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Ecophysiology of Sulfate-Reducing Bacteria and Syntrophic Communities in Marine Anoxic Sediments” Derya Özüölmez Wageningen, 12 September 2017

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Ecophysiology of Sulfate-Reducing Bacteria and Syntrophic Communities in Marine Anoxic Sediments” Derya Özüölmez Wageningen, 12 September 2017 Propositions 1. Prolonged incubation is a key strategy toward the enrichment of marine syntrophs. (this thesis) 2. Hydrogen-consuming methanogens can effectively compete with hydrogen- consuming sulfate reducers even at high sulfate concentration. (this thesis) 3. The plastic-eating wax worm, Galleria mellonella, can help cleaning up existing plastic mass (Bombelli et al. 2017, Current Biology 27(8): 292-293), but the real solution to environmental pollution still relies on shifting from disposable plastics to reusable and biodegradable materials. 4. With the discovery of abundant molecular hydrogen in Enceladus’ salty ocean (Waite et al. (2017) Science 356:6334, 155-159) extraterrestrial life in our solar system has become highly probable, and should shift our life-hunting focus from distant stars to our nearby neighbors. 5. With the "Help me to do it myself" motto, the Montessori education leads children to grow into mature, creative and self-confident adults. 6. Nothing is impossible as long as the dream is held close to the heart and patience and persistence are applied for the accomplishment. Propositions belonging to the PhD thesis entitled: “Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments” Derya Özüölmez Wageningen, 12 September 2017 Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments Derya Özüölmez Thesis committee Promotor Prof. Dr Alfons J.M. Stams Personal chair at the Laboratory of Microbiology Wageningen University & Research Co-promotor Dr Caroline M. Plugge Associate professor, Laboratory of Microbiology Wageningen University & Research Other members Prof. Dr Tinka Murk, Wageningen University & Research Prof. Dr Gerard Muyzer, University of Amsterdam, The Netherlands Prof. Dr Stefan Schouten, Utrecht University and Netherlands Institute for Sea Research, Texel, The Netherlands Dr Verona Vandieken, University of Oldenburg, Germany This research was conducted under the auspices of the Graduate School for SocioEconomic and Natural Sciences of the Environment (SENSE). Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments Derya Özüölmez Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus, Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 12 September 2017 at 4 p.m. in the Aula. Derya Özüölmez Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments, 231 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2017) With references, with summary in English and Dutch ISBN: 978-94-6343-654-0 DOI: 10.18174/420757 Table of Contents Chapter 1 General Introduction 1 Chapter 2 Methanogenic archaea and sulfate reducing bacteria co- 19 cultured on acetate: teamwork or coexistence? Chapter 3 Butyrate degradation by sulfate-reducing and methanogenic 45 communities in anoxic sediments of Aarhus Bay, Denmark Chapter 4 Propionate conversion under sulfidogenic and methanogenic 85 conditions in different biogeochemical zones of Aarhus Bay, Denmark Chapter 5 Membrane lipid composition in enrichments from the sulfate 119 and methane zones of Aarhus Bay, Denmark Chapter 6 Physiological and molecular characterization of anaerobic 139 marine propionate- and butyrate-converting syntrophic cultures Chapter 7 General Discussion 167 Appendices 182 References 184 Summary 212 Samenvatting 214 Author affiliations 217 Acknowledgements 218 About the author 221 List of publications 222 SENSE Diploma 223 Chapter 1 General Introduction Derya Özüölmez Chapter 1 1.1 Global carbon cycle Carbon is the major element of all life forms, and it is actively cycled in the biosphere. The carbon cycle reflects the flow and exchange of carbon among living organisms and the environment through a series of chemical, physical and biological reactions (Figure 1). Inorganic carbon that is formed from organic matter or weathered from limestone enters the atmosphere as CO2 or in − aquatic environments mostly as HCO3 . Atmospheric CO2 is in equilibrium with the carbonate − system of the oceans (Takahashi et al., 1997; Fasham et al., 2001). Atmospheric CO2 or CO2/HCO3 in the oceans or lakes can be fixed by autotrophic or photolithotrophic organisms (e.g. plants, phytoplankton and marine algae) to synthesize organic carbon. By decay of these organisms, organic carbon is converted back to inorganic carbon through hydrolysis, fermentation and mineralization by the combined action of different organisms (Canfield, 1993; Kristensen and Holmer, 2001). Figure 1. Global carbon cycle. Figure is adapted from