13
Extracellular electron transfer via microbial nanowires Gemma Reguera 1 , Kevin D. McCarthy 2 *, Teena Mehta 1 *, Julie S. Nicoll 1 , Mark T. Tuominen 2 & Derek R. Lovley 1 Microbes that can transfer electrons to extracellular electron acceptors, such as Fe(III) oxides, are important in organic matter degradation and nutrient cycling in soils and sediments 1,2 . Pre- vious investigations on electron transfer to Fe(III) have focused on the role of outer-membrane c-type cytochromes 1,3 . However, some Fe(III) reducers lack c-cytochromes 4 . Geobacter species, which are the predominant Fe(III) reducers in many environments 1 , must directly contact Fe(III ) oxides to reduce them 5 , and produce monolateral pili 6 that were proposed 1,2 , on the basis of the role of pili in other organisms 7,8 , to aid in establishing contact with the Fe(III) oxides. Here we report that a pilus-deficient mutant of Geobacter sulfurreducens could not reduce Fe(III) oxides but could attach to them. Conducting-probe atomic force microscopy revealed that the pili were highly conductive. These results indicate that the pili of G. sulfurreducens might serve as biological nanowires, transferring electrons from the cell surface to the surface of Fe(III) oxides. Electron transfer through pili indi- cates possibilities for other unique cell-surface and cell–cell interactions, and for bioengineering of novel conductive materials. The role of pili in Fe(III ) oxide reduction was studied with Geobacter sulfurreducens because a genetic system 9 and the complete genome sequence 10 are available. As expected from previous studies 6 , G. sulfurreducens produced pili during growth on Fe(III ) oxide (Fig. 1a) but not on soluble Fe(III ) (Fig. 1b), and the pili were localized to one side of the cell. The formation of pili could also be induced during growth on the alternative electron acceptor fumarate if the cells were grown at the suboptimal temperature of 25 8C (Fig. 2a), indicating that pilin production in G. sulfurreducens might be growth-regulated as it is in other bacteria 11 . The genome sequence of G. sulfurreducens contained two open reading frames (ORFs), GSU1496 and GSU1776, predicted to code for pilin domain proteins with the conserved amino-terminal amino acid characteristics of type IV pilins 12 . Phylogenetic analyses placed the protein encoded by ORF GSU1776 among bacterial pseudopilins of type II secretion systems, and subsequent studies have confirmed the role of this gene, termed oxpG, in protein secretion to the outer membrane 13 . The protein encoded by ORF GSU1496 formed an independent line of descent along with pilin subunits of other members of the Geobacteraceae such as Geobacter metallireducens and Pelobacter propionicus (Fig. 1c). The predicted length of these Geobacter pilin proteins was considerably shorter than other bacterial pilins (see Supplementary Fig. S1) and was restricted to the highly conserved N-terminal domain of bacterial type IV pilins, which functions in inner membrane insertion, signal processing and pilin polymerization, and forms the central helical core of the pilus filament 12,14 . The degree of conservation of geopilins at this region was lower than other bacterial pilins and, as a result, geopilins were LETTERS Figure 1 | Geobacter sulfurreducens pili. a, b, Transmisssion electron micrographs of cells grown with poorly crystalline Fe(III ) oxides (a) or soluble Fe(III) citrate (b). Arrows indicate pili. Scale bars, 0.5 mm. c, Phylogenetic distance tree derived from amino- terminal amino acid sequence alignments (see Supplementary Information and Supplementary Fig. S1) showing the relationship of annotated G. sulfurreducens pilin- domain proteins, encoded by GSU1496 and GSU1776, and pilins (blue branches) and pseudopilins (green branches) of other bacteria. d, Genomic organization of pilus biosynthesis genes surrounding GSU1496 in G. sulfurreducens and the pilA gene in M. xanthus 17 . 1 Department of Microbiology and 2 Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA. *These authors contributed equally to this work. Vol 435|23 June 2005|doi:10.1038/nature03661 1098 © 2005 Nature Publishing Group

Lovley Nanowires

Embed Size (px)

