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ECOLOGY
Microb Ecol (2000) 39:153-167
DOI: 10.1007/s002480000018
? 2000 Springer-VerlagNew York Inc.
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.
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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
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156 O.L. Snoeyenbos-Westet al.
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
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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)
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].
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
100
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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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SubsurfaceFe(III)-ReducingCommunity Structure 167
actions in aquatic sediments. Geochim Cosmochim Acta genes from natural ecosystems. Curr Opin Microbiol 2:317-
52:2993-3003 322
33. LovleyDR, Phillips EJP(1986) Organicmatter mineralization 45. MuyzerG, Wall ECD, UitterlindenG (1993) Profilingof com-
with reduction of ferric iron in anaerobic sediments. Appl plex microbialpopulationsby denaturinggradientgel electro-
Environ Microbiol 51:683-689 phoresisanalysisof polymerasechain reaction-amplifiedgenes
34. Lovley DR, Phillips EJP (1992) Bioremediation of uranium coding for 16S rRNA. Appl Environ Microbiol 59:695-700
contamination with enzymatic uranium reduction. Environ 46. Nevin KP, Lovley DR (2000) Potential for nonenzymatic re-
Sci Technol 26:2228-2234 duction of Fe(IJJ)during microbialoxidation of organic mat-
35. Lovley DR, Phillips EJP (1989) Requirementfor a microbial ter coupled to Fe(III) reduction. Environ. Sci. Technol.
consortium to completely oxidize glucose in Fe(IIJ)-reducing 47. Picard C, Ponsonnet C, Paget E, Nesme X, Simonet P (1992)
sediments. Appl Environ Microbiol 55:3234-3236 Detection and enumerationof bacteriain soil by direct DNA
36. Lovley DR, Phillips EJP,Gorby YA, LandaER (1991) Micro- extraction and polymerasechain reaction. Appl Environ Mi-
bial reduction of uranium. Nature 350:413-416 crobiol 58:2717-2722
37. Lovley DR, Phillips EJP,Lonergan DJ (1989) Hydrogen and 48. RaskinL, StromleyJM,RittmannBE,StahlDA (1994) Group-
formate oxidation coupled to dissimilatoryreduction of iron specific 16S rRNA hybridization probes to describe natural
or manganeseby Alteromonasputrefaciens.Appl Environ Mi- communities of methanogens. Appl and Environ Microbiol
crobiol 55:700-706 60:1232-1240
38. Lovley DR, Woodward JC (1996) Mechanisms for chelator 49. RobertsMS, Cohan FM (1995) Recombinationand migration
stimulation of microbial Fe(IlI)-oxide reduction. Chem Geol rates in natural populations of Bacillus subtilis and Bacillus
132:19-24 mojavensis.Evolution 49:1081-1094
39. LovleyDR, WoodwardJC, ChapelleFH (1996) Rapidanaero- 50. Rooney-VargaJN, AndersonRT, FragaJL,RingelbergD, Lov-
bic benzene oxidation with a varietyof chelatedFe(III) forms. ley DR (1999) Microbialcommunities associatedwith anaero-
Appl Environ Microbiol 62:288-291 bic benzene mineralization in a petroleum-contaminated
40. Lovley DR, Woodward JC, Chapelle FH (1994) Stimulated aquifer.Appl Environ Microbiol 65:3056-3063
anoxic biodegradationof aromatichydrocarbonsusing Fe(III) 51. SwoffordDL (1998) PAUP*,PhylogeneticAnalysisUsing Par-
ligands. Nature 370:128-131 simony (* and other methods) Version 4. SinauerAssociates,
41. Maclntyre WG, Boggs M, Antworth CP, StaufferTB (1993) Sunderland,MA
Degradationkinetics of aromatic organics solutes introduced 52. Van de PeerY, De WachterY (1994) TREECONfor Windows:
into a heterogeneousaquifer.WaterResourRes 20:4045-4051 A softwarepackagefor the construction and drawingof evo-
42. MaidakBL, Cole JR, CharlesT, ParkerJ, GarrityGM, Larsen lutionary trees for the Microsoft Windows environment.
N, Li B, LilburnTG, McCaugheyMJ, Olsen GJ, OverbeekR, Comput Applic Biosci 10:569-570
PramanikS, SchmidtTM, TiedjeJM,Woese CR (1999) A new 53. VargasM, KashefiK, Blunt-HarrisEL,Lovley DR (1998) Mi-
version of the RDP (Ribosomal DatabaseProject). Nucl Acid crobiological evidence for Fe(IIJ) reduction on early Earth.
Res 27:171-173 Nature 395:65-67
43. Methe BA, Hiorns WD, Zehr JP (1998) Contrasts between 54. ZwartG, Hiorns WD, Methe BA, AgterveldMP, HuismansR,
marine and freshwater bacterial community composition: Nold SC, Zehr JP, LaanbroekHJ (1998) Near-identical 16S
Analysesof communities in Lake George and six other lakes. rRNA sequences recoveredfrom lakes in North America and
Limnol Oceanog 43:368-374 Europe indicate the existence of clades of freshwaterbacteria
44. Muyzer G (1999) DGGE/TGGE,a method for identifying with global distribution.Syst Appl Microbiol 21:546-556
This content downloaded from 128.119.49.10 on Fri, 18 Sep 2015 16:35:12 UTC
All use subject to JSTOR Terms and Conditions
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