Microbial Ecology

, Volume 48, Issue 2, pp 178–190 | Cite as

Microbial Communities Associated with Electrodes Harvesting Electricity from a Variety of Aquatic Sediments

  • D.E. Holmes
  • D.R. Bond
  • R.A. O’Neil
  • C.E. Reimers
  • L.R. Tender
  • D.R. LovleyEmail author


The microbial communities associated with electrodes from underwater fuel cells harvesting electricity from five different aquatic sediments were investigated. Three fuel cells were constructed with marine, salt-marsh, or freshwater sediments incubated in the laboratory. Fuel cells were also deployed in the field in salt marsh sediments in New Jersey and estuarine sediments in Oregon, USA. All of the sediments produced comparable amounts of power. Analysis of 16S rRNA gene sequences after 3–7 months of incubation demonstrated that all of the energy-harvesting anodes were highly enriched in microorganisms in the δ-Proteobacteria when compared with control electrodes not connected to a cathode. Geobacteraceae accounted for the majority of δ-Proteobacterial sequences or all of the energy-harvesting anodes, except the one deployed at the Oregon estuarine site. Quantitative PCR analysis of 16S rRNA genes and culturing studies indicated that Geobacteraceae were 100-fold more abundant on the marine-deployed anodes versus controls. Sequences most similar to microorganisms in the family Desulfobulbaceae predominated on the anode deployed in the estuarine sediments, and a significant proportion of the sequences recovered from the freshwater anodes were closely related to the Fe(III)-reducing isolate, Geothrix fermentans. There was also a specific enrichment of microorganisms on energy harvesting cathodes, but the enriched populations varied with the sediment/water source. Thus, future studies designed to help optimize the harvesting of electricity from aquatic sediments or waste organic matter should focus on the electrode interactions of these microorganisms which are most competitive in colonizing anodes and cathodes.


Fuel Cell Clone Library Current Production Freshwater Sediment Control Electrode 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This research was supported by the Office of Naval Research (ONR) (grant N00014-00-1-0776), the Defense Advanced Research Project’s Agency (DARPA) Defense Sciences Office (DSO) (grant N66001-02-C-8044), and the Office of Science (BER), U.S. Department of Energy (cooperative agreement No. DE-FC02-02ER63446).