Citation preview

Page 1: Lovley Nanowires

Extracellular electron transfer via microbialnanowiresGemma Reguera1, Kevin D. McCarthy2*, Teena Mehta1*, Julie S. Nicoll1, Mark T. Tuominen2 & Derek R. Lovley1

Microbes that can transfer electrons to extracellular electronacceptors, such as Fe(III) oxides, are important in organic matterdegradation and nutrient cycling in soils and sediments1,2. Pre-vious investigations on electron transfer to Fe(III) have focused onthe role of outer-membrane c-type cytochromes1,3. However, someFe(III) reducers lack c-cytochromes4. Geobacter species, which arethe predominant Fe(III) reducers in many environments1, mustdirectly contact Fe(III) oxides to reduce them5, and producemonolateral pili6 that were proposed1,2, on the basis of the roleof pili in other organisms7,8, to aid in establishing contact with theFe(III) oxides. Here we report that a pilus-deficient mutant ofGeobacter sulfurreducens could not reduce Fe(III) oxides but couldattach to them. Conducting-probe atomic force microscopyrevealed that the pili were highly conductive. These resultsindicate that the pili of G. sulfurreducensmight serve as biologicalnanowires, transferring electrons from the cell surface tothe surface of Fe(III) oxides. Electron transfer through pili indi-cates possibilities for other unique cell-surface and cell–cellinteractions, and for bioengineering of novel conductivematerials.The role of pili in Fe(III) oxide reduction was studied with

Geobacter sulfurreducens because a genetic system9 and the completegenome sequence10 are available. As expected from previous studies6,G. sulfurreducens produced pili during growth on Fe(III) oxide

(Fig. 1a) but not on soluble Fe(III) (Fig. 1b), and the pili werelocalized to one side of the cell. The formation of pili could also beinduced during growth on the alternative electron acceptor fumarateif the cells were grown at the suboptimal temperature of 25 8C(Fig. 2a), indicating that pilin production in G. sulfurreducensmight be growth-regulated as it is in other bacteria11.The genome sequence of G. sulfurreducens contained two open

reading frames (ORFs), GSU1496 and GSU1776, predicted to codefor pilin domain proteins with the conserved amino-terminal aminoacid characteristics of type IV pilins12. Phylogenetic analyses placedthe protein encoded by ORF GSU1776 among bacterial pseudopilinsof type II secretion systems, and subsequent studies have confirmedthe role of this gene, termed oxpG, in protein secretion to the outermembrane13. The protein encoded by ORF GSU1496 formed anindependent line of descent along with pilin subunits of othermembers of the Geobacteraceae such as Geobacter metallireducensand Pelobacter propionicus (Fig. 1c). The predicted length of theseGeobacter pilin proteins was considerably shorter than other bacterialpilins (see Supplementary Fig. S1) and was restricted to the highlyconserved N-terminal domain of bacterial type IV pilins, whichfunctions in inner membrane insertion, signal processing and pilinpolymerization, and forms the central helical core of the pilusfilament12,14. The degree of conservation of geopilins at this regionwas lower than other bacterial pilins and, as a result, geopilins were

LETTERS

Figure 1 | Geobacter sulfurreducenspili. a, b, Transmisssion electronmicrographs of cells grown with poorlycrystalline Fe(III) oxides (a) or solubleFe(III) citrate (b). Arrows indicate pili.Scale bars, 0.5 mm. c, Phylogeneticdistance tree derived from amino-terminal amino acid sequencealignments (see SupplementaryInformation and SupplementaryFig. S1) showing the relationship ofannotated G. sulfurreducens pilin-domain proteins, encoded by GSU1496and GSU1776, and pilins (bluebranches) and pseudopilins (greenbranches) of other bacteria. d, Genomicorganization of pilus biosynthesis genessurrounding GSU1496 in G.sulfurreducens and the pilA gene inM. xanthus17.

1Department of Microbiology and 2Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA.*These authors contributed equally to this work.

