Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2001 Role of the dominant phototrophic bacterium in anaerobic swine waste lagoons, Rhodobacter sp PS9, in odor remediation Young Sub Do Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Bioresource and Agricultural Engineering Commons, Ecology and Evolutionary Biology Commons, Environmental Engineering Commons, Environmental Sciences Commons, and the Microbiology Commons Recommended Citation Do, Young Sub, "Role of the dominant phototrophic bacterium in anaerobic swine waste lagoons, Rhodobacter sp PS9, in odor remediation " (2001). Retrospective Theses and Dissertations. 915. https://lib.dr.iastate.edu/rtd/915 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Role of the dominant phototrophic bacterium in anaerobic swine waste lagoons, Rhodobacter sp. PS9, in odor remediation by Young Sub Do A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Microbiology Program of Study Committee: Alan DiSpirito, Major Professor D. L. "Hank" Harris Thomas Moorman Anthony Pometto III Thaddeus Stanton Iowa State University Ames, Iowa 2001 Copyright © Young Sub Do, 2001. All rights reserved. UMI Number: 3143526 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. UMI UMI Microform 3143526 Copyright 2004 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, Ml 48106-1346 ii Graduate College Iowa State University This is to certify that the doctoral dissertation of Young Sub Do has met the dissertation requirements of Iowa State University Signature was redacted for privacy. Committee Member Signature was redacted for privacy. Committee Member Signature was redacted for privacy. Committee Member Signature was redacted for privacy. ommittee Member Signature was redacted for privacy. Major Professor Signature was redacted for privacy. For the Major Program iii To Haekyong, Kyongmin, and Kun iv TABLE OF CONTENTS LIST OF FIGURES ix LIST OF TABLES xiv ABSTRACT xviii CHAPTER 1. INTRODUCTION 1 Biological Treatment Systems 2 Aerobic treatment 3 Anaerobic treatment 4 Microbiology and Biochemistry of Odor Production 5 Odor producing microorganisms 5 Fermentation reactions 7 Sulfate reducing bacteria 8 Odor consuming bacteria 9 Anoxygenic phototrophic bacteria 9 Non-photosynthetic sulfur oxidizing bacteria 9 Deodorant microorganisms 10 Evaluation of Odor 10 Olfactometry 11 Chemical analysis 11 Electronic methods 12 CHAPTER 2. MATERIALS AND METHODS 13 Description of Anaerobic Waste Storage Lagoon 13 Field Monitoring 13 Collection of Liquid Samples 14 V Collection of Environmental Odor Pollutants 14 Chemical Characterization of Liquid in Swine Waste Lagoon 15 Analysis of Environmental Odor Pollutants in the Air 15 Isolation and Identification of Bacteriochlorophylls 18 Isolation of Phototrophic Bacteria from Lagoon Samples 18 Electron Microscopy 20 Analysis of Fatty Acids from Purple Phototrophic Bacteria 21 Strains Used for Quantitative Filter Hybridization 22 Nucleic Acid Extraction and Analysis 23 Oligonucleotide Probes and Labeling 24 Quantitative Filter Hybridization 24 CHAPTER 3. CHARACTERIZATION OF VOLATILE ORGANIC COMPOUNDS IN ENVIRONMENTAL ODOR POLLUTANTS FROM SWINE WASTE LAGOONS 27 Evaluation of Chemical Odor Monitoring System 27 Analysis of Airborne Odor Pollutants by Thermal Desorption Method 28 Discussion 32 CHAPTER 4. ISOLATION AND CHARACTERIZATION OF PURPLE PHOTOTROPHIC BACTERIA FROM SWINE WASTE LAGOONS 34 Isolation of Phototrophic Bacteria 35 Morphology and Ultrastructure 35 Spectral Identification of Photopigment 36 Fatty Acid Analysis of Purple Phototrophic bacteria 39 Phylogenetic Properties 39 Electron Donors and Carbon Sources 41 Discussion 44 vi CHAPTER 5. MICROBIAL COMMUNITY STRUCTURE IN ANAEROBIC SWINE WASTE LAGOONS: ABUNDANCE OF DOMINANT PHOTOSYNTHETIC BACTERIA AND THEIR ROLE IN ODOR REMEDIATION 46 Field Observations 46 Quantification of Rhodobacter sp. PS9 in Anaerobic Swine Waste Lagoons by Oligonucleotide probe Hybridization 47 Correlation of Photosynthetic Bloom to Emission Rate of Volatile Organic Compounds 52 Discussion 53 CHAPTER 6. CONCLUSION 56 Summary of Results 56 Odor Remediation by Using Indigenous Phototrophic Bacteria 59 APPENDIX A. CHARACTERIZATION OF VOLATILE ORGANIC