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Nitrogen Removal at the Expense of Methane Generation THESIS

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The Wetland Dilemma: Nitrogen Removal at the Expense of Methane Generation THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Michael R Brooker Graduate Program in Environmental Science The Ohio State University 2013 Master's Examination Committee: Paula Mouser, Advisor, Gil Bohrer, Jay Martin Copyrighted by Michael R Brooker 2013 Abstract Wetlands in the United States were subject to draining or dredging leading to substantial losses prior to gaining legal protection. Combined with increased fertilization and drainage tile use on agricultural fields, drainage basins have been affected by increased nutrient loads. Nitrogen introduction to large water bodies contributes to the development of hypoxic conditions and harming the ecosystem. To solve this issue, reconstruction of wetlands has been suggested as they are known nutrient sinks. However, wetlands also produce large amounts of the greenhouse gas, methane, giving rise to a dilemma: are the benefits worth the harm? Essentially, denitrification is the initial process which ultimately leads to the conditions necessary for methanogenesis, both being the result of microbial metabolisms present within the sediments. The potential for methane production from sediments collected at three distinct wetland biomes was investigated. Further processing investigated the methanogenic abilities of the upper and lower fifteen centimeter layers from the two hydric soils. Environmental indicators including effect of temperature and nutrient availability was ii investigated pertaining to their effect on microbial-source carbon cycling in an incubation experiment. Sediments collected from the same sites were analyzed for their microbial community in order to explain spatial variations of biogeochemical processes. Potential methane and carbon dioxide fluxes were highest at the open water site. Deep sediments lacked some innate component in its ability to produce methane. A change in temperature from 20°C to 30°C caused potential methane and carbon dioxide fluxes to double, on average. Carbon, especially acetate, was likely the factor limiting methane production in these sediments. Microbial assemblages showed that the open water site had the highest abundance of methanogenic organisms while the vegetated site showed somewhat higher ratios of organisms supposedly involved in nitrogen cycling. Isolations of pure cultures from wetland sediments provided several organisms which are serviceable as model-organisms. A methanogen and several dissimilatory nitrate reducers can be used to supply standards for quantification of genetic materials in future studies. They may also provide use in laboratory studies used to predict interactions between functional groups. iii Acknowledgments This research was supported by the US Geological Survey through the Ohio Water Resource Center, grant#60030648, as I was supported through positions as a graduate research/teaching associate position in part funded by the Environmental Science Graduate Program. My graduate committee (Paula Mouser, Gil Bohrer, and Jay Martin) provided me with invaluable insight and direction. My advisor, Paula Mouser, trained me in the techniques needed for field sampling and laboratory analysis. Gil Bohrer gave me practical knowledge by training me in modeling and giving me the ability to formulate hypotheses derived from field-data. Numerous lab members (Mengling Stuckman, Matt Noerpel, Raiyung Xiao, Zuzana Bohrerova) assisted me with training of protocols used for this research. Bill Mitsch and the Wetland Research Center (Jorge Villa-Betancur, Kay Stefanik, Blanca Bernal, Lynn McCready) allowed me access to equipment, research sites, and information. Purnima Kumar provided me with a foundation of knowledge skill, and connections. Matt Mason, Shareef Dabdoub, and iv Terry Camerlengo were instrumental in teaching bioinformatics analysis. I could not have completed my goals without the support of family, especially my parents and Molly. v Vita 2003................................................................Northwest High School 2007................................................................B.S. Microbiology, The Ohio State University 2013................................................................M.S. Environmental Science, The Ohio State University 2011 to present ..............................................Graduate Teaching/Research Associate, Department of Environmental Engineering, The Ohio State University Publications Kumar, P. S., Brooker, M. R., Dowd, S. E., and Camerlengo, T. (2011). Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing. Plos One, 6(6) vi Kumar, P. S., Mason, M. R., Brooker, M. R., and O'Brien, K. (2012). Pyrosequencing reveals unique microbial signatures associated with healthy and failing dental implants. Journal of Clinical Periodontology, 39(5) Brooker, M.R., Bohrer, G., and Mouser, P.J. (in prep). Potential carbon cycling derived from the microbial component of wetland sediments. Journal of Biogeochemical Cycles Fields of Study Major Field: Environmental Science vii Table of Contents Abstract ............................................................................................................................... ii Acknowledgments.............................................................................................................. iv Vita ..................................................................................................................................... vi List of Tables .................................................................................................................... xii Chapter 1: Introduction ....................................................................................................... 1 1.1 Wetlands in America ................................................................................................. 1 1.2 Major Biochemical Processes in Wetlands ............................................................... 4 1.2.1 Aerobic Processes ............................................................................................... 5 1.2.2 Suboxic Processes............................................................................................... 8 1.2.3 Anaerobic Processes ......................................................................................... 10 1.3 Microbial Communities in Wetland Environments ................................................ 14 1.3.2 Microorganisms Involved in Methane Production ........................................... 19 viii 1.3.3 Microorganisms Involved in Methane Oxidation ............................................. 20 1.4 Environmental Factors Influencing Wetland Microbial Activity ........................... 22 1.4.1 Hydrology ......................................................................................................... 22 1.4.2 Temperature ...................................................................................................... 24 1.4.3 Nutrient Availability ......................................................................................... 25 1.4.4 Vegetation ......................................................................................................... 27 1.4.5 Redox Potential and Sediment pH .................................................................... 29 1.4.6 Incorporation of Factors into Models Estimating Biogeochemical Flux ......... 30 1.5 Conclusions ............................................................................................................. 31 Chapter 2: Factors Affecting the Anaerobic Microbial Respiration Potential of Wetland Sediments .......................................................................................................................... 33 2.1 Abstract ................................................................................................................... 33 2.2 Introduction ............................................................................................................. 34 2.3 Materials and Methods ............................................................................................ 39 2.3.1 Site Description and Sample Collection ........................................................... 39 2.3.2 Experimental Design and Analysis ................................................................... 42 2.3.3 DNA extraction and processing ........................................................................ 44 2.3.4 Data Reduction and Statistical Analyses .................................................... 45 ix 2.4 Results ..................................................................................................................... 50 2.4.1 Factors Affecting Potential Carbon Fluxes ...................................................... 50 2.4.2 Biogeochemical Trends .................................................................................... 55 2.4.3 Microbial Community Dynamics ..................................................................... 58 2.5 Discussion ................................................................................................................... 63 2.5.1 Methane and Carbon Dioxide Flux Potentials .................................................. 63 2.5.2 Factors Affecting Microbial Activity ..............................................................
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