Vol 435|23 June 2005|doi:10.1038/nature03661

1098© 2005 Nature Publishing Group

Page 2: Lovley Nanowires

phylogenetically distant from other bacterial pilins, including a typeIV pilin of another metal reducer, Shewanella oneidensis (Fig. 1c).Homologues of genes required for the formation and assembly of piliin other Gram-negative bacteria15,16 are upstream of the GeobacterpilA gene (Fig. 1d), in a genetic arrangement similar to that of the piligenes inMyxococcus xanthus17, a d-proteobacterium distantly relatedto Geobacter. These results indicate that the GSU1496 gene encodes apilin subunit, which was designated PilA.When pilA was deleted, G. sulfurreducens failed to produce pili

(Fig. 2b) and could no longer reduce insoluble electron acceptorssuch as poorly crystalline Fe(III) oxides (Fig. 3) and Mn(IV) oxides(data not shown). In contrast, the mutant could reduce solubleelectron acceptors, such as fumarate and Fe(III) citrate as well as thewild type. The mutant also grew in medium containing Fe(III) oxideif the chelator nitrilotriacetate was added to solubilize some of theFe(III) or in the presence of anthraquinone-2,6-disulfonate (AQDS)(Supplementary Fig. S2). AQDS serves as a soluble electron shuttleand transfers electrons between the cell surface and the surface of theFe(III) oxide18, alleviating the need for direct contact for Fe(III) oxidereduction5. Complementation of the pilAmutation with a functionalcopy of the pilA gene in trans restored the capacity for assembling pili(Fig. 2c) and for Fe(III) oxide reduction (Fig. 3a). These resultsshowed thatG. sulfurreducens required the assembly of functional pilito reduce insoluble Fe(III) oxides.One known function of type IV pili in other microorganisms is

establishing contact with surfaces7,8. Fe(III) oxides are typicallysmaller than G. sulfurreducens cells (Fig. 1a), but it was possible toquantify the potential for attachment of G. sulfurreducens to Fe(III)by inoculating fumarate-grown cells into medium in which Fe(III)oxide, attached to glass coverslips, was provided as the sole electronacceptor. Within the first 24 h, the cells of the pilA-deficient strainthat were added initially attached to Fe(III) oxides as well as the wildtype (Fig. 3b), but whereas the wild type grew on the Fe(III) oxide, asindicated by an increase in biomass on the Fe(III) oxide over the next24 h, the pilA mutant could not grow, as shown by a decrease inbiomass (Fig. 3b). The pilA-deficient mutant did grow on the surfaceif fumarate was provided as an alternative electron acceptor (data notshown). These results showed that pili are not required for Fe(III)oxides to attach to cells and confirmed the necessity for pili forgrowth with Fe(III) oxides as the sole electron acceptor. Furtherevaluation of the nature of the association of the Fe(III) oxides withthe cells revealed that, when Fe(III) oxides were added to fumarate-grown cells, the outer surface of the pilA-deficient mutant still hadthe ability to bind Fe(III) oxides (Fig. 3d) but in the wild type therewas substantial association of Fe(III) oxides with the pili (Fig. 3c).It has previously been proposed that Geobacter’s pili might

mediate surface motility, which might aid G. sulfurreducens inlocating Fe(III) or Mn(VI) oxides1,2,6, but no twitching motility ofthe wild-type cells was observed on glass surfaces coated with Fe(III)oxide. Furthermore, deleting a putative pilT gene (SupplementaryInformation), which is required for twitching motility in otherorganisms19, had no effect on Fe(III) oxide reduction.These results indicated that the pili might have a more direct role

in electron transfer to Fe(III) oxides. To evaluate this wemeasured theelectrical conductivity through the pili. Pili and other proteinsreleased from the outer surface of G. sulfurreducens grown withfumarate (Supplementary Fig. S3) were immobilized on a graphitesurface and analysed with an atomic force microscope (AFM)equipped with a conductive tip and electronics that permittedmapping of the local conductance from the tip to the substrate(Fig. 4). Topographic analysis revealed pili as well as other, uni-dentified, more globular, proteins which were also sheared off theouter cell surface (Fig. 4a). When a voltage was applied to the tipthere was a strong current response along the pilus filament, whichwas positive when a positive voltage was applied and negative with anegative voltage (Fig. 4b, c). In contrast, the non-pilin proteins hadno detectable conductivity and in instances in which the non-pilin

