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Genomes of Three Arsenic Metabolizing Bacteria Xue Chen

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Genomes of Three Arsenic Metabolizing Bacteria Xue Chen Duquesne University Duquesne Scholarship Collection Electronic Theses and Dissertations 2015 Genomes of Three Arsenic Metabolizing Bacteria Xue Chen Follow this and additional works at: https://dsc.duq.edu/etd Recommended Citation Chen, X. (2015). Genomes of Three Arsenic Metabolizing Bacteria (Master's thesis, Duquesne University). Retrieved from https://dsc.duq.edu/etd/398 This Immediate Access is brought to you for free and open access by Duquesne Scholarship Collection. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Duquesne Scholarship Collection. For more information, please contact [email protected]. GENOMES OF THREE ARSENIC METABOLIZING BACTERIA A Thesis Submitted to the Bayer School of Natural and Environmental Sciences Duquesne University In partial fulfillment of the requirements for the degree of Master of Science By Xue Chen August 2015 Copyright by Xue Chen 2015 ii GENOMES OF THREE ARSENIC METABOLIZING BACTERIA By Xue Chen Approved July 15, 2015 ________________________________ ________________________________ Dr. John F. Stolz Dr. Nancy Trun Professor of Biology Associate Professor of Biology (Committee Chair) (Committee Member) ________________________________ Dr. Partha Basu Professor of Chemistry & Biochemistry (Committee Member) ________________________________ ________________________________ Dr. Philip Reeder Dr. John F. Stolz Dean, Bayer School Director, CERE iii ABSTRACT GENOMES OF THREE ARSENIC METABOLIZING BACTERIA By Xue Chen August 2015 Dissertation supervised by Dr. Stolz Although arsenic is toxic to most living cells, many microbes live in environments with high concentrations of arsenic. In addition to being resistant to arsenic, some actively couple arsenic oxidation/reduction reactions to respiration gaining energy in the process. Following a current review of the literature, the genomes of the three such bacteria, one arsenite oxidizer, Alkalilimnicola ehrlichii MLHE-1, and two arsenate reducers, Alkaliphilus oremlandii OhILAs, and Bacillus selenitireducens MLS- 10 are presented. The genome of Alkalilimnicola ehrlichii MLHE-1 consists of 3,275,944 bp with a 67.53% GC content; the genome of Alkaliphilus oremlandii OhILAs consists of 3,123,558 bp with a 36.26% GC content; and the genome of Bacillus selenitireducens MLS-10 consists of 3,592,478 bp with a 48.46% GC content. The arsenic genes in A. iv oremlandii were clustered in an “arsenic island”, while the genes for arsenic resistance (i.e., ars) and respiration (arr, arx) in Al. ehrlichii and B. selenitireducens were not. v DEDICATION Thanks to the supports from my parents and my dear sister Katt. vi ACKNOWLEDGEMENT I would like to thank Dr. Stolz and the entire Stolz lab group for their guidance and assistance throughout the process. Without their support, this thesis paper would have never been accomplished. I would like to specifically express my gratitude and appreciation to Dr. Stolz for the mentorship, understanding and teaching me the new knowledge and skills to push me to accomplish the thesis paper. vii TABLE OF CONTENTS Page Abstract .............................................................................................................................. iv Dedication .......................................................................................................................... vi Acknowledgement ............................................................................................................ vii List of Tables .................................................................................................................... xii List of Figures .................................................................................................................. xiii List of Abbreviations .........................................................................................................xv Chapter 1 Introduction .........................................................................................................1 1.1 General ..........................................................................................................................1 1.2 Source of Arsenic ..........................................................................................................2 1.3 Toxicity Effects on Human Health ................................................................................4 1.3.1 Respiratory effects ......................................................................................................6 1.3.2 Cardiovascular effects .................................................................................................6 1.3.3 Gastrointestinal effects ................................................................................................7 1.3.4 Hematological effects .................................................................................................7 1.3.5 Hepatic effects ............................................................................................................8 1.3.6 Renal effects................................................................................................................8 1.3.7 Dermal effects .............................................................................................................9 1.3.8 Neurological effects ....................................................................................................9 1.3.9 Reproductive effects .................................................................................................10 1.3.10 Genotoxic effects ....................................................................................................10 1.3.11 Mutagenetic effects .................................................................................................10 viii 1.3.12 Carcinogenic effects................................................................................................11 1.3.13 Biochemical effects .................................................................................................11 1.3.14 Diabetes mellitus .....................................................................................................12 1.4 Arsenic Contamination around the World ...................................................................13 1.4.1 Argentina...................................................................................................................14 1.4.2 Bangladesh ................................................................................................................14 1.4.3 Brazil .........................................................................................................................15 1.4.4 Canada.......................................................................................................................15 1.4.5 Chile ..........................................................................................................................16 1.4.6 Hungary.....................................................................................................................16 1.4.7 India ..........................................................................................................................17 1.4.8 Mexico ......................................................................................................................17 1.4.9 United States of America ..........................................................................................18 1.4.10 Vietnam ...................................................................................................................18 1.5 Arsenic Standard for Drinking Water ..........................................................................19 1.6 Methods of Removing Arsenic from Water.................................................................19 1.6.1 Precipitation processes ..............................................................................................19 1.6.2 Membrane process ....................................................................................................20 1.6.3 Adsorption processes ................................................................................................20 1.7 Arsenic Contamination and Adverse Health Effects in China .....................................21 1.8 Microbial Reponses to Environmental Arsenic ...........................................................27 Chapter 2 Hypotheses, Aims and Methods ........................................................................39 2.1 Hypotheses ...................................................................................................................39 ix 2.1.1 Hypothesis1: Arsenic metabolism is encoded by arsenic specific genes .................39 2.1.2 Hypothesis2 Arsenic genes are organized in cluster as “arsenic island” in the three bacteria ...............................................................................................................................40 2.2 Aims .............................................................................................................................41 2.2.1 Aim1: Identify the arsenic genes in the genomes of A. ehrlichii, A. oremlandii and B. selenitireducens. ...........................................................................................................41 2.2.2 Aim2 Determine the existence of “arsenic islands” in the three bacteria .................41 2.2.3 Aim3: Draft genome announcements for
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