without the production of 14CH4,and '4C02 Fe(IIJ)reduction appearedto be the dominant TEAPin the
a)3
production
-0)
0 10 was not inhibited in the presence of molybdate sediments at all three sampling sites of the Borden aquifer.
(data not shown). These results indicated that Fe(III) was All three sediments contained Fe(JI), but there was also
the predominantTEAP in these sediments [26]. Fe(III) availablefor microbial reduction in that Fe(II) ac-
counted for the following percentagesof the HCl-extractable
iron in the sediments:backgroundcontrol site, 63%;gate 2,
63%;and gate 3, 66%. Dissolvedhydrogenconcentrationsat
6r
ate
men 1
2a3s4 the Gate 2 samplingsite were generallyin the concentration
range typicallyfound for sediments in which Fe(II) reduc-
tion is the predominant TEAP (Fig. 9). Hydrogen was not
measured in the control sediments because of a lack of ap-
Fig.e9 hydoge
Dissolvedat over four-
conentrationsedmeatsured
propriatewells. The periodic additions of benzoate to gate 3
prdepthsion ihbthed oaionsofeprsedimen cfollecionate
welsjutaosdto indicatedthat metabolismwas not at steady-stateconditions
the BoredemnaqufesTE.Pi hs eiet and thus the hydrogen concentrationscould not be consid-
2]
ered to be diagnostic of the TEAP at this gate [28, 32].
However, hydrogen concentrations in gate 3 were higher
theBodenaqifGaste3 than in gate 2, which suggested that anaerobicmetabolism
had been stimulated in gate 3.
The apparentstimulation of anaerobicmetabolism with
the addition of benzoate to gate 3 was associatedwith much
higher numbers of Geobacteraceae sequences in this zone in
comparisonto gate 2, which receivedthe low concentrations
of chlorinatedcontaminantsand toluene but no benzoate,or
the control site, which receivedno additions (Fig. 10). Num-
bers of Geobacteraceae sequences in sediments from Gate 2

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Subsurface Fe(III)-Reducing Community Structure 163

108 to those that are readily available in pure culture. As dis-


l) I
0 1~07 July 1997 cussed earlier, the two methods that were used here to
stimulate Fe(III) reduction, the addition of electron donors
liX10_ 1 November 19 and the addition of electron shuttles, are the two most likely
CD~
OD 0 10?. -
101 strategies for stimulating dissimilatory metal reduction in
metal-contaminatedsubsurfaceenvironments.Thus, the re-
10
ICP
sults suggest that the design of strategiesfor the use of dis-
similatory metal reduction as a bioremediation tool should
102 consider that Geobacaer species are likely to be integralcom-
Z 101 ponents of the metal-reducingcommunity.

100

CONTAMINANTS BENZOATE& UNCONTAMINATED Effectof AddedElectronDonorson Fe(lIl)Reductionand


