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HORIZONTAL GENE TRANSFER and BIOGEOGRAPHY of ISOLATED THERMAL ACIDIC BACTERIAL COMMUNITIES by MIRATUL MAGHFIROH a Thesis Presen

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HORIZONTAL GENE TRANSFER and BIOGEOGRAPHY of ISOLATED THERMAL ACIDIC BACTERIAL COMMUNITIES by MIRATUL MAGHFIROH a Thesis Presen HORIZONTAL GENE TRANSFER AND BIOGEOGRAPHY OF ISOLATED THERMAL ACIDIC BACTERIAL COMMUNITIES By MIRATUL MAGHFIROH A Thesis Presented to The Faculty of Humboldt State University In Partial Fulfillment of the Requirements for the Degree Master of Science in Biology Committee Membership Dr. Mark Wilson, Professor, Committee Chair Dr. Patricia Siering, Professor Dr. Edward Metz, Associate Professor Dr. Jianmin Zhong, Associate Professor Dr. Erik Jules, Professor, Graduate Coordinator December 2015 ABSTRACT HORIZONTAL GENE TRANSFER AND BIOGEOGRAPHY OF ISOLATED THERMAL ACIDIC BACTERIAL COMMUNITIES Miratul Maghfiroh A number of isolated high temperature, low pH geothermal sites exist in Lassen Volcanic National Park (LVNP) and Hawai’i Volcanoes National Park (HVNP) that allow for the growth of thermoacidophilic microbial communities. Horizontal gene transfer (HGT) may be particularly important in these communities because it allows for ecotype divergence of closely related organisms. Previous work with LVNP isolates suggested that HGT has been occurring within species of Alicyclobacillus and between Alicyclobacillus spp. and other bacterial genera within hydrothermal communities. It was found that bacteria which possessed divergent 16S rRNA gene sequences had nearly identical protein-coding genes. Isolated thermal acidic systems also provide an opportunity to test hypotheses about microbial dispersal and biogeography, as the sites have island-like characteristics (localized regions of specialized habitats surrounded by inhospitable habitat). This thesis project aimed to 1) investigate whether HGT was occurring among a set of Alicyclobacillus tolerans and A. acidocaldarius isolates from HVNP, 2) determine whether there were geographical limits to the spread of alleles among sites within a park and between LVNP and HVNP, and 3) investigate the mechanisms by which HGT might be occurring in Alicyclobacillus. A phylogenetic tree based on cpn60 gene sequences was consistent with HGT of the cpn60 gene. A Bacillus isolate possessed a cpn60 allele that was identical to that of HVNP A. tolerans isolates. One A. tolerans isolate which possesses 16S rRNA, gyrB, keto, and eftu genes that ii cluster with those of the other HVNP A. tolerans isolates, possesses a cpn60 allele that belongs to distantly related Gram positive bacteria. Numerous examples of incongruent phylogenetic trees likely caused by HGT were also found among LVNP isolates. Evidence for rapid dispersal between HVNP and LVNP was evident in the A. tolerans dataset; identical alleles were found in A. tolerans isolates from sites that are separated by ~4000 km. However, biogeographical clustering of alleles was found in A. acidocaldarius isolates, including in LVNP sites separated by ~3 km. The traC gene, associated with conjugation, was found in A. tolerans and A. acidocaldarius LVNP isolates, and pulsed-field gel electrophoresis detected the presence of a 100-150 kbp plasmid in an A. tolerans isolate. SEM of filter-mated pairs of isolates showed the presence of the pili-like structures, but not in pure cultures of these strains. Analysis of a draft genome of an A. acidocaldarius isolate revealed the presence of numerous genes related to transformation and conjugation. Collectively, the results support a high rate of HGT among the Alicyclobacillus isolates and suggest that conjugation may be an important process of HGT among these Gram positive species in these environments. The A. tolerans data suggest that rapid dispersal between HVNP and LVNP sites is likely, but the A. acidocaldarius data suggest that in some cases this dispersal is not enough to overcome forces favoring local biogeographical specialization. The difference between the A. tolerans and the A. acidocaldarius results is surprising and suggests that even among closely related species the forces of dispersal, HGT and ecotype divergence are operating in strikingly different ways. iii ACKNOWLEDGEMENT I thank Dr. Mark Wilson for the guidance and support, the committee members : Dr. Patricia Siering, Dr. Edward Metz, and Dr. Jianmin Zhong, HEAT lab members : Angela McCartney, Kathryn Wiles, Kevin Amses, Gabriel Ross, the students in Genetic Lab – Spring 2014, Dr. Casey Lu, and Marty Reed. iv TABLE OF CONTENTS ABSTRACT .................................................................................................................................... ii ACKNOWLEDGEMENT ............................................................................................................. iv TABLE OF CONTENTS ................................................................................................................ v LIST OF TABLES ........................................................................................................................ vii LIST OF FIGURES ..................................................................................................................... viii CHAPTER 1 : SITE DESCRIPTIONS AND PROJECT GOALS ................................................. 1 CHAPTER 2 : LITERATURE REVIEW ....................................................................................... 3 1. Horizontal gene transfer (HGT) ........................................................................................... 3 2. Mechanisms of HGT ............................................................................................................ 4 3. Detection of HGT ................................................................................................................ 7 4. Microbial communities of thermal acidic environments ................................................... 11 5. Microbial biogeography ..................................................................................................... 17 CHAPTER 3 : HORIZONTAL GENE TRANSFER AND GENE BIOGEOGRAPHY ............. 21 Introduction ............................................................................................................................... 21 Materials and Methods .............................................................................................................. 23 Results ....................................................................................................................................... 28 Discussion ................................................................................................................................. 49 CHAPTER 4 : CONJUGATION AS A POSSIBLE MECHANISM OF HGT IN Alicyclobacillus. ....................................................................................................................................................... 55 Introduction ............................................................................................................................... 55 Materials and Methods .............................................................................................................. 57 Results ....................................................................................................................................... 62 Discussion ................................................................................................................................. 71 CHAPTER 5 : POSSIBLE MECHANISMS OF HORIZONTAL GENE TRANSFER USING THE ANALYSIS OF GENOMIC SEQUENCES ........................................................................ 74 Introduction ............................................................................................................................... 74 Materials and methods .............................................................................................................. 76 Results ....................................................................................................................................... 77 Discussion ................................................................................................................................. 88 CHAPTER 6 : SUMMARY.......................................................................................................... 91 v REFERENCES ............................................................................................................................. 92 APPENDICES ............................................................................................................................ 113 vi LIST OF TABLES Page Table 1. Genes contributing to transformation and conjugation. ........................................ 6 Table 2. Target genes and PCR primers ........................................................................... 26 Table 3. HVNP isolates, identity by 16S rRNA gene sequencing, and the corresponding sequences analyzed. .......................................................................................................... 30 Table 4. LVNP isolates identified as A. tolerans on the basis of 16S rRNA gene sequence, and sequences available. .................................................................................. 32 Table 5. LVNP isolates identified as A. acidocaldarius on the basis of 16S rRNA gene sequence, isolation site, and sequences available. ............................................................ 33 Table 6. Primers used to search for traC homologs in LVNP and HVNP isolates. ......... 58 Table 7. Homolog genes contributed in conjugation and transformation present in Alicyclobacillus acidocaldarius chromosomal genome and plasmids ............................. 78 Table 8. Genes involved in conjugation
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