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A study of dissolved organic matter in peatlands: molecular characterisation of a dynamic carbon reservoir Luke McDonald Ridley A thesis submitted for the degree of Doctor of Philosophy, 2012 University of Edinburgh Declaration Ruth Flerus carried out the ESI-FT-ICR-MS analysis and data acquisition (discussed in Chapter 6). CuO oxidation GC-MS analysis and quantification of phenolic compounds in the solid phase was carried out Jason Dallas-Ross and Dafydd Elias, who also assisted in the field in June 2010. All subsequent data analysis and interpretation was carried out by the candidate. All other sample analysis and data collection was carried out by the candidate. The candidate declares that: (a) that the thesis has been composed by the candidate, and (b) either that the work is the candidate's own, or, if the candidate has been a member of a research group, that the candidate has made a substantial contribution to the work, such contribution being clearly indicated, and (c) that the work has not been submitted for any other degree or professional qualification except as specified. Signed: Abstract Northern peatlands represent a significant carbon reservoir, containing approximately a third of the terrestrial carbon pool. The stability of these carbon stores is poorly understood, and processes of accumulation and degradation appear to be finely balanced. Over the last decade, it has become increasingly clear that losses of dissolved organic carbon (DOC) from peatlands can be of considerable size and this flux appears to have increased substantially over the last 20 years. Despite its significance, the chemical composition of peatland-derived DOC remains poorly understood. This study aimed to characterise dissolved organic matter (DOM) at the molecular level using a novel combination of techniques. The study site (Cors Fochno, Wales, UK) is an ombrotrophic bog on which a number of studies into carbon cycling and hydrology have been carried out, providing a useful context for this project. The size and compositions of the DOC pool was monitored over 18 months, from three banks of piezometers, sampling from depths of 15 cm to 6 m. DOM which is representative of bog runoff was also monitored. DOC concentrations varied considerably between locations, spanning an order of magnitude (11.4 to 114 mgC l-1). Several relationships between DOC concentration and environmental and physical factors were established: DOC levels near the surface of the peatland varied with temperature, those in the runoff were most affected by recent rainfall events and the apparent DOC concentration at depth was related to the hydraulic conductivity of peat at that depth. The annual flux of DOC from the site was estimated at 113 tonnes, or 17.4 gC m-2. Only a small portion of the DOC pool could be characterised by analysis of dissolved combined amino acids (DCAA) and dissolved carbohydrates (as neutral sugars). Non-protein amino acids were most abundant in runoff samples, suggesting microbial reworking of DOM on entering drainage systems. DCAA yields decreased with depth, and the DCAA pool in deeper peat layers was characterised by more hydrophobic compounds. Interpretation of semi-quantitative results from TMAH thermochemolysis GC-MS analysis suggested oxidative degradation of organic matter near the surface of the peatland and photochemical degradation where DOM entered drainage networks, and this was supported by novel interpretation of results from ultrahigh resolution mass spectrometry analysis. The deepest porewaters were dominated by n- alkanes, with notable contributions from fatty acids, suggesting a plant wax source for this DOM. The highest DOC concentrations were found at intermediate depth from a site midway between the centre of the bog and the southern boundary where hydraulic conductivities were low, and DOM from these piezometers were characterised by high contributions from a suite of phenolic compounds (with mainly para-hydroxyphenyl structures). These compounds have been linked to Sphagnum species, and are known to be functionally important to the development and maintenance of the unusual chemical environment in peatlands which slows decay rates, reduces microbial activity, and allows the sequestration of the large carbon reservoir. The findings of this study highlight