Pidwirny, 2012. Carbon is stored in our planet (a) as living and dead biomass in the biosphere; (b) as carbon dioxide gas in the atmosphere, (c) as organic matter in soils and sediments, (d) in the lithosphere as fossil fuels like coal, oil, and natural gas, and as carbonate-based sedimentary rock deposits such as limestone and dolomite; and (e) in the oceans as dissolved atmospheric carbon dioxide and as 2 General Introduction calcium carbonate shells in marine organisms (Figure 1) (Pidwirny, 2012). The majority of the carbon is fixed as inorganic carbon in limestone or in fossil organic pools, largely as CO2, whereas organic carbon represents only about 0.1% of the total carbon cycles through the active pool on Earth (Harvey, 2006). Soils represent the largest pool within this active cycle. This is followed by land biota, dissolved organic matter in seawater, and surficial marine sediments with decreasing amounts of organic matter. The smallest fraction includes marine biota and particulate pools (Harvey, 2006). Although the particulate organic carbon reservoir is small, it is dynamic and plays a central role in both amount and composition of organic matter which reaches underlying sediments (Harvey, 2006). 1.2 Degradation of organic matter in marine sediments Coastal marine ecosystems receive regular inputs of organic matter and nutrients from primary production of phytoplankton, rivers, coastal erosion, and the atmosphere (Jørgensen, 1982). Mineralization of the particulate organic matter starts already in the water column. On the other hand, the organic matter that is not decomposed in the water column rapidly sinks down to the sediment in coastal shelf sediments and part of it gets buried in the sediment (Jørgensen, 1983). It is shown that 10 – 50 % of carbon from primary production was deposited on the bottom in coastal shelf sediments (0-200 m depth), whereas this fraction decreases to about 1% in pelagic sediments (5000-6000 m) (Jørgensen, 1983). The coastal shelfs comprise 8.6% of the total area of the oceans, and it is estimated that 83% of the mineralization in the sea bottom takes place in these shelf areas (Jørgensen, 1983). This reflects the importance of coastal and shelf areas in the carbon cycle. High microbial activity in the upper sediment layers leads the formation of distinct biogeochemical zones. The depth range of each zone varies strongly depending on the supply of organic matter from overlying seawater and the sedimentation rate which have an effect on accumulation of organic matter (Jørgensen, 1983). In coastal marine sediments, the oxic surface layer constitutes a thin layer due to the rapid consumption of oxygen for aerobic mineralization. Therefore, the remaining organic matter will be degraded by anaerobic microbes and part of it will be buried in the sediment where mineralization continues albeit slow. In the anoxic part of the sediment, nitrate, manganese, iron, sulfate and carbon dioxide serve as terminal electron acceptors for the mineralization processes (Figure 2). The depth sequence of electron acceptors reflects a gradual decrease in redox potential and thus a decrease in the free energy available by respiration. 3 Chapter 1 It is estimated that 25-50% of the organic carbon is mineralized through sulfate reduction, which makes sulfate an important electron acceptor in anoxic part of the sediments (Jørgensen, 1982). Primary production CO , NH +, O2 2 4 Ocean 2- HPO4 etc Flux into overlying water Oxic Zone N2 Macromolecular O2 respiration - Organic Matter NO3 reduction Mn2+ Suboxic Zone Exoenzymatic Hydrolysis Mn(IV) reduction Propionate Fe2+ Butyrate Fe(III) reduction Sugars Amino Lactate Acids + H2S Sulfate Zone NH4 Long Chain 2- Fatty Acids acetate SO4 reduction CH4 Fermentation Methane Zone H2 + CO2 Methanogenesis Buried Organic Material Figure 2. Organic carbon degradation pathways in marine sediments and their relation to the biological redox zonation. Figure is adapted from Parkes et al., 2014 and Jørgensen, 2006. Anaerobic degradation of organic matter in marine sediments is a complex sequential process in which a variety of physiologically different microorganisms takes part. The first step is an extracellular hydrolysis of polymers (polysaccharides, proteins, nucleic acids and lipids) (Fig 2, Fig 3). Primary fermenting bacteria ferment the monomers and oligomers to fatty acids, branched- chain fatty acids, alcohols, aromatic acids, H2 and CO2. Some of these fermentation products, such as acetate, H2, CO2, and other one-carbon compounds, can be converted directly to methane and carbon dioxide by methanogens. In methanogenic environments, secondary fermenters or proton reducers convert alcohols, long-chain, branched-chain and aromatic fatty acids to acetate, formate, H2
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