Molecular Characterization of Spinach (Spinacia
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MOLECULAR CHARACTERIZATION OF SPINACH (SPINACIA OLERACEA) MICROBIAL COMMUNITY STRUCTURE AND ITS INTERACTION WITH ESCHERICHIA COLI O157:H7 IN MODIFIED ATMOSPHERE CONDITIONS Gabriela Lopez-Velasco Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Food Science and Technology Monica A. Ponder, Committee Chair. Renee R. Boyer, Committee Member. Joseph O. Falkinham III, Committee Member. Gregory Welbaum, Committee Member. Robert C. Williams, Committee Member. March 31, 2010 Blacksburg, VA Keywords: spinach, microbial diversity, bacterial interaction, microbial community. Copyright © 2010, Gabriela Lopez-Velasco unless otherwise stated MOLECULAR CHARACTERIZATION OF SPINACH (SPINACIA OLERACEA) MICROBIAL COMMUNITY STRUCTURE AND ITS INTERACTION WITH ESCHERICHIA COLI O157:H7 IN MODIFIED ATMOSPHERE CONDITIONS Gabriela Lopez-Velasco ABSTRACT Leafy greens like lettuce and spinach are a common vehicle for foodborne illness in United States. It is unknown if native plant epiphytic bacteria may play a role in the establishment of enteric pathogens on leaf surfaces. The objective of this study was to characterize the bacterial communities of fresh and packaged spinach leaves and to explore interactions with E. coli O157:H7. We assessed the bacterial diversity present on the spinach leaf surfaces and how parameters such as spinach cultivar, field conditions, post-harvest operations and the presence of E. coli O157:H7 affected its diversity. Differences in bacterial population size and species richness were associated with differences in plant topography; flat leaves had smaller bacterial populations than savoy leaves, which correlated with larger number of stomata and trichomes in savoy leaves. During spinach growing season shifts in environmental conditions affected richness and population size of the spinach bacterial community. Decreases in the overall soil and ambient temperature and increased rainfall decreased richness and bacterial population size. Fresh spinach richness and composition assessed by parallel pyrosequencing of 16S rRNA elucidated 600 operational taxonomic units, with 11 different bacterial phyla. During postharvest operations diversity indexes and evenness tended to decrease, likely attributed to storage at low temperature and time of storage (4°C and 10°C), that promoted the dominance of -Proteobacteria. Bacteria isolated from fresh spinach elicited growth inhibition of E. coli O157:H7 in vitro, which was associated with nutrient competition. In contrast growth enhancement produced by epiphytes was associated to low correlations in carbon source utilization and the ability of E. coli O157:H7 to rapidly utilize carbon resources. In packaged spinach, E. coli O157:H7 altered the composition of the bacterial community and its growth was promoted on packaged spinach when a disinfection and temperature abuse occurred, removal of the epiphytic bacteria resulted in significant increases in numbers of E. coli O157:H7 at 10°C and was associated with increased expression of E. coli O157:H7 virulence and stress response genes. The large diversity present on the surface of spinach leaves significantly impacted the ecology of enteric pathogens like E. coli O157:H7 on the phyllosphere. iii ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Monica Ponder for all your guidance and support. I learned a lot from you and with you. Thank you for sharing your experience with me and for giving me the opportunity of being your student. To my committee: Dr. Joe, Dr. Greg, Dr. Renee and Dr. Rob. Thank you for always being available to talk and discuss my project, for all your support and guidance. I really enjoyed all the moments we shared. To my lab mates: Heather Totty, Heather Tydings, Phyllis Carder, Peter Ziegler, Twyla Smith and Megan Shepherd. It was a great experience to work with each one of you. Thank you for your friendship and support. To the National Council for Science and Technology (CONACyT) that provided financial support for my postgraduate education. To all students, staff and professors from the Department of Food Science and Technology and the Fralin Life Institute, thank you for the great environment that made my graduate studies a great experience. I would like to thank to Dr. Marcy, Dr. Sumner, Jennifer, Julie, Joell, Trina, Kim and Walter for all your help and support. To all my friends in Blacksburg, Umesh, Elaine, Tyler, Roberto, Seba, Heather, Gabi, Laurita, Agustin, Naiara, Hedie, Marianne, Chucho, Zara, Jose, David, Andrea, Fulvia and Gulden. This would not have been possible without your friendship. I love you very much. To my family in Mexico, Alma, Gonzo, Jorge, Miri, Margarita, Rafael, for