the dynamic nature of peatland derived DOM, both in the size of the carbon pool and its composition which change dramatically with both season and depth. This thesis is dedicated to my dad who was dauntlessly fighting his own battles throughout this project, and whose victory gives our family much to smile about every day. "Si ce n'est pas toi, petit, qui commence a changer le monde, qui le fera?" Unknown author Given to me on a postcard by my mum before I left home for university. Acknowledgements Thank you to NERC for funding this project, and to DAAD and the British Council for giving me the opportunity to collaborate with European colleagues, resulting in the ESI-FT- ICR-MS work presented in Chapter 6 of this thesis. In addition to acknowledging the support and advice of all my supervisory team, Greg Cowie, Geoff Abbott, Andy Baird and Maurizio Mencucinni, I would like to say a special thank you to Andy, whose help in the field and during the writing process has been invaluable. Mike Bailey at CCW was also a huge help, and great champion of scientific studies at Cors Fochno. A special thanks must also be given to Steve Mowbray, who introduced me to the wonders of working in an organic geochemistry lab, and whose expert knowledge I called upon countless times. Thanks also to Paul Donohoe at Newcastle University for his help with the acquisition of TMAH thermochemolysis data, and to Alan Pike and Jim Sm ith for their help with the manufacture of field equipment (with some entertainment along the way). Thanks also to Ruth Flerus, Philippe Schmitt-Kopplin and Boris Koch for their generosity, inspiration and help while I was getting to grips with ESI-FT-ICR-MS. For their huge efforts in the field, both manual and morale boosting, I’d like to thank Alice Milner, Alun Evans, Daf Elias, Jason Dallas-Ross and Terry Alexander. A special mention goes to Alun, who has helped immeasurably over the past three and a half years. Thanks also to Imalda Stamp for her support on and off the bog, to Rhona and Phil at Borth House B&B, and to Walter Geibert who was always willing to offer advice and support over coffee. And thanks to my informal peat network (AKA Kathleen Allan and Antony Phin) for all the peatmeets, and for proof reading chapters. On that front, thanks also to Drs Antony Bloom, Bronwen Whitney, Tom Russon and Gillian McCay for their very helpful comments and advice. Finally, a huge thanks to my friends, housemates and office buddies, without whom this would not have been four of the most enjoyable and rewarding years of my life. I can’t mention everyone, but Matthew Unterman, Amber Annett, Tom, Gillian, Sian Henley, Rachel Kilgallon, Johanass Miocic, Robyn Tuerena, Lizzie Entwhistle, Maddy Berg, Nancy Burns, Rhian Meara, Luke Smallman, Catherine Harper, Andrew Schurer and Dan Hobley all deserve special mentions. Contents 1 Introduction and project rationale 1 1.1 Northern peatlands as a carbon reservoir 1 1.2 Peatland dynamics: the possible impact of future climate change 4 1.2.1 Increased DOC fluxes – possible climatic controls 5 1.2.2 Increased DOC fluxes – possible non-climatic controls 7 1.3 Mechanisms for the production and export of DOC in peatlands 8 1.4 Research questions and aims of the project 11 2 Methods and site description 14 2.1 Site description 14 2.2 Sampling design and protocol 17 2.3 Sampling methods 19 2.3.1 Porewater sampling and preservation 23 2.3.2 Solid peat sampling, preparation and preservation 24 2.4 Chemical analysis of samples – overview and rationale 25 2.4.1 CN analysis 28 2.4.2 DOC and TDN 28 2.4.3 Carbohydrate analysis 29 2.4.4 Amino acid analysis 31 2.4.4.1 Amino acid analysis of solid peat 31 2.4.4.2 Amino acid analysis of DOM from water samples 31 2.4.4.3 Amino acid analysis – quantification by HPLC 32 2.4.5 Phenol analysis of solid peat 33 2.4.6.TMAH thermochemolysis GC MS 34 2.4.6.1 TMAH thermochemolysis sample preparation and instrumental set-up 34 2.4.6.2 Quantification and coeluting peaks 35 2.4.7 ESI-FT-ICR-MS 41 3 DOC dynamics with season and location and an estimate of DOC loss 44 3.1 Objectives and approaches taken 44 3.2DOC concentrations – variations with depth, location and season 45 3.2.1Other locations – Investigating those samples with high DOC 48 3.2.2 Other locations –DOC concentrations at the Lake site 48 3.3 DOC concentrations – comparison to water table and