ONLY CONTAMINANTSBACKGROUND MicrobialCommunities
GATE2 GATE3
The addition of electrondonors effectivelystimulatedFe(III)
Fig. 10. Numbersof targetsequencesper gramof sedimentcor- reductionin both the laboratoryand field experiments.Elec-
respondingto membersof the Geobacteraceaedetectedby MPN-
tron donors used directly by a variety of microorganisms
PCRin Bordensedimentssampledat two differenttime points.
that conserve energy to support growth via metal reduction
include acetateand other short-chainfatty acids;long-chain
and the control site were similar,indicatingthat the addition fatty acids; monoaromatic compounds, and hydrogen [23,
of the low concentrationof chlorinatedsolvents and toluene 25]. Long-chain fatty acids are generallyinsoluble and thus
had little impact on this Fe(III)-reducingpopulation. can not be readilyadded to groundwater.Hydrogen is both
In order to determinewhich Geobacteraceae were present poorly soluble and explosive, and these characteristicspre-
in the Borden aquifersediments, 16S rDNA sequences were sent technical problems when introducing it into the sub-
amplified as described above, and the PCR products were surface. Although, as shown here, formate can serve as an
separatedwith DGGE. Although each sediment treatment electron donor for Fe(III) reduction, it did not stimulate
had a somewhat different complement of Geobacteraceae Fe(III) reduction as well as the other known electron donors
bands, no single band was found to be unique to the ben- that were evaluated.Formatehas additional potential draw-
zoate-treatedsediments in either position or intensity on the backs in that it is the salt of a corrosive acid and is also
gel (data not shown). Sequence analysis revealed that 11 rapidly disproportionatedto hydrogen and carbon dioxide
bands from the Borden gel form a monophyletic group in sediments. Therefore,formate is probably a poor choice
within the Geobactercluster of the Geobacteraceae, whereas as an electron donor for stimulation of Fe(III) reduction in
one sequence that was recovered from the control site falls the subsurface.
within the Desulfuromonascluster (Fig. 3). Glucose significantly stimulated Fe(III) reduction, but
this and other fermentable compounds have the potential
drawbackthat they may stimulate the excessive growth of
Discussion fermentative bacteria. The enrichment of microorganisms
with sequencessimilarto fermentativeClostridiain the sedi-
The results demonstrate that the stimulation of Fe(III) re- ments amendedwith glucose, but not in sediments amended
duction in sandy aquifer sediments was associated with a with other electron donors, suggests that the added glucose
specific enrichment of Geobacterspecies. This was true in did stimulate the growth of fermentativebacteria.Although
field as well as laboratorystudies, regardlessof the electron at least one Fe(III)-reducingShewanellaspecies can use glu-
donors or electron shuttles used to stimulate Fe(III) reduc- cose as an electron donor [10], it was apparentlynot com-
tion. This finding is of interest not only because of the petitive with the fermentative Clostridiaas no Shewanella
consistency of the enrichment for Geobacterspecies under sequenceswere detected. Fe(III) reducerscan be expected to
diverse conditions, but also because it represents a rare utilize the fermentation products that fermentativemicro-
instance in which microorganismsfound to be environmen- organismsproduce, as evidencedhere by the increasednum-
tally significantwith moleculartechniquesare closely related bers of Geobacterin the glucose-amendedsediments. How-

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164 O.L. Snoeyenbos-Westet al.