all your love and support. iv DEDICATORY To Jose Manuel, I do not have words to thank you all what we have lived together here. Thank you for being always so supporting, for sharing with me this great experience, for your patience and for your love. I love you very much. v ATTRIBUTIONS Dr. Monica Ponder was the principal advisor in the development of this research project, providing advice, guidance and resources. Dr. Joseph Falkinham III provided important input and guidance in the development of techniques to screen bacterial interactions with E. coli O157:H7 and spinach phyllosphere as well and provided his expertise in microbial ecology. Dr. Gregory Welbaum provided his expertise in horticultural crops and assistance in spinach production and analysis of spinach anatomical features. Dr. Renee R. Boyer and Dr. Robert C. Williams provided guidance and assistance in the experiments associated with bagged spinach and the behavior of E. coli O157:H7 and provided their expertise in food safety. Brinkley Benson actively participated in the production of spinach during Fall of 2007 and Spring of 2008. Dr. Glenda Gillaspy provided her expertise and assistance in the utilization of DIC microscopy. Dr. Jose Herrera-Alonso and MS. Roberto Franco collaborated with spinach harvest and irrigation operations during the spinach production. MS. Gabriela Marquez, MS. Sebastian Arriola and MS. Ciro Velasco provided advise in statistical analysis. Mss. Heather Tydings was involved in the collection and screening of isolates from spinach during the summer of 2008 as undergraduate intern. She actively participated in the media preparation and packaging of spinach. vi Dr. Mane Shrinivasrao, Dr. Monica Ponder and Dr. Clive Evans provided their expertise in the analysis of sequencing obtained from 454-pyrosequencing of 16S rRNA microbiomes gene amplicons from spinach, by providing guidance and assistance in metagenomic analysis. vii Table of contents Page Abstract ii Acknowledgements iv Dedicatory v Attributions vi Table of contents viii List of tables xiii List of figures xvi Chapter 1. Introduction and Justification 1 References 2 Chapter 2. Literature review 4 Produce as part of a healthy diet 4 Trends in produce consumption 4 Produce and food safety 5 Outbreaks associated with the consumption of produce items 5 E. coli O157:H7 outbreaks 9 Consequences of foodborne illnesses 9 The reality of food safety 10 E. coli O157:H7 as human pathogen 11 Mechanisms of pathogenicity of EHEC 11 Emergence of recently recognized foodborne pathogens 13 Changes in transmission vehicles associated with microbial adaptation 13 Societal factors associated with emergence of foodborne pathogens 14 Globalization of the food supply 14 viii Factors that contribute to the increased emergence of E. coli O157:H7 as foodborne 15 pathogen Contamination of produce with Escherichia coli O157:H7during pre-harvest operations 16 Animal Manure 18 Irrigation Water 19 Contaminated soils 20 Wild life and other sources of produce contamination 21 Ecology of foodborne pathogens on plant surfaces 21 Persistence of foodborne pathogens on edible plants surfaces 22 Establishment of foodborne pathogens on edible plants 23 Plant surface as environment for bacterial growth 23 Factors that contribute to plant colonization and fitness of the phylloepiphytic bacteria 25 and enteric pathogens 26 Survival strategies of phylloepiphytic bacteria on leaf surfaces under environmental stress conditions 28 Overlapping mechanisms for survival and establishment of enteric pathogens on plant surfaces Interactions of enteric pathogens with the phyllosphere members 30 34 Biodiversity of the phyllosphere Study of microbial communities 34 38 Fingerprinting techniques to study microbial communities: Denaturant gradient gel electrophoresis Phyla specific amplification through real-time PCR 39 ix Pyrosequencing 40 Studies of diversity on the phyllosphere 41 Studies of population dynamics on the phyllosphere 46 Spinach as vegetable crop 47 Botany and production requirements 47 Harvest and post-harvest of spinach 49 49 Spinach cultivars Spinach production in United States 50 Trends of spinach consumption 51 Produce post-harvest and implications in food safety 51 Strategies to reduce microbial load and microbial growth on post-harvested produce 55 Preventive strategies to minimize the risk of produce contamination with foodborne pathogens 60 References 62 Chapter 3. Phylloepiphytic microbial community structure on spinach (Spinacia oleracea) 91 leaves at harvest as affected by cultivar and environment Abstract 91 Introduction 93 Materials and Methods 94 Results 99 Discussion 101 Acknowledgements 104 References 105 Chapter 4. Growth of E. coli O157:H7 is influenced by interactions