ORIGINAL ARTICLE Bacterial community structure, compartmentalization and activity in a microbial fuel cell G.T. Kim 1 , G. Webster 1 , J.W.T. Wimpenny 1 , B.H. Kim 2 , H.J. Kim 3 and A.J. Weightman 1 1 Cardiff School of Biosciences, Cardiff University, Cardiff, UK 2 Water Environment & Remediation Research Center, Korea Institute of Science and Technology, Seoul, Korea 3 Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul, Korea Introduction A microbial fuel cell (MFC) is an electrochemical device that converts chemical energy to electrical energy using the catalytic action of electrochemically active micro- organisms (EAM; Park and Zeikus 2000; Kim et al. 2002). Several electron-transfer mediators have been used to faci- litate electron transfer between an electrode and electro- chemically inactive micro-organisms (Kim and Kim 1988; Kim et al. 2000; Park and Zeikus 2000; McKinlay and Zeikus 2004); however, the so-called mediatorless MFCs (Park et al. 2001; Kim et al. 2005) utilize bacteria that can transfer electrons directly to the electrode. Recently, a number of Fe(III)-reducing bacteria (FRB) with electrochemical activity were isolated from a MFC, marine aquatic sediment and submerged soil, e.g. Clos- tridium butyricum (Park et al. 2001), Rhodoferax ferriredu- cens (Chaudhuri and Lovley 2003) and Enterococcus gallinarum (Kim et al. 2005). Iron is universally present in most ecosystems and the microbial reduction of Fe(III) plays an important role in the biogeochemistry of these systems (Lovley et al. 2004). Many micro-organisms are able to conserve energy for growth by coupling the oxida- tion of organic acids, aromatic hydrocarbons and H 2 to Fe(III) reduction (Nielsen et al. 2002). These include spe- cies of the genera Geobacter (Lovley et al. 1993; Caccavo et al. 1996; Bond et al. 2002), Shewanella (Lovley et al. 1989, 1992; Hyun et al. 1999) and the sulfate-reducing bac- terium, Desulfotomaculum reducens (Tebo and Obraztsova 1998). The enterobacterium, Klebsiella oxytoca, isolated Keywords 16S rRNA, anaerobic respiration, biofilm, denaturing gradient gel electrophoresis, electrochemical activity, Fe(III)-reducing bacteria, Klebsiella oxytoca, microbial fuel cell. Correspondence Gwang Tae Kim, Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3TL, UK. E-mail: kimgt@cardiff.ac.uk Present address G. Webster, School of Earth, Ocean and Planetary Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3YE, UK. 2005/0859: received 29 July 2005, accepted 17 January 2006 doi:10.1111/j.1365-2672.2006.02923.x Abstract Aims: To characterize bacterial populations and their activities within a micro- bial fuel cell (MFC), using cultivation-independent and cultivation approaches. Methods and Results: Electron microscopic observations showed that the fuel cell electrode had a microbial biofilm attached to its surface with loosely asso- ciated microbial clumps. Bacterial 16S rRNA gene libraries were constructed and analysed from each of four compartments within the fuel cell: the plank- tonic community; the membrane biofilm; bacterial clumps (BC) and the anode biofilm. Results showed that the bacterial community structure varied signifi- cantly between these compartments. It was observed that Gammaproteobacteria phylotypes were present at higher numbers within libraries from the BC and electrode biofilm compared with other parts of the fuel cell. Community struc- ture of the MFC determined by analyses of bacterial 16S rRNA gene libraries and anaerobic cultivation showed excellent agreement with community profiles from denaturing gradient gel electrophoresis (DGGE) analysis. Conclusions: Members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and other Gammaproteobacteria with Fe(III)-reducing and electrochemical activity had a significant potential for energy generation in this system. Significance and Impact of the Study: This study has shown that electrochemi- cally active bacteria can be enriched using an electrochemical fuel cell. Journal of Applied Microbiology ISSN 1364-5072 698 Journal compilation ª 2006 The Society for Applied Microbiology, Journal of Applied Microbiology 101 (2006) 698–710 ª 2006 The Authors