  1. 1.
    Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ 1990Basic local alignment search tool.J Mol Biol215403410CrossRefPubMedGoogle Scholar
  2. 2.
    Amann, RI, Ludwig, W, Schleifer, KH 1995Phylogenetic identification and in situ detection of individual microbial cells without cultivation.Microbiol Rev59143169PubMedGoogle Scholar
  3. 3.
    Anderson, RT, Rooney-Varga, J, Gaw, CV, Lovley, DR 1998Anaerobic benzene oxidation in the Fe(III)-reduction zone of petroleum-contaminated aquifers.Environ Sci Technol3212221229CrossRefGoogle Scholar
  4. 4.
    Atlas, RM 1984Diversity of microbial communities.Adv Microb Ecol7147Google Scholar
  5. 5.
    Atlas, RM 1984Use of microbial diversity measurements to assess environmental stress.Klug, MJReddy, CA eds. Current Perspectives in Microbial EcologyAmerican Society for MicrobiologyWashington, DC540545Google Scholar
  6. 6.
    Atlas, RM, Bartha, R 1998Microbial Ecology: Fundamentals and Applications, 4th ed.Benjamin/Cummings Publishing Company, Inc.Menlo Park, CAGoogle Scholar
  7. 7.
    Ausubel, FM, Brent, R, Kingston, RE, Moore, DD, Seidhan, JG, Smith, JA, Struhl, K 1997Current Protocols in Molecular BiologyJohn Wiley and SonsNew YorkGoogle Scholar
  8. 8.
    Bond, DR, Holmes, DE, Tender, LM, Lovley, DR 2002Electrode-reducing microorganisms that harvest energy from marine sediments.Science295483485CrossRefPubMedGoogle Scholar
  9. 9.
    Bond, DR, Lovley, DR 2003Electricity generation by Geobacter sulfurreducens attached to electrodes.Appl Environ Microbiol6915481555CrossRefPubMedGoogle Scholar
  10. 10.
    Brettar, I, Moore, ER, Hofle, MG 2001Phylogeny and abundance of novel denitrifying bacteria isolated from the water column of the central Baltic Sea.Microb Ecol42295305CrossRefPubMedGoogle Scholar
  11. 11.
    Chandler, DP, Fredrickson, JK, Brockman, FJ 1997Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries.Mol Ecol6475482CrossRefPubMedGoogle Scholar
  12. 12.
    Childers, SE, Ciufo, S, Lovley, DR 2002Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis.Nature416767769CrossRefPubMedGoogle Scholar
  13. 13.
    Dang, H, Lovell, CR 2000Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes.Appl Environ Microbiol66467475CrossRefPubMedGoogle Scholar
  14. 14.
    Dang, H, Lovell, CR 2002Numerical dominance and phylotype diversity of marine Rhodobacter species during early colonization of submerged surfaces in coastal marine waters as determined by 16S ribosomal DNA sequence analysis and fluorescence in situ hybridization.Appl Environ Microbiol68496504CrossRefPubMedGoogle Scholar
  15. 15.
    Emde, R, Schink, B 1990Oxidation of glycerol, lactate, and propionate by Propionibacterium freudenrichii in a poised-potential amperometic culture system.Arch Microbiol153506512Google Scholar
  16. 16.
    Emde, R, Swain, A, Schink, B 1989Anaerobic oxidation of glycerol by Escherichia coli in an amperometric poised-potential culture system.Appl Microbiol Biotechnol32170175Google Scholar
  17. 17.
    Farrelly, V, Rainey, FA, Stackebrandt, E 1995Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species.Appl Environ Microbiol6127982801PubMedGoogle Scholar
  18. 18.
    Furlong, MA, Singleton, DR, Coleman, DC, Whitman, WB 2002Molecular and culture-based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus.Appl Environ Microbiol6812651279CrossRefPubMedGoogle Scholar
  19. 19.
    Holmes, DE, Finneran, KT, O’Neil, RA, Lovley, DR 2002Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments.Appl Environ Microbiol6823002306CrossRefPubMedGoogle Scholar
  20. 20.
    Lane, DL 199116S/23S rRNA sequencing.Stackebrandt, EGoodfellow, M eds. Nucleic Acid Techniques in Bacterial SystematicsWileyChichester, England115175Google Scholar
  21. 21.
    Lane, DL, Pace, B, Olsen, GJ, Stahl, D, Sogin, ML, Pace, NR 1985Rapid determination of 16S ribosomal RNA sequences for phylogenetic analysis.Proc Natl Acad Sci USA8269556959PubMedGoogle Scholar
  22. 22.
    Liesack, W, Finster, K 1994Phylogenetic analysis of five strains of gram-negative, obligately anaerobic, sulfur-reducing bacteria and description of Desulfuromusa gen. nov., including Desulfuromusa kysingii sp. nov., Desulfuromusa bakii sp. nov., and Desulfuromusa succinoxidans sp. nov.Int Syst Bacteriol44753758Google Scholar
  23. 23.
