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The Microbial Ecology and Horticultural Sustainability of Organically and Conventionally Managed Apples

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The Microbial Ecology and Horticultural Sustainability of Organically and Conventionally Managed Apples ABSTRACT Title of Document: THE MICROBIAL ECOLOGY AND HORTICULTURAL SUSTAINABILITY OF ORGANICALLY AND CONVENTIONALLY MANAGED APPLES. Andrea R. Ottesen, PhD, 2008 Directed By: Professor, Dr. Christopher S. Walsh, Plant Sciences and Landscape Architecture Objectives Organically and conventionally managed apple trees (Malus domestica Borkh) were evaluated for three growing seasons (2005-2007) to examine the impact of organic and conventional pesticide applications on the microbial ecology of phyllosphere and soil microflora. An important objective was to establish if organic or conventional selection pressures contribute to an increased presence of enteric pathogens in phyllosphere microflora. The horticultural and economic sustainability of the organic crop was also compared to the conventional crop with regard to fruit yield and input costs. Methods Microbial populations from phyllosphere and soil environments of apple trees were evaluated using clone libraries of 16S rRNA gene fragments. Clones were sequenced and software was used to assess diversity indices, identify shared similarities and compute statistical differences between communities. These measurements were subsequently used to examine treatment effects on the microbial libraries. Phyllosphere Results Eight bacterial phyla and 14 classes were found in this environment. A statistically significant difference between organically and conventionally managed phyllosphere bacterial microbial communities was observed at four of six sampling time points. Unique phylotypes were found associated with each management treatment but no increased human health risk could be associated with either treatment with regard to enteric pathogens. Soil Results Seventeen bacterial phyla spanning twenty-two classes, and two archaeal phyla spanning eight classes, were seen in the 16S rRNA gene libraries of organic and conventional soil samples. The organic and conventional soil libraries were statistically different from each other although the sampling depth was not sufficient to make definitive inference about this environment. Horticultural Results Fruit yields from organically managed apple trees were from one half to one third of the yields from conventionally managed trees. Based on input costs, organic fruit was about twice as expensive to produce. Asian pears (Prunus serotina) were also included in this horticultural analysis and showed greater field tolerance as an organic specialty niche crop than apples. THE MICROBIAL ECOLOGY AND HORTICULTURAL SUSTAINABILITY OF ORGANICALLY AND CONVENTIONALLY MANAGED APPLES. By Andrea Ruth Ottesen Dissertation submitted to the Faculty of the Graduate School of the University of Maryland, College Park, in partial fulfillment of the requirements for the degree of Doctor of Philosophy 2008 Advisory Committee: Dr. Christopher S. Walsh, Chair Dr. Jocelyne DiRuggiero Dr. Kim Kroll Dr. James Hanson Dr. Mark Walderhaug © Copyright by Andrea R. Ottesen 2008 Acknowledgements First and foremost I would like to thank Dr. Chris Walsh (PSLA-UMD) for his endless support and encouragement. I would also like to acknowledge and thank Dr. Arthur Miller and Brian Shawn Eblen for their important contributions to the preliminary microbiological questions and training that eventually evolved into this dissertation research. Also sincere thanks to Joint Institute for Food Safety and Applied Nutrition (JIFSAN) for financial support. Most profound thanks are due to Dr. Jocelyne DiRuggiero for her elegant guidance and inspirational mentoring. She has been an invaluable mentor and a role model as I have matured as a scientist. Sincere thanks to Dr. Kim Kroll for his identification of this project for gracious research support by the Sustainable Agriculture Research and Education (SARE) organization and for focusing my education towards the sustainable stewardship of agricultural lands. None of this work would have been remotely possible without the highly capable efforts of Michael Newell (WREC-UMD) and his staff, who researched and managed the organic and conventional logistics at the Wye Research and Education Center in Queenstown, Maryland. I’d also like to acknowledge the gracious support of the Harry R. Hughes Center for AgroEcology, Inc. ii I want to sincerely thank the wise Dr. Mark Walderhaug for his intelligent interest and “outside the box” support of my research despite its more ecological and academic approach to food safety epidemiology. I am also deeply grateful to Dr. James Hanson for providing his economic expertise to analyze the financial bottom line of the organic and conventional crops (Appendix 2). My committee as a whole was very gracious, intelligent and supportive and (apparently) I am lucky to have had such a good experience in this realm! Sincere thanks to Dr. Cecile Parmentier-Line, Dr. Julie Enticknap and the Russel Hill lab at COMB for training in various molecular techniques. I am also deeply appreciative of the highly capable undergraduate student that assisted me with various aspects of the lab work in 2007 and 2008 – Demetra Skaltsas (PLSC-UMD). I am also grateful to many members of the Plant Science and Landscape Architecture Department in the College of Agriculture for an equally supportive experience. I cannot fail to mention the brilliant James Robert White (Center for Computational Biology – UMD) who single handedly brought me out of the Bioinformatic Dark Ages and took our research to a very exciting place – 2008! iii Table of Contents Acknowledgements................................................................................................... ii Table of Contents..................................................................................................... iv List of Tables.......................................................................................................... vii List of Figures........................................................................................................ viii Chapter 1: Introduction ............................................................................................. 1 Sustainable Agriculture, Food Safety and Microbial Ecology................................ 1 Sustainable Agriculture ..................................................................................... 1 Food Safety....................................................................................................... 4 Microbial Ecology............................................................................................. 5 Phyllosphere ..................................................................................................... 6 Soil ................................................................................................................... 6 Research Objectives.............................................................................................. 8 Sustainable Agriculture ..................................................................................... 8 Food Safety and Public Health .......................................................................... 9 Microbial Ecology: Phyllosphere ...................................................................... 9 Microbial Ecology: Soil ...................................................................................10 Chapter 2: Horticultural Sustainability of Organic and Conventional Apples............11 Introduction .........................................................................................................11 Agriculture in America.....................................................................................11 Organic Agriculture .........................................................................................13 Economics .......................................................................................................13 Research Goals for Sustainable Agriculture..........................................................15 Materials and Methods.........................................................................................16 Experimental Design of the Organic and Conventional Orchard.......................16 Organic and Conventional Materials ................................................................18 Cultivars ..........................................................................................................21 Apples..............................................................................................................21 Asian Pears ......................................................................................................22 Harvest.............................................................................................................23 Analysis of Variance ........................................................................................23 Results .................................................................................................................24 Yield................................................................................................................24 Discussion............................................................................................................26 Economics .......................................................................................................28 Chapter 3: Microbial Ecology of the Phyllosphere of Organic and Conventionally Managed ‘Enterprise’ Apples...................................................................................29 Microbial Ecology, Historical
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