proteins covered the pili filaments they insulated the pili from theconductive tip. This general response, initially observed in relativelylarge-scale scans (Fig. 4a–c), was even clearer in cross-sections inwhich high current was associated with the slight increase intopography associated with the pilus filament, but the highertopography, associated with non-pilin material, had no detectablecurrent (Fig. 4d, middle panel). A scan across a portion of the pilinfilament overlain by other material also yielded no detectable current(Fig. 4d, bottom panel). Current line scans generated after applyingdifferent voltages while scanning the same region of a pilus demon-strated a linear, ohmic, correspondence between current and voltageapplied (Fig. 4e, f). When similar studies were performed with pilifrom the metal reducer Shewanella oneidensis or the non-metalreducer Pseudomonas aeruginosa (Supplementary Fig. S4 and S5),no conductance was detected.These results show that the pili of G. sulfurreducens are highly

conductive. This indicates thatG. sulfurreducens requires pili in orderto reduce Fe(III) oxides because pili are the electrical connectionbetween the cell and the surface of the Fe(III) oxides. This contrastswith the nearly universal concept that outer-membrane cytochromesare the proteins that transfer electrons to Fe(III) oxide in Fe(III)

Figure 2 | Transmission electronmicroscopy analyses. Shown are cells of awild-type strain (a), a pilA-deficient mutant strain (b) and a complementedmutant strain (c) of G. sulfurreducens. Cells were grown in medium withacetate and fumarate at 25 8C to induce the formation of pili, then negativelystained. Insets in a and c show details of pili produced by the wild-type andcomplemented mutant strains, respectively. Scale bars, 0.2 mm.

NATURE|Vol 435|23 June 2005 LETTERS

1099© 2005 Nature Publishing Group

Page 3: Lovley Nanowires

reducers1,3. However, the outer-membrane cytochrome model forFe(III) reduction has serious limitations. For example, whereasGeobacter and Desulfuromonas species in the Geobacteraceae familyof Fe(III)-reducing microorganisms contain abundant c-type cyto-chromes, no c-type cytochromes could be detected in Pelobacterspecies4, which are phylogenetically intertwined with Geobacter

and Desulfuromonas species20,21. Yet Pelobacter species—which, likeGeobacter species, contain pili localized on one side of the cell—alsoare capable of reducing Fe(III) oxides4.The conductive pili provide the opportunity to extend electron

transfer capabilities well beyond the outer surface of the cells, whichmight be especially important in soils in which Fe(III) oxides exist as

Figure 3 | Effect of a mutation in pilinproduction on reduction of Fe(III)oxide and attachment. a, Cells(open symbols) of the wild-type(circles), DpilA mutant (triangles)and complemented DpilA mutant(squares) strains and Fe(II) producedfrom Fe(III) reduction (filledsymbols). Plus signs, Fe(II) inuninoculated medium; crosses, cellsin uninoculated medium. b, Biomassof cells attached to Fe(III) oxide-coated coverslips over time; inset,confocal scanning laser microscopyof biomass attached in the first 24 hto the Fe(III) oxide, which is at thebottom of each image. Scale bar,20mm. Solid bars, wild type (WT);open bars, DpilA mutant (PilA2).Error bars show s.d. c, d,Transmission electron micrographsof fumarate-grownWT (c) and PilA2

(d) cells amended with Fe(III) oxides(indicated by arrows). Scale bars,0.5mm. Inset in (c) shows WT piliintertwined with Fe(III) oxides.

Figure 4 | Conducting-probe atomic forcemicroscopy. a, Topography of a pilus (indicatedby arrows) and non-pilin globular proteins. b, c,Current image (b) of the same field when a slow,triangular sweep bias voltage (c) was applied to thetip. d, Image showing both the topography andcurrent of a pilus (top); the top and bottom whitelines show the locations of the scans in the middleand bottom panels, respectively. Thick line (blueopen circles where visible), height; red line,current. e, Results from disabling the slow axis torepeatedly scan horizontally across the sameportion of a pilus filament. The apparent increasedwidth of the pilus is an artefact of this form ofscanning. f, Correspondence between current andapplied voltage. Scale bars, 100 nm.