    Lonergan, DJ, Jenter, H, Coates, JD, Phillips, EJP, Schmidt, T, Lovley, DR 1996Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria.J Bacteriol17824022408PubMedGoogle Scholar
  24. 24.
    Lovley, DR 2000Fe(III)- and Mn(IV)-reducing prokaryotes.Dworkin, MFalkow, SRosenberg, ESchleifer, KHStackebrandt, E eds. The ProkaryotesSpringer-VerlagNew YorkGoogle Scholar
  25. 25.
    Lovley, DR, Chapelle, FH 1995Deep subsurface microbial processes.Rev Geophys33365381CrossRefGoogle Scholar
  26. 26.
    Lovley, DR, Coates, JD, Blunt-Harris, EL, Phillips, EJP, Woodward, JC 1996Humic substances as electron acceptors for microbial respiration.Nature382445448CrossRefGoogle Scholar
  27. 27.
    Lovley, DR, Fraga, JL, Blunt-Harris, EL, Hayes, LA, Phillips, EJP, Coates, JD 1998Humic substances as a mediator for microbially catalyzed metal reduction.Acta Hydrochim Hydrobiol26152157CrossRefGoogle Scholar
  28. 28.
    Lovley, DR, Fraga, JL, Coates, JD, Blunt-Harris, EL 1999Humics as an electron donor for anaerobic respiration.Environ Microbiol18998CrossRefPubMedGoogle Scholar
  29. 29.
    Lovley, DR, Klug, MJ 1986Model for the distribution of sulfate reduction and methanogenesis in fresh water sediments.Geochim Cosmochim Acta501118CrossRefGoogle Scholar
  30. 30.
    Lovley, DR, Klug, MJ 1983Sulfate reducers can outcompete methanogens at freshwater sulfate concentrations.Appl Environ Microbiol45187192Google Scholar
  31. 31.
    Lovley, DR, Phillips, EJP 1994Novel processes for anoxic sulfate production from elemental sulfur by sulfate-reducing bacteria.Appl Environ Microbiol6023942399Google Scholar
  32. 32.
    Lovley, DR, Phillips, EJP 1986Organic matter mineralization with reduction of ferric iron in anaerobic sediments.Appl Environ Microbiol51683689Google Scholar
  33. 33.
    Lovley, DR, Phillips, EJP 1989Requirement for a microbial consortium to completely oxidize glucose in Fe(III)-reducing sediments.Appl Environ Microbiol5532343236Google Scholar
  34. 34.
    Lovley, DR, Phillips, EJP 1987Competitive mechanisms for inhibition of sulfate reduction and methane production in the zone of ferric iron reduction in sediments.Appl Environ Microbiol5326362641Google Scholar
  35. 35.
    Lovley, DR, Phillips, EJP 1988Manganese inhibition of microbial iron reduction in anaerobic sediments.Geomicrobiol J6145155Google Scholar
  36. 36.
    Lovley, DR, Phillips, EJP 1988Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese.Appl Environ Microbiol5414721480Google Scholar
  37. 37.
    Lovley, DR, Roden, EE, Phillips, EJP, Woodward, JC 1993Enzymatic iron and uranium reduction by sulfate-reducing bacteria.Mar Geol1134153CrossRefGoogle Scholar
  38. 38.
    Magnuson, TS, Isoyama, N, Hodges Myerson, AL, Davidson, G, Maroney, MJ, Geesey, GG, Lovley, DR 2001Isolation, characterization and gene sequence analysis of a membrane- associated 89 kDa Fe(III) reducing cytochrome c from Geobacter sulfurreducens.Biochem J359147152CrossRefPubMedGoogle Scholar
  39. 39.
    Maidak, BL, Cole, JR, Lilburn, TG, Parker, CT, Saxman, PR, Farris, RJ, Garrity, GM, Olsen, GJ, Schmidt, TM, Tiedje, JM 2001The RDP-II (Ribosomal Database Project).Nucleic Acids Res29173174CrossRefPubMedGoogle Scholar
  40. 40.
    Marchesi, JR, Sato, T, Weightman, AJ, Martin, TA, Fry, JC, Hiom, SJ, Wade, WG 1998Design and evaluation of useful bacterium specific PCR primers that amplify genes coding for bacterial 16S rRNA.Appl Environ Microbiol64795799PubMedGoogle Scholar
  41. 41.
    Myers, EW, Miller, W 1988Optimal alignments in linear-space.Comput Appl Biol Sci41117PubMedGoogle Scholar
  42. 42.
    Nevin, KP, Lovley, DR 2000Lack of production of electron-shuttling compounds or solubilization of Fe(III) during reduction of insoluble Fe(III) oxide by Geobacter metallireducens.Appl Environ Microbiol6622482251CrossRefPubMedGoogle Scholar
  43. 43.
    Nevin, KP, Lovley, DR 2002Mechanisms for Fe(III) oxide reduction in sedimentary environments.Geomicrobiol J19141159CrossRefGoogle Scholar
  44. 44.
    Nevin, KP, Lovley, DR 2002Novel mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans.Appl Envioron Microbiol6822942299CrossRefGoogle Scholar
  45. 45.
    Newman, DK, Kolter, R 2000A role for excreted quinones in extracellular electron transfer.Nature4059497CrossRefPubMedGoogle Scholar
  46. 46.
    Park, DH, Laivenieks, M, Guettler, MV, Jain, MK, Zeikus, JG 1999Microbial utilization of electrically reduced neutral red as the sole electron donor for growth and metabolite production.Appl Environ Microbiol6529122917PubMedGoogle Scholar
