Metabolism of Microbial Communities in the Environment

Metabolism of microbial communities in the environment A compound-specific stable hydrogen isotope approach O OH Sandra M. Heinzelmann Metabolism of microbial communities in the environment: A compound-specific stable hydrogen isotope approach Sandra Mariam Heinzelmann ISBN: 978-94-6203-959-9 Printed by Wöhrmann Print Service, Zutphen Cover design: Sandra Heinzelmann Metabolism of microbial communities in the environment: A compound-specific stable hydrogen isotope approach Component-specifieke stabiele waterstofisotopen als gereedschap voor de bepaling van het metabolisme van microbiële gemeenschappen in het milieu (met een samenvatting in het Nederlands) Metabolismus von mikrobiellen Gemeinschaften in der Umwelt: Ein komponentenspezifischer stabiler Wasserstoff Isotopen Ansatz (mit einer Zusammenfassung in deutscher Sprache) Proefschrift ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag van de rector magnificus, prof.dr. G.J. van der Zwaan, ingevolge het besluit van het college voor promoties in het openbaar te verdedigen op maandag 21 december 2015 des middags te 4.15 uur door Sandra Mariam Heinzelmann geboren op 18 mei 1985 te Mainz, Duitsland Promotoren: Prof. dr. ir. S. Schouten Prof. dr. ir. J.S. Sinninghe Damsté Copromotor: Dr. M.T.J. van der Meer „Keine Panik auf der Titanic“ Für meine Eltern Table of contents Chapter 1 7 Introduction PART I Chapter 2 25 Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids Chapter 3 45 Comparison of the effect of salinity on the D/H ratio of fatty acids of heterotrophic and photoautotrophic microorganisms PART II Chapter 4 59 Critical assessment of glyco- and phospholipid separation by using silica chromatography Chapter 5 75 Seasonal changes in the D/H ratio of fatty acids of pelagic microorganisms in the coastal North Sea Chapter 6 97 Assessing the metabolism of sedimentary microbial communities using hydrogen isotopic compositions of fatty acids 6 References 117 Summary/Samenvatting/Zusammenfassung 141 Supplementary Data 153 Acknowledgement 185 About the Author 187 7 Chapter 1 Introduction Chapter 1 1.1. Microbial metabolism and diversity Microorganisms and their metabolic activity shape and affect the environment both on a global and local scale as they are key-players in all elemen- tal cycles (Madigan et al., 2012). It has been estimated that microorganisms contribute up to 60 % to the biomass of the whole biosphere (Singh et al., 2009) with prokaryotic cells alone containing 350-550 Pg of cellular carbon, approximately 60-100% of the estimated total carbon in plants (Whitman et al., 1998). The marine water column and surface sediments contain a major part of all microorganisms (Whitman et al., 1998). One of the most important players in the carbon cycle are marine phytoplankton, contributing half the global primary production (Field et al., 1998) with one of the highest cellular production rates on earth (Whitman et al., 1998). Photo credit: T.E. Letain, Photo credit: Y. Tsukii S.I. Martin, H.R. Beller Pediastrum boryanum light CO2 + 2 H2O CH2O + O2 + H2O Thiobacillus denitrificans 2- 2- + S2O3 + H2O + 2 O2 2 SO4 + 2 H Light photo- Energy source Chemical chemo- Inorganic -litho- Electron donor -organo- Organic -troph -auto- CO2 Carbon Organic -hetero- source Both -mixo- Escherichia coli C6H12O6 + 6 O2 6 CO2 + 6 H2O Photo credit: F. Sauvager Figure 1: Classification of microbial metabolism regarding energy source, electron donor and carbon source. 10 Introduction Understanding the impact of microorganisms on their environment re- quires studying their metabolic capabilities and activities. The metabolism of microorganisms can be distinguished based on their energy source, electron donor and carbon source (Figure 1). Organisms can either be metabolical- ly flexible and able to express different metabolic pathways depending on environmental conditions or be restricted to just one (Lengeler et al., 1999; Madigan et al., 2012). One of the first approaches to study microorganisms and their metabolism involved the isolation or enrichment of organisms from environmental samples using specific growth conditions, e.g. different energy and carbon sources and to study the physiological properties of the isolates in culture. While this has led to a large number of microorganisms available in pure culture (e.g. ~10600 species in the Deutsche Sammlung von Mikro- organismen und Zellkulturen [DSMZ] in 2015), it has nevertheless been estimated that only ~1% of all microorganisms in the environment can be cul- tivated with standard techniques (Amann et al., 1995). Additionally, those microorganisms that are brought into pure culture are not necessarily the most abundant microorganisms present in nature or do not play an important role in