LETTERS NATURE|Vol 435|23 June 2005

1100© 2005 Nature Publishing Group

Page 4: Lovley Nanowires

heterogeneously dispersed coatings on clays and other particulatematter. The pilus apparatus is anchored in the periplasm and outermembrane of Gram-negative cells, thus offering the possibility thatpili accept electrons from periplasmic and/or outer membraneelectron transfer proteins. These intermediary electron transferproteins need not be the same in all organisms, which is consistentwith the differences in cytochrome content and/or composition indifferent Fe(III) reducers1. The likely function of the pili is tocomplete the circuit between these various intermediary electroncarriers and the Fe(III) oxide.In addition to serving as a conduit for electron transfer to Fe(III)

oxides, pili could conceivably be involved in other electron transferreactions. For example, pili of individual Geobacter cells are oftenintertwined, raising the possibility of cell-to-cell electron transferthrough pili. These biologically produced nanowires might be usefulin nanoelectronic applications22,23, with the possibility of geneticallymodifying pilin structure and/or composition to generate nanowireswith different functionalities.

METHODSBacterial strains and culture conditions. All G. sulfurreducens strains wereisogenic with the wild-type strain PCA (ATCC 51573). A PilA2 mutant strainwas generated by replacement of theþ61 toþ159 coding region of the pilA gene(GSU1496) with a chloramphenicol cassette, as described previously9. The pilAmutation was complemented in trans by introducing plasmid pRG5-pilA, apRG5 derivative24 carrying a wild-type copy of the coding region of pilA.

Cells were routinely cultured at 30 or 25 8C under strictly anaerobic con-ditions in freshwater medium supplemented with acetate as electron donor, withfumarate, Fe(III)-citrate or poorly crystalline Fe(III) oxides (100mM) as theelectron acceptor25, and in the presence of chloramphenicol (15mgml21) orspectinomycin (150–300mgml21) for cultures of the PilA2 and pRG5-pilAstrains, respectively. Rates of Fe(III) oxide reduction were determined bymeasuring the production of Fe(II), and growth was determined as cell countsof acridine-orange-stained cells. For attachment assays, cells were grown in thepresence of coverslips coated with Fe(III) oxide; the attached biomass wasdetermined with crystal violet (see Supplementary Information).Conducting-probe atomic force microscopy analyses. Pili and other outer-surface proteins that were sheared from the cell surface (see SupplementaryInformation) were left to adsorb for 20min on the surface of freshly cleaved,highly oriented pyrolytic graphite, fixed with 1% glutaraldehyde for 5min,washed twice with double deionized water and blotted dry. Samples wereexamined with a Veeco Dimension 3100 AFM equipped with a Nanoscope IVcontroller and a SAM III signal access module to enable electrical interfacingwith the tip. A gold-coated AFM tip (nominal spring constant 0.06Nm21; VeecoInc.) was used for the imaging. The AFM was operated in contact mode withsimultaneous tip–substrate conductivity mapping. While imaging, a slow‘triangle-sweep’ bias voltage was applied to the tip in reference to the graphitesurface by using a low-noise battery-powered ramping circuit. Current wasmeasured with a DL Instruments 1211 current preamplifier.

Received 31 October 2004; accepted 21 April 2005.

1. Lovley, D. R., Holmes, D. E. & Nevin, K. P. in Advances in Microbial PhysiologyVol. 49 (ed. Poole, R. K.) 219–-286 (Elsevier Academic, London, 2004).

2. Lovley, D. R. Cleaning up with genomics: applying molecular biology tobioremediation. Nature Rev. Microbiol. 1, 35–-44 (2003).

3. Richardson, D. J. Bacterial respiration: a flexible process for a changingenvironment. Microbiology 146, 551–-571 (2000).