  47. 47.
    Park, DH, Zeikus, JG 2000Electricity generation in microbial fuel cells using neutral red as an electronophore.Appl Environ Microbiol6612921297CrossRefPubMedGoogle Scholar
  48. 48.
    Park, HS, Kim, BH, Kim, HS, Kim, HJ, Kim, GT, Kim, M, Chang, IS, Park, YK, Chang, HI 2001A novel electrochemically active and Fe(III)-reducing bacterium phylogenetically related to Clostridium butyricum isolated from a microbial fuel cell.Anaerobe7297306CrossRefGoogle Scholar
  49. 49.
    Polz, MF, Cavanaugh, CM 1998Bias in template-to-product ratios in multitemplate PCR.Appl Environ Microbiol6437243730PubMedGoogle Scholar
  50. 50.
    Purkhold, U, Pommerening-Roser, A, Juretschko, S, Schmid, MC, Koops, HP, Wagner, M 2000Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys.Appl Environ Microbiol6653685382CrossRefPubMedGoogle Scholar
  51. 51.
    Qiu, X, Wu, L, Huang, H, McDonel, PE, Palumbo, AV, Tiedje, JM, Zhou, J 2001Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning.Appl Environ Microbiol67880887CrossRefPubMedGoogle Scholar
  52. 52.
    Reimers, CE, Tender, LM, Fertig, S, Wang, W 2001Harvesting energy from the marine sediment–water interface.Environ Sci Technol35192195CrossRefPubMedGoogle Scholar
  53. 53.
    Roling, WF, van Breukelen, BM, Braster, BL, van Verseveld, HW 2001Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer.Appl Environ Microbiol6746194629CrossRefPubMedGoogle Scholar
  54. 54.
    Roller, SD, Bennetto, HP, Delaney, GM, Mason, JR, Stirling, JL, Thurston, CF 1984Electron-transfer coupling in microbial fuel cells: 1. Comparison of redox-mediator reduction rates and respiratory rates of bacteria.J Chem Technol Biotechnol34312Google Scholar
  55. 55.
    Rooney-Varga, JN, Anderson, RT, Fraga, JL, Ringelberg, D, Lovley, DR 1999Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer.Appl Environ Microbiol6530563063PubMedGoogle Scholar
  56. 56.
    Snoeyenbos-West, OL, Nevin, KP, Anderson, RT, Lovley, DR 2000Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments.Microb Ecol39153167CrossRefPubMedGoogle Scholar
  57. 57.
    Speksnijder, AG, Kowalchuk, GA, De Jong, S, Kline, E, Stephen, JR, Laanbroek, HJ 2001Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences.Appl Environ Microbiol67469472CrossRefPubMedGoogle Scholar
  58. 58.
    Stein, LY, La Duc, MT, Grundl, TJ, Nealson, KH 2001Bacterial and achaeal populations associated with freshwater ferromanganous micronodules and sediments.Environ Microbiol31018CrossRefPubMedGoogle Scholar
  59. 59.
    Stults, JR, Snoeyenbos-West, O, Methe, B, Lovley, DR, Chandler, DP 2003Application of the 5′ fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments.App Environ Microbiol6727812789CrossRefGoogle Scholar
  60. 60.
    Suzuki, M, Giovannoni, S 1996Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR.Appl Environ Microbiol62625630PubMedGoogle Scholar
  61. 61.
    Swofford, DL (1998) PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods), Version 4. Sinauer Associates, Sunderland, MA.Google Scholar
  62. 62.
    Tender, LM, Reimers, CE, Stecher, HA, Holmes, DE, Bond, DR, Lowy, DA, Pilobello, K, Fertig, SJ, Lovley, DR 2002Harnessing microbially generated power on the seafloor.Nat Biotechnol20821825PubMedGoogle Scholar
  63. 63.
    Valentine, DL 2002Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review.Antonie Van Leeuwenhoek81271282CrossRefPubMedGoogle Scholar
  64. 64.
    Wang, GC, Wang, Y 1996The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species.Microbiology14211071114PubMedGoogle Scholar
  65. 65.
    Widdel, F, Pfennig, N 1982Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids II. Incomplete oxidation of propionate by Desulfobulbus propionicus gen. nov., sp. nov.Arch Microbiol131360365Google Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • D.E. Holmes
    • 1
  • D.R. Bond
    • 1
  • R.A. O’Neil
    • 1
  • C.E. Reimers
    • 2
  • L.R. Tender
    • 3
  • D.R. Lovley
    • 1
    Email author
  1. 1.Department of MicrobiologyUniversity of MassachusettsAmherstUSA
  2. 2.Hatfield Marine Science CenterOregon State UniversityNewportUSA
  3. 3.Center for Bio/molecular Science and Engineering, Code 6900Naval Research LaboratoryWashingtonUSA

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