ever, stimulatingthe growthof fermentativemicroorganisms 50], it was found that there was a significantenrichment of
with glucose or other more complex fermentablesubstrates Geobacterin the zone where the most rapid oxidation of
could increase the possibility of plugging the aquifer with aromatichydrocarbonssuch as benzene [5] and toluene [4]
biomass that does not directly contribute to Fe(III) reduc- was taking place. DGGE analysis indicated that Geobacter
tion. species were major components of the community in those
In contrast to fermentable sugars, acetate, lactate, and aromatichydrocarbon-degradingsediments,and MPN-PCR
monoaromatic compounds can be directly oxidized to car- demonstratedthat the Geobacteraceae sequencesin the most
bon dioxide by Fe(III)-reducingmicroorganisms[23, 24]. It active Fe(III)-reducingsediments were four orders of mag-
was previously speculated [23] that Fe(III) reducerswith a nitude more numerous than in the uncontaminatedback-
metabolismlike that of the various Shewanellaspecies might ground sediments. This increase in Geobacterin the con-
first partiallyoxidize lactateto acetateand carbon dioxide in taminatedsedimentswas attributedto Geobacterspecies oxi-
Fe(III)-reducing environments. However, it has subse- dizing the aromatic hydrocarbonsat that site. The findings
quently been found that some Fe(III) reducers, including reported here that the growth of Geobacterspecies was en-
Geobacterspecies [11], can completely oxidize lactateto car- hanced with the addition of benzoate to Bemidji sediments,
bon dioxide. The finding that a Geobacterpopulation be- with the addition of benzoate to the Borden aquifer,and in
came dominant in the lactate-amendedsediments and that the presence of petroleum hydrocarbonsat the Columbus
there was no enrichmentof Shewanellasequencesin lactate- site demonstratethat Geobacterspecies are likely to be im-
amended sediments suggests that Geobacterspecies capable portant components of the Fe(JII)-reducingcommunity in a
of completely oxidizing lactate were most effective at scav- varietyof sandy aquifersin which Fe(III)reductionis stimu-
enging the added lactate. lated with monoaromatic compounds.
Acetate was very effective in stimulating Fe(III) reduc-
tion. Numerous members of the Geobacteraceae family can
oxidize acetate with the reduction of Fe(III) [24], as can Stimulation
of Fe(lIl)ReductionwithExtracellular
Quinones
Geovibrioferrireducens[9], Ferribacteriumlimneticum [12],
and Geothrixfermentans[10]. However,acetateadditionsled Recent studies have suggested that another strategy for
primarilyto the enrichment of a Geobacterpopulation. No stimulatingFe(III) reduction in subsurfaceenvironmentsis
sequences related to the other known acetate-oxidizing the addition of humics or other extracellularquinones [30,
Fe(III)-reducing microorganisms were among the most 31, 39, 46]. Fe(III)reducerscan reducethe quinones in these
prominent sequences recoveredin the DGGEanalysisof the organics to the hydroquinone state, and the hydroquinones
sediments. Enumeration of Geothrix 16S rDNA sequences can then abioticallyreduceFe(III) [30, 31] as well as Mn(IV)
with specific PCR primers indicated that the growth of this and contaminant metals such as uranium and technetium
bacterium was stimulated with the addition of acetate and (unpublished data). The Fe(III) reduction step oxidizes the
other electron donors. However, Geobactersequences were hydroquinone to the quinone, which can then undergo an-
typicallythree to five ordersof magnitudegreaterthan those other cycle of reduction and oxidation. This alleviatesthe
of Geothrix. need for Fe(III)-reducingmicroorganismsto come into di-
Benzoate additions stimulated Fe(III) reduction in the rect physicalcontactwith insolubleFe(III)oxides in orderto
laboratorystudies, and benzoate and aromatichydrocarbons reduce them. In addition, hydroquinonesgeneratedvia qui-
resulted in the development of Fe(III)-reducingconditions none reductionby Fe(III)reducersmay be able to enter pore
in the field studies. This result might have been expected spaces that are too small for Fe(III) reducers to enter and
based on previous studies,which have demonstratedthat the permit reduction of Fe(III) and other metals that would
releaseof monoaromatichydrocarbonsinto groundwateras otherwise be inaccessible [31]. Although there has not yet
the result of hydrocarboncontamination greatly stimulates been an opportunityto conduct a field trial on the effect of
Fe(III) reduction in aquifers [27, 26]. Geobacterspecies are the addition of extracellularquinones on Fe(III) reduction
the only Fe(III)-reducingmicroorganismsthat are known to in sandy aquifers, the laboratory results suggest that the
have the ability to oxidize monoaromatic compounds with addition of humics and other extracellularquinones will
the reduction of Fe(III) [24]. In previous studies of the pe- stimulate the growth and activity of Geobacterspecies in
troleum-contaminated portion of the Bemidji aquifer [5, aquifer sediments.

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SubsurfaceFe(III)-ReducingCommunity Structure 165