4. Lovley, D. R., Phillips, E. J., Lonergan, D. J. & Widman, P. K. Fe(III) and S0

reduction by Pelobacter carbinolicus. Appl. Environ. Microbiol. 61, 2132–-2138(1995).

5. Nevin, K. P. & Lovley, D. R. Lack of production of electron-shuttling compoundsor solubilization of Fe(III) during reduction of insoluble Fe(III) oxide byGeobacter metallireducens. Appl. Environ. Microbiol. 66, 2248–-2251 (2000).

6. Childers, S. E., Ciufo, S. & Lovley, D. R. Geobacter metallireducens accessesinsoluble Fe(III) oxide by chemotaxis. Nature 416, 767–-769 (2002).

7. Nassif, X. et al. Type-4 pili and meningococcal adhesiveness. Gene 192,149–-153 (1997).

8. Doig, P. et al. Role of pili in adhesion of Pseudomonas aeruginosa to humanrespiratory epithelial cells. Infect. Immun. 56, 1641–-1646 (1988).

9. Coppi, M. V., Leang, C., Sandler, S. J. & Lovley, D. R. Development of a geneticsystem for Geobacter sulfurreducens. Appl. Environ. Microbiol. 67, 3180–-3187(2001).

10. Methe, B. A. et al. Genome of Geobacter sulfurreducens: metal reduction insubsurface environments. Science 302, 1967–-1969 (2003).

11. Sahu, S. N. et al. The bacterial adaptive response gene, barA, encodes a novelconserved histidine kinase regulatory switch for adaptation and modulation ofmetabolism in Escherichia coli. Mol. Cell. Biochem. 253, 167–-177 (2003).

12. Strom, M. S. & Lory, S. Structure-function and biogenesis of the type IV pili.Annu. Rev. Microbiol. 47, 565–-596 (1993).

13. Childers, S. E., Mehta, T., Ciufo, S. & Lovley, D. R. Abstracts 103rd GeneralMeeting 361 (American Society for Microbiology, Washington DC, 2003).

14. Parge, H. E. et al. Structure of the fibre-forming protein pilin at 2.6 A resolution.Nature 378, 32–-38 (1995).

15. Alm, R. A. & Mattick, J. S. Genes involved in the biogenesis and function oftype-4 fimbriae in Pseudomonas aeruginosa. Gene 192, 89–-98 (1997).

16. Aho, E. L., Murphy, G. L. & Cannon, J. G. Distribution of specific DNAsequences among pathogenic and commensal Neisseria species. Infect. Immun.55, 1009–-1013 (1987).

17. Wall, D. & Kaiser, D. Type IV pili and cell motility. Mol. Microbiol. 32, 1–-10(1999).

18. Lovley, D. R., Coates, J. D., Blunt-Harris, E. L., Phillips, E. J. P. & Woodward, J. C.Humic substances as electron acceptors for microbial respiration. Nature 382,445–-448 (1996).

19. Merz, A. J., So, M. & Sheetz, M. P. Pilus retraction powers bacterial twitchingmotility. Nature 407, 98–-102 (2000).

20. Holmes, D. E., Nevin, K. P. & Lovley, D. R. Comparison of 16S rRNA, nifD, recA,gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. Int. J. Syst.Evol. Microbiol. 54, 1591–-1599 (2004).

21. Lonergan, D. J. et al. Phylogenetic analysis of dissimilatory Fe(III)-reducingbacteria. J. Bacteriol. 178, 2402–-2408 (1996).

22. Davis, J. J. Molecular bioelectronics. Phil. Trans. R. Soc. Lond. A 361, 2807–-2825(2003).

23. Sayler, G. S., Simpson, M. L. & Cox, C. D. Emerging foundations: nano-engineering and bio-microelectronics for environmental biotechnology. Curr.Opin. Microbiol. 7, 267–-273 (2004).

24. Butler, J. E. et al. A single bifunctional enzyme for fumarate reduction andsuccinate oxidation in Geobacter sulfurreducens and Geobacter metallireducens.J. Bacteriol. (submitted).

