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Bacterial Diversity of the Gut of <Em>Cotinis Nitida</Em>

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Bacterial Diversity of the Gut of <Em>Cotinis Nitida</Em> Clemson University TigerPrints All Theses Theses December 2019 Bacterial Diversity of the Gut of Cotinis nitida Roy Attila Kucuk Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_theses Recommended Citation Kucuk, Roy Attila, "Bacterial Diversity of the Gut of Cotinis nitida" (2019). All Theses. 3218. https://tigerprints.clemson.edu/all_theses/3218 This Thesis is brought to you for free and open access by the Theses at TigerPrints. It has been accepted for inclusion in All Theses by an authorized administrator of TigerPrints. For more information, please contact [email protected]. BACTERIAL DIVERSITY OF THE GUT OF Cotinis nitida A Thesis Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Master of Science Plant and Environmental Science by Roy Attila Kucuk December 2019 Accepted by: Dr. Michael Caterino, Committee Chair Dr. Peter Adler Dr. Sharon Bewick Dr. Matthew Turnbull ABSTRACT Adult and larval Holometabolous insects exhibit radically different gut morphologies tied to their differing natural histories. Additionally, like other animals, these organisms frequently show distinctive morphological and physiological partitioning of their digestive systems, and this reflects on resident microbial communities. A review of the literature reveals bacteria have formed various symbioses with holometabolous hosts, differing widely in the context of host-symbiont services and patterns of colonization. The significance of these organisms in shaping host evolution and vice- versa is, at present, unclear, but intriguing in the context of host phylogeny. Using high throughput 16S amplicon sequencing, the bacterial community of the digestive tract of adults and larvae of the common North American scarab species Cotinis nitida is characterized according to life stage, gut structure, and adult sex. Through statistical analysis of sequence data, I show that the bacterial communities of the digestive system differ significantly between adults and larvae in both taxon richness and relatedness, and that no major differences exist between adult male and adult female beetles in terms of bacterial community. Significant differences are observed between the midgut and hindgut regions in adult beetles. The partitioning between communities of bacteria in the digestive system of larvae is displayed through significant differences in two distinct hindgut regions, the ileum and the expanded paunch., while there is no significant difference between the midgut and ileum portion of the hindgut region in larvae. ii ACKNOWLEDGMENTS I thank my advisor Dr. Michael Caterino for providing both professional expertise and steadfast and amiable guidance, and facilitating freedom in my research pursuits. I thank the other members of my committee, Dr. Peter Adler, Dr. Sharon Bewick, and Dr. Matthew Turnbull for adding novel perspectives on my work that ranged across physiology, morphology, and community ecology, and thus kept its aims and application as holistic as possible. I thank Dr. Barbara Campbell for providing lab space and equipment to carry out some of my methods, but also for providing constant technical advice and encouragement. I thank Lauren O’Connell for providing valuable suggestions and assistance in terms of molecular work and bioinformatics. I thank Matt Green for his assistance in carrying out statistical measures, as well as ready and regular advice. I thank Dr. Vincent Richards for permitting me to carry out some of my methods in his lab as well as for providing access to his MiSeq machine. iii TABLE OF CONTENTS Page TITLE PAGE .................................................................................................................... i ABSTRACT .................................................................................................................... ii ACKNOWLEDGMENTS .............................................................................................. iii LIST OF TABLES ......................................................................................................... vi LIST OF FIGURES ....................................................................................................... vii CHAPTER I. BACTERIAL COMMUNITIES OF HOLOMETABOLOUS INSECTS ARE SHAPED BY INTERACTIONS WITH HOST PHYSIOLOGY AND MORPHOLOGY .................................... 1 Abstract .................................................................................................... 1 Introduction ............................................................................................. 1 Host morphology ..................................................................................... 3 Host sexual dimorphism .......................................................................... 4 Mechanisms of transmission ................................................................... 5 Host nutrition ........................................................................................... 7 Host development and defense .............................................................. 12 Host behavior ......................................................................................... 14 Host lineage ........................................................................................... 16 Concluding remarks ............................................................................... 21 II. BACTERIAL DIVERSITY OF THE GUT OF Cotinis nitida ................... 23 Introduction ........................................................................................... 23 Materials and methods ........................................................................... 28 Results ................................................................................................... 35 Discussion .............................................................................................. 39 Conclusion ............................................................................................. 50 APPENDICES ............................................................................................................... 53 iv Table of Contents (Continued) Page A: Tables .......................................................................................................... 54 B: Figures ......................................................................................................... 55 REFERENCES .............................................................................................................. 73 v LIST OF TABLES Table Page A-1 Kruskal-Wallis pairwise comparison of bacterial communities of the gut of C. nitida ....................................................... 54 A-2 Pairwise permanova of bacterial communities of the gut of C. nitida ............................................................................................. 54 vi LIST OF FIGURES Figure Page B-1 The gut of an adult C. nitida ........................................................................ 55 B-2 The gut of a larval C. nitida ......................................................................... 55 B-3 Detail of the midgut of the larval C. nitida ................................................. 56 B-4 Detail of the ileum of the larval C. nitida .................................................... 56 B-5 Detail of the exterior paunch of the larval hindgut C. nitida ....................... 57 B-6 Alpha diversity measures of adult and larval C. nitida ...................................................................................................... 58 B-7 Alpha diversity of the gut of two life stages of C. nitida according to the Shannon diversity index and Chao1 .................................................................................... 59 B-8 Alpha diversity of the gut regions of C. nitida according to the Shannon diversity index and Chao1 ..................................................................................................... 60 B-9 Beta diversity of the gut of two life stages of C. nitida according to unweighted Unifrac ................................................ 61 B-10 Beta diversity of the gut regions of C. nitida according to unweighted Unifrac .......................................................... 62 B-11 Beta diversity of the gut of the sexes of C. nitida according to unweighted Unifrac .......................................................... 63 B-12 Beta diversity of the gut of two life stages of Cotinis nitida according to Bray-Curtis dissimilarity ........................................ 64 B-13 Beta diversity of the gut regions of C. nitida according to Bray-Curtis dissimilarity .................................................. 65 vii List of Figures (Continued) Figure Page B-14 Beta diversity of the gut of the sexes of C. nitida according to Bray-Curtis dissimilarity .................................................. 66 B-15 Beta diversity of the gut of two life stages of C. nitida according to NMDS (Bray-Curtis dissimilarity) ................................... 67 B-16 Beta diversity of the gut of the gut regions of C. nitida according to NMDS (Bray-Curtis dissimilarity) ................................... 68 B-17 Relative frequency of bacterial phyla in the gut of C. nitida according to gut region ........................................................... 69 B-18 Relative frequency of bacterial phyla in the gut of C. nitida according to gut region
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