Implications
of the ApparentUbiquityof GeobacterSpeciesin reducing enrichment culture (Benz-76) from this site (Fig.
Fe(lIl)-Reducing
Sedimentsof SandyAquifers 3). An additionalGeobactersequence (BordenGeo-101) that
is 98% similar to Geo-83 was recovered from the Borden
The enrichment of Geobacterspecies in response to the sediments when the 16S rDNA was amplified with the PCR
stimulation of Fe(IIL)reduction in the studies reportedhere primer set designed to amplify the 16S rDNA of most Bac-
is consistent with the known physiologicalcharacteristicsof teria (Fig. 3). Although Desulfuromonassequenceswere less
Geobacterspecies that have been studied in pure culture. predominant than Geobactersequences, three partial 16S
However, it was not necessarilyexpected that stimulation of rDNA sequences (Humics Dsf-1, Columbus Dsf-1, and Bor-
Fe(III) reduction in sandy aquifersediments would result in den Dsf- 1) that fall within the DesulfuromonasClusterof the
the growth of organismsso closely relatedto those alreadyin family Geobacteraceae[21] were retrievedfrom each of the
pure culture. For example, it is commonly considered diffi- aquifer sites (Fig. 3). They are very similar to one another
cult to culture the microorganismsthat are the most envi- and to those found in a previousstudy of the Bemidjiaquifer
ronmentally significant [3]. Yet, the Geobactersequences [50] and are designated here as the "SubsurfaceDesulfu-
that predominatein the aquifersediments are closely related romonasCluster"(Fig. 3).
to Geobacterspecies in pure culture, and we have been able It is becoming increasinglyapparent[14, 15] that similar
to recover organisms in culture from the Bemidji aquifer microbial species may be ubiquitous in freshwater[43, 54],
that are closely related to the sequences that predominate marine [16, 17], and aerobicsoil environments [19, 49]. The
there. results presentedhere indicate that such microbial ubiquity
The consistent enrichment of similar Geobacterspecies, may also be extended to the anaerobiczones of sandy aqui-
regardlessof the method for stimulating Fe(JII) reduction, fers.
also could not have been anticipated in advance. For ex-
ample, from the known physiological characteristicsof the
Fe(III)-reducingmicroorganismsin pure culture it seemed Conclusions
possible that Shewanellaspecies that can oxidize lactate and
formate with the reduction of Fe(III) [8, 37] might have
The resultsof this study, as well as previousinvestigationsof
been stimulated when these electron donors were added.
a petroleum-contaminatedaquifer [5, 50], demonstratethat
The finding with moleculartechniques that Shewanellaspe-
organisms with 16S rDNA sequences closely related to
cies were either absentfrom the sediments or presentin very
known species of Geobacterspecies are significantlyenriched
low numbers is in accordancewith recent culturing studies,
under a variety of conditions that promote dissimilatory
which have indicated that even when lactate or formate are
Fe(III) reduction in sandy aquifers.The finding that it may
used as the electron donor, Geobacterspecies rather than
be possible to isolate the most important Fe(III)-reducing
Shewanellaare recoveredfrom soils (Coates, manuscriptin
microorganismsin pure culture provides a unique oppor-
preparation).
tunity to combine environmentaland culture studies to si-
One of the most interesting results was the finding that
multaneously investigate the biochemical and geochemical
the Geobacterspecies that predominated in the Fe(III)-
factorsinfluencingthe rate and extent of Fe(III)reductionin
reducing sediments from three geographicallydistinct aqui-
the subsurface.
fers had 16S rDNA sequences that were very similar, desig-
nated here as the "SubsurfaceGeobacterCluster."The Geo-
bactersequences that predominatedin the Fe(III)-reducing
sediments from Columbus (Columbus Geo-1 and Geo-2) Acknowledgments
and the Borden (Borden Geo-1 through Geo-11) aquifer
sediments were not only closely related to the Geobacter The NABIR Program of the Department of Energy (Grant
sequences in the Bemidji sediments from the laboratory DEFG0297ER62475)supportedthis work. We thank G. De-
studies reportedhere, but were also very similar to the pre- lin and W. Larsonfor Bemidjisediment samplecollection,T.
viously reported [50] Geobactersequences that were abun- Staufferand R. Stapletonfor coordinatingsample collection
dant in the Fe(III)-reducing zone of the Bemidji aquifer at the Columbus site, and B.J.Butlerfor sample collection at
(Geo-60 and Geo-83) and in a benzene-oxidizing, Fe(III)- Borden.

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166 O.L. Snoeyenbos-Westet al.

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