25. Lovley, D. R. & Phillips, E. J. P. Novel mode of microbial energy metabolism:organic carbon oxidation coupled to dissimilatory reduction of iron ormanganese. Appl. Environ. Microbiol. 54, 1472–-1480 (1988).

Supplementary Information is linked to the online version of the paper atwww.nature.com/nature.

Acknowledgements We thank T. Russell and D. Bryant for helpful suggestions.This research was supported by grants to D.R.L. from the Department ofEnergy’s Genomics:GTL and NABIR programmes and DARPA, by a grant toM.T.T. from the National Science Foundation, and by a postdoctoral fellowshipto G.R. from the Ministerio de Educacion y Ciencia of Spain.

Author Information Reprints and permissions information is available atnpg.nature.com/reprintsandpermissions. The authors declare no competingfinancial interests. Correspondence and requests for materials should beaddressed to D.R.L. ([email protected]).

NATURE|Vol 435|23 June 2005 LETTERS

1101© 2005 Nature Publishing Group

Page 5: Lovley Nanowires

S1

Supplementary Material

Methods

Phylogenetic analyses. Amino acid sequence alignments of G. sulfurreducens

pilin domain proteins, GSU1496 and GSU1776, and pilin and pseudopilin

proteins from other bacteria were generated using the Clustal X (1.8) program

and manually optimized using the SeAl v. 2.0a11 Carbon program (University of

Oxford). Phylogenetic trees were inferred from the optimized alignment by

distance analysis using the PAUP 4.0 4a software package. Distance and

branching order were determined by the neighbor-joining method (S3) using the

BioNJ algorithm (S1). Bootstrap values were determined from 100 replicates by

the neighbor method using the PAUP 4.0 4a software. The optimized alignment

used to generate the phylogenetic tree is shown in supplementary Fig. S1. The

Pelobacter propionicus pilA sequence was obtained from the Joint Genome

Institute (www.jgi.doe.gov). The complete genome sequence of G.

sulfurreducens can be found at www.tigr.org. Abbreviations: PilA, Geobacter

sulfurreducens (gi:399996596); PilA, G. metallireducens (gi:23053459); OxpG,

G. sulfurreducens (gi:41152675); GspG, G. sulfurreducens (gi:399995435); PilA,

P. propionicus (Joint Genome Institute; www.jgi.doe.gov); PilA, Pseudomonas

aeruginosa PA302025 (gi:21629635); PilA, Pseudomonas fluorescens PfO-1

(gi:23058745); NE1308, Nitrosomonas europaea ATCC 19718 (gi:30249287);

PilE, Neisseria gonorrhoeae FA1090 (gi:2921589); PilE, Neisseria meningitidis

FAM18 (gi:2228578); PilA, P. aeruginosa PA5196 (gi:21464534); PilA, Ralstonia

Page 6: Lovley Nanowires

S2

metallidurans (gi:15642724); SO0854, S. oneidensis (gi:24346423); PilA,

Myxococcus xanthus (gi:950654); EspG, Vibrio cholerae El Tor N16961

(gi:15642724); GspG, Mesorhizobium loti MAF 303099 (gi:13475692); GspG,

Burkholderia cepacia KF1 (gi:22978954); PilA, Dichelobacter nodosus N2

(gi:16118465); PulG, P. fluorescens PfO-1 (gi:23059410); GspG,

Thermoanaerobacter tengcongensis MB4T (gi:20807714); HofG, Synechocystis

sp. PCC6803 (gi:16330343); Yts1G, Yersinia enterocolitica WA-314

(gi:27529239).

Attachment assays

For Fe(III) oxides attachment assays, cells were grown in FW-acetate medium in

the presence or absence of the soluble electron acceptor, fumarate, and

incubated at 30oC with Fe(III) oxide-coated borosilicate coverslips (S6). The

bacterial biomass that attached to the Fe(III)-coated coverslips was stained with

1 % crystal violet (S2), and the cell-associated dye was then solubilized in

dimethyl sulfoxide (DMSO) and quantified by measuring the OD580 of the dye-

DMSO solution. Attached cells also were stained with the BacLight‰

fluorescence dyes (Molecular Probes) and examined with a Zeiss LSM510

inverted confocal scanning laser microscope (CSLM) equipped with a 63X long

working distance objective.

