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Diversity and Function of the Microbial Community on Anodes of Sediment Microbial Fuel Cells Fueled by Root Exudates

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Diversity and Function of the Microbial Community on Anodes of Sediment Microbial Fuel Cells Fueled by Root Exudates Diversity and Function of the Microbial Community on Anodes of Sediment Microbial Fuel Cells fueled by Root Exudates Doctoral thesis Submitted in partial fulfillment of the requirement for a doctoral degree “Doktorgrad der Naturwissenschaften (Dr. rer. nat.)” to the faculty of biology – Philipps-Universität Marburg by Angela Cabezas da Rosa from Montevideo, Uruguay Marburg / Lahn | 2010 The research for the completion of this work was carried out from April 2007 to September 2010 at the Max-Planck Institute for Terrestrial Microbiology under the supervision of Prof. Michael W. Friedrich Thesis was submitted to the Faculty of Biology, Philipps-Universität, Marburg Doctoral thesis accepted on: 24.11.2010 Date of oral examination: 26.11.2010 First reviewer: Prof. Dr. Michael W. Friedrich Second reviewer: Prof. Dr. Wolfgang Buckel The following manuscripts originated from this work and were published or are in preparation: De Schamphelaire L, Cabezas A, Marzorati M, Friedrich MW, Boon N & Verstraete W (2010) Microbial Community Analysis of Anodes from Sediment Microbial Fuel Cells Powered by Rhizodeposits of Living Rice Plants. Applied and Environmental Microbiology 76: 2002-2008. Cabezas A, de Schamphelaire L, Boon N, Verstraete W, Friedrich MW. Rice root exudates select for novel electrogenic Geobacter and Anaeromyxobacter populations on sediment microbial fuel cell anodes. In preparation. Cabezas A, Köhler T, Brune A, Friedrich MW. Identification of β-Proteobacteria and Anaerolineae as active populations degrading rice root exudates on sediment microbial fuel cell anodes. In preparation. Cabezas A, Breidenbach B, Friedrich MW. Taming methane emissions from rice field soil with microbial fuel cells. In preparation. A mis amores Marcelo e Irene Table of Contents Summary III Zusammenfassung V CHAPTER 1 GENERAL INTRODUCTION 1 1.1 MICROBIAL FUEL CELLS 1 1.2 THE RICE WETLAND ECOSYSTEM AND METHANE EMISSION 15 1.3 STABLE ISOTOPE PROBING AND NEXT GENERATION SEQUENCING TECHNOLOGIES IN MICROBIAL ECOLOGY 17 1.4 AIMS OF THIS STUDY 19 1.5 REFERENCES 21 CHAPTER 2 MATERIALS AND METHODS 30 2.1 SEDIMENT MICROBIAL FUEL CELLS - SMFC 30 2.2 STABLE ISOTOPE PULSE LABELING 33 2.3 MOLECULAR ANALYSIS OF BACTERIAL AND ARCHAEAL COMMUNITIES 35 2.4 REFERENCES 41 CHAPTER 3 MICROBIAL COMMUNITY ANALYSIS OF ANODES FROM SEDIMENT MICROBIAL FUEL CELLS POWERED BY RHIZODEPOSITS OF LIVING PLANTS 43 3.1 ABSTRACT 44 3.2 INTRODUCTION 44 3.3 MATERIALS AND METHODS 46 3.4 RESULTS 51 3.5 DISCUSSION 59 3.6 CONCLUSIONS 64 3.7 REFERENCES 64 3.8 SUPPLEMENTARY DATA 69 CHAPTER 4 RICE ROOT EXUDATES SELECT FOR NOVEL ELECTROGENIC GEOBACTER AND ANAEROMYXOBACTER POPULATIONS ON SEDIMENT MICROBIAL FUEL CELL ANODES 70 4.1 ABSTRACT 71 4.2 INTRODUCTION 71 4.3 MATERIALS AND METHODS 73 4.4 RESULTS 77 4.5 DISCUSSION 87 4.6 CONCLUSIONS 92 4.7 REFERENCES 93 4.8 SUPPLEMENTARY DATA 96 CHAPTER 5 IDENTIFICATION OF Β-PROTEOBACTERIA AND ANAEROLINEAE AS ACTIVE POPULATIONS DEGRADING ROOT EXUDATES ON SEDIMENT MICROBIAL FUEL CELL ANODES 101 5.1 ABSTRACT 102 5.2 INTRODUCTION 102 5.3 MATERIALS AND METHODS 104 5.4 RESULTS 108 5.5 DISCUSSION 121 5.6 CONCLUSIONS 123 5.7 REFERENCES 124 5.8 SUPLEMENTARY DATA 127 CHAPTER 6 TAMING METHANE EMISSIONS FROM RICE FIELD SOIL WITH MICROBIAL FUEL CELLS 130 6.1 ABSTRACT 131 6.2 INTRODUCTION 131 6.3 MATERIAL AND METHODS 133 6.4 RESULTS AND DISCUSSION 135 6.5 REFERENCES 142 6.6 SUPPLEMENTARY DATA 143 CHAPTER 7 GENERAL DISCUSSION AND PERSPECTIVES 146 7.1 MICROBIAL DIVERSITY ON ANODES FROM SMFCS FUELED BY RICE ROOT EXUDATES 146 7.2 MODEL FOR CARBON FLOW ON ANODES 150 7.3 SMFCS AS METHANE EMISSION MITIGATION STRATEGY 153 7.4 PERSPECTIVES 155 7.5 REFERENCES 156 CHAPTER 8 GENERAL CONCLUSIONS 158 APPENDICES 159 PHOTOS OF SETUPS 159 LIST OF ABBREVIATIONS 163 CURRICULUM VITAE ACKNOWLEDGMENTS Summary Anode microbial communities are essential for current production in microbial fuel cells. Anode reducing bacteria are capable of using the anode as final electron acceptor in their respiratory chain. The electrons delivered to the anode travel through a circuit to the cathode where they reduce oxygen to water generating an electric current. A novel type of sediment microbial fuel cell (SMFC) harvest energy from photosynthetically derived compounds released through the roots. Nothing is known about anode microbial communities of this type of microbial fuel cell. This work consists of three parts. The first part focuses on the study of bacterial and archaeal community compositions on anodes of SMFCs fueled by rice root exudates. By using terminal restriction fragment length polymorphism (T-RFLP), a profiling technique, and cloning / sequencing of 16S rRNA, we determined that the support type used for the plant (vermiculite, potting soil or rice field soil) is an important factor determining the composition of the microbial community. Finally, by comparing microbial communities of current producing anodes and non-current producing controls we determined that Desulfobulbus- and Geobacter-related populations were probably most important for current production in potting soil and rice field soil SMFCs, respectively. However, δ-proteobacterial Anaeromyxobacter spp., unclassified δ-proteobacteria and Anaerolineae were also part of the anode biofilm in rice field soil SMFCs and these populations might also play a role in current production. Moreover, distinct clusters of Geobacter and Anaeromyxobacter populations were stimulated by rice root exudates. Regarding Archaea, uncultured Euryarchaea were abundant on anodes of potting soil SMFCs indicating a potential role in current production. In both, rice field soil and potting soil SMFCs, a decrease of Methanosaeta, an acetotrophic methanogen, was detected on current producing anodes. In the second part we focused our study on identifying the bacteria capable of rice root exudate assimilation on anodes of planted SMFCs. Using stable isotope probing (SIP) with 13C-CO2 combined with high throughput sequencing, we detected that labeled bacteria belonged to β-proteobacteria and Anaerolineae indicating their relevance in root exudate degradation. The main current producing bacteria, belonging to δ-proteobacteria were not able to assimilate root exudates. A microbial “food chain” combining activities of anode reducing bacteria with root exudate degrading bacteria is necessary for current III Summary production. However, we cannot dismiss the possibility that some bacteria might be able to directly use root exudates for current production. In the last part, we found that by submerging an anode into rice field soil up to 50% methane emission was reduced compared with open circuit controls. This mitigation could not only be explained by competition for common electron donors like acetate. We suggest that the anode, even in non-current controls, can be used as electron acceptor capturing electrons and transferring them from one part of the sediment to a spatially distant one, communicating biogeochemical processes occurring in different parts of the sediment. Our work is a first approach in understanding the microbial diversity on anodes of SMFCs fueled by rice root exudation and their potential as methane emission mitigation strategy. IV Zusammenfassung Voraussetzung für einen Stromfluss in Bio-Brennstoffzellen (microbial fuel cell; MFC) ist die Besiedlung der Anode durch mikrobielle Gemeinschaften. Anoden-reduzierende Bakterien sind in der Lage, die Anode als terminalen Elektronenakzeptor in ihrer Atmungskette zu nutzen. Die an der Anode abgegebenen Elektronen fließen in einem Stromkreis zur Kathode, an der Sauerstoff durch Aufnahme der Elektronen zu Wasser reduziert und ein elektrischer Strom erzeugt wird. Ein neuer Typ von mikrobiellen Brennstoffzellen im Sediment (sediment microbial fuel cell; SMFC) nutzt die Energie von photosynthetisch assimilierten Verbindungen, die von Reiswurzeln ausgeschieden werden, wobei die Zusammensetzung der mikrobielle Gemeinschaft auf der Anode bisher nicht bekannt war. Die vorliegende Arbeit besteht aus drei Teilen. Der erste Teil beschäftigt sich mit der Analyse der Zusammensetzung bakterieller und archaeeller Gemeinschaften auf der Anode von Boden-basierten mikrobiellen Brennstoffzellen, die durch Reiswurzelexsudate angetrieben werden. Durch Anwendung von terminalem Restriktionsfragmentlängenpolymorphismus (T-RFLP), Klonierung und Sequenzierung der 16S rRNA fanden wir heraus, dass das Trägermaterial für Pflanzen (Vermikulit, Pflanzerde oder Reisfeldboden) ein wichtiger Faktor für die Zusammensetzung der mikrobiellen Gemeinschaft ist. Beim Vergleich der mikrobiellen Besiedlung von stromerzeugenden Anoden und nicht-stromerzeugenden Kontrollen fanden wir Desulfobulbus- und Geobacter- verwandte als wahrscheinliche Hauptproduzenten in auf Pflanzerde und Reisfeldboden basierten Biobrennstoffzellen (SMFC). Allerdings waren auch zu den δ-Proteobacteria gehörende Anaeromyxobacter spp., nicht-klassifizierte δ- Proteobacteria und Anaerolineae im Biofilm der Anode von Reisfeldboden basierten Biobrennstoffzellen vertreten und könnten ebenfalls eine Rolle in der Stromerzeugung spielen. Darüber hinaus wurden bestimmte Gruppen von Geobacter and Anaeromyxobacter durch Reiswurzelexsudate stimuliert. Bezüglich der Archaea waren nicht-kultivierbare Euryarchaea auf der Anode von mikrobiellen Brennstoffzellen mit Pflanzerde nachweisbar, was auf eine potentielle Rolle dieser Population in der Stromerzeugung hindeutet. In mikrobiellen Brennstoffzellen basierend auf Reisfeldboden oder Pflanzerde nahm der Anteil von Sequenzen der Methanosaeta,
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