EMISSIONS AND WASTES FROM A SWINE PRODUCTION FACILITY 61 Abstract 61 Introduction 62 Materials and Methods 64 Description of swine waste storage basin and placement of air monitoring equipment 64 Capture and analysis of volatile organic compounds from the air 65 Physical and chemical characterization of stored waste in the slurry basin 67 Results and Discussion 68 Physical and chemical characterization of stored waste in the slurry basin 68 Atmospheric transport measurements for volatile organic compounds 70 Evaluation of air sampling methodology 73 Conclusions 74 vii Acknowledgements 76 Literature Cited 76 APPENDIX B. CORRELATION OF HUMAN OLFACTORY RESPONSES TO AIRBORNE CONCENTRATIONS OF MALODOROUS VOLATILE ORGANIC COMPOUNDS EMITTED FROM SWINE EFFLUENT 89 Abstract 89 Introduction 90 Materials and Methods 92 Composition of odorant solutions 92 Emission chamber design and operational parameters 93 Scale development and sensory panel design 95 Results and Discussion 97 Development and validation of synthetic swine odor Z2 97 Operational parameters of dynamic emission chamber 99 Panel and scale development 100 Conclusions 105 Acknowledgements 106 References 106 APPENDIX C. FUNCTIONAL CLASSIFICATION OF SWINE MANURE MANAGEMENT SYSTEMS BASED ON EFFLUENT AND GAS EMISSION CHARACTERISTICS 122 Abstract 122 Introduction 123 Materials and Methods 124 Physical and chemical characterization of stored manure 124 Description of swine manure storage facilities, placement of air monitoring equipment and statistical analyses 125 viii Capture and analysis of air pollutants from swine manure management systems 125 Evaluation of the odor intensity associated with swine manure management systems 127 Measurement of CH4 flux, VOC concentration, and odor intensity from 29 swine manure management systems 128 Detailed studies of gas flux rates from four swine manure management systems 129 Results and discussion 131 Initial evidence that methane emission rate is dependent upon manure management system environment 131 Classification of 29 swine manure management systems based on solution-phase chemistry and methane emission rate 133 Relationships between emission chemistry and odor intensity 136 Emission rates of air pollutants from swine manure management systems 139 Conclusions 142 Acknowledgements 143 Literature Cited 144 APPENDIX D. ADDITIONAL OLFACTOMETRY DATA 158 Developing a Measurement Scale for Swine Waste Odor 158 Results and Discussion 160 REFERENCES 166 ACKNOWLEDGEMENTS 180 ix LIST OF FIGURES Figure 1.1 Microbial decomposition of livestock wastes under anaerobic conditions. 6 Figure 3.1 Volatile organic compounds emitted from anaerobic swine waste lagoon eluted from Tenax TA-Carbopack C resins by thermal desorption, separated on a HP-Innowax capillary column. Gas chromatography-mass spectrometry (GC-MS) chromatogram was acquired using electron impact ionization. 32 Figure 4.1 Electron micrographs of negatively stained (A) and ultrathin-sectioned (B) cells of phototrophically grown Rhodobacter sp. PS9, showing ovoid cells with subpolar flagellum and vesicular type of intracytoplasmic membrane arrangement, respectively. 36 Figure 4.2 Spectrophotometry analysis of (A) anaerobic swine waste lagoons prior to (photo A, trace c) and following (photo B, trace a) the purple photosynthetic bloom compared with phototrophically grown Rhodobacter sp. PS9 (trace b), and (B) methanol extracts of bacteriochlorophyll from purple photosynthetic lagoon (trace a) and Rhodobacter sp. PS9 (trace b). Insert, lagoon liquid samples were taken on April 2nd, 2001 and incubated for 20 days under the light (photo B) or dark (photo A) at room temperature. 38 Figure 4.3 Primary structure of the 16S ribosomal RNA gene of Rhodobacter sp. PS9. 40 Figure 4.4 Distance matrix tree showing phylogenetic relationships between Rhodobacter sp. PS9 and phototrophic and nonphototrophic relatives belonging to the alpha subclass of the Proteobacteria, based on 16S X ribosomal RNA gene sequences; 1419 bases were used in the alignments. Scale bar represents 10 nucleotide substitutions per 100 nucleotides. 41 Figure 5.1 Chromatographic profiles of airborne volatile organic compounds emitted from anaerobic swine