Attachment also was assayed by growing cells of the WT and PilA- mutant under

pili-inducing conditions in the absence of Fe(III) oxides (i.e., growth in FW-

acetate/fumarate medium and incubation at 25 oC for 48-72 h) and transferring

Page 7: Lovley Nanowires

S3

the cells to FW medium with poorly crystalline Fe(III) oxides (100 mmol/L) and

with no electron donor. After 24 h of incubation at 25 oC, cells were negatively

stained with uranyl acetate and visualized by transmission electron microscopy.

G.sulfurreducens pilT gene and twitching motility assays

A potential role of twitching motility in Fe(III) oxide reduction by G. sulfurreducens

was studied by constructing a deletion mutant in the putative pilT gene of G.

sulfurreducens (GSU1492, pilT-4), which clusters with G. sulfurreducens pilA

gene and is homologous in sequence and genomic organization to the functional

pilT gene of M. xanthus (S7). The G. sulfurreducens genome contains three

additional pilT homologs in unrelated chromosomal positions. A potential role for

any of these genes in type IV pilus retraction in G. sulfurreducens remains to be

elucidated.

Twitching motility in the wild-type strain of G. sulfurreducens was assayed in

plate assays as previously described (S4), except that FW-fumarate/acetate solid

(1.5% agar) medium was used and glass coverslips or Fe(III)-coated coverslips

also were used as surfaces to study pili-mediated motility in G. sulfurreducens.

Potential halos of twitching motility around the points of inoculation were

visualized by staining the surface-attached biomass with crystal violet and by

microscopic observation of the expansion edge.

Pili preparation for CP-AFM

For CP-AFM analyses, G. sulfurreducens was grown in FW medium

supplemented with acetate and fumarate and incubated at 25 oC for 48 h. S.

Page 8: Lovley Nanowires

S4

oneidensis strain MR-1 was grown in Luria Bertani (LB) medium and incubated at

30 oC for 24 h to induce pili expression (S5). Pseudomonas aeruginosa strain K

was also grown in LB medium and incubated overnight at 37 oC. Pili were

isolated by repeated passages through a 26G1/2 hyperdermic needle or

mechanically sheared with glass beads. Freshly prepared pili preparations were

adsorbed and fixed to a graphite block for CP-AFM analyses as described in the

methods section.

References

S1. Gascuel, O. 1997. BIONJ: an improved version of the NJ algorithm basedon a simple model of sequence data. Mol. Biol. Evol. 14:685-95.

S2. O'Toole, G. A., and R. Kolter. 1998. Initiation of biofilm formation inPseudomonas fluorescens WCS365 proceeds via multiple, convergentsignalling pathways: a genetic analysis. Mol. Microbiol. 28:449-61.

S3. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a newmethod for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-25.

S4. Semmler, A. B., C. B. Whitchurch, and J. S. Mattick. 1999. A re-examination of twitching motility in Pseudomonas aeruginosa.Microbiology 145:2863-2873.

S5. Thormann, K. M., R. M. Saville, S. Shukla, D. A. Pelletier, and A. M.Spormann. 2004. Initial Phases of biofilm formation in Shewanellaoneidensis MR-1. J. Bacteriol. 186:8096-104.

S6. van Schie, P. M., and M. Fletcher. 1999. Adhesion of biodegradativeanaerobic bacteria to solid surfaces. Appl. Environ. Microbiol. 65:5082-8.

S7. Wall, D., and D. Kaiser. 1999. Type IV pili and cell motility. Mol. Microbiol.32:1-10.

Page 9: Lovley Nanowires

S5

FIGURE S1

Page 10: Lovley Nanowires

S6

FIGURE S2

Page 11: Lovley Nanowires

S7

FIGURE S3

Page 12: Lovley Nanowires

S8

FIGURE S4

Page 13: Lovley Nanowires

S9

FIGURE S5