the environment (Overmann, 2006). Furthermore, microorganisms express- ing novel metabolic pathways can be overlooked because of e.g. use of inap- propriate selection conditions for cultivating efforts (Overmann, 2006; Madi- gan et al., 2012). Thus, studying activity, diversity and metabolism in situ is essential to be able to understand the complete picture of metabolic dynamics within microbial communities. Over the past decades, a wide range of cultivation-independent approaches have been used to study and understand the metabolic activity of microbial communities in the natural environment. These techniques use a wide range of organic and inorganic molecules, including biomarker molecules like DNA, RNA and lipids. A selection of the most common techniques includes stable isotope probing (SIP), functional gene analysis, microelectrode profiling, incorporation of radiolabeled tracers into macromolecules (DNA or proteins), microautoradiography fluorescence in situ hybridization (MAR-FISH), and secondary ion mass spectrometry in situ hybridization (SIMSISH) (Table 1). However, several limitations for these methods have been observed including e.g. targeting only a small selection of microorganisms with specific metabolic capabilities, inducing artificial changes in microbial communities and cross labelling of secondary metabolites (e.g. Radajewski et al., 2000; Rastogi and Sani, 2011). In addition, methods targeting specific genes require knowledge of the DNA sequences for genes coding for enzymes involved in 11 Chapter 1 12 Table 1: Selected examples for cultivation independent methods and their limitations to assess metabolic activity in microbial communities in situ. Method Target Aim Potential problems Example literature Stable isotope prob- DNA, RNA, lipids - identification of microorganism - incubation time (incorporation in secondary (Boschker et al., 1998; Radajew- ing (SIP) metabolising isotopic labelled metabolites, low signal) ski et al., 2000; Radajewski et substrate al., 2003; Dumont and Murrell, - concentration ( artificial changes of microbi- 2005) al activity, low signal) Functional gene mRNA, 16S rRNA - estimation of relative abundance - pre-knowledge of gene sequences required (Corredor et al., 2004; Henry activity analysis of specific groups et al., 2004; Jensen et al., 2008; Agrawal and Lal, 2009) - estimation of metabolic activity Microelectrode concentration respi- - analysis of microbial processes - no identification of metabolic active organ- (Nielsen et al., 1990; Schramm profiling ration gases e.g. O2, like photosynthesis, respiration, ism possible et al., 1996; Pepper et al., 2014) H2S, H2 sulfur reduction - only on very small scale, does not assess the whole community Incorporation of DNA, protein - measuring metabolic activity - limited to heterotrophic microorganisms (Kirchman and Hoch, 1988; radiolabeled tracers of heterotrophic microorganisms Tibbles and Harris, 1996; Pepper into macromolecules by incorporation of radiolabeled - concentration, incubation time, nonspecific et al., 2014) thymidine or leucin labelling of non-target molecules - not all targeted microorganisms take up exogenously supplied molecules Microautoradiogra- DNA - identification of active cells that - added substrate can be metabolised by (Okabe et al., 2005; Overmann, phy fluorescence in metabolise the added radioactive non-target organisms 2006; Rogers et al., 2007; Rasto- situ hybridization substrate gi and Sani, 2011) (FISH- MAR) - probes require pre-knowledge of gene se- quence - natural radioactive isotopes with long half- life necessary Secondary ion mass DNA - direct observation and identifi- - added substrate can be metabolised by (Behrens et al., 2008; Li et al., spectrometry in situ cation of active cells that metabo- non-target organisms 2008; Rastogi and Sani, 2011) hybridization (SIM- lise added labelled substrate SISH) - probes require pre-knowledge of gene se- quence Introduction different metabolic pathways, which makes it difficult to identify novel metabolic pathways. Furthermore, recent studies have shown that a higher tran- scriptional activity of a gene does not always correlate with a higher activity of the pathway in which the protein-coding gene is involved (Bowen et al., 2014). Therefore, it is desirable to develop additional techniques for studying microbial activity in the environment in order to complement existing ones. 1.2. Isotopic composition of microbial lipids A possible alternative for DNA-based techniques is the use of the natural stable isotope abundance of different biomarker molecules, especially lipids. An advantage of lipids compared to DNA is their stability over geological timescales, making them ideal biomarkers also for paleostudies.

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