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Lessons from The Pennsylvania State University The Graduate School Eberly College of Science MICROBES IN LIFE HISTORY TRANSITIONS: LESSONS FROM THE UPSIDE-DOWN JELLYFISH CASSIOPEA XAMACHANA A Dissertation in Biology by Aki Ohdera © 2018 Aki Ohdera Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2018 The Dissertation of Aki Ohdera was reviewed and approved* by the following: Mónica Medina Associate Professor of Biology Dissertation Advisor Todd C. LaJeunesse Associate Professor of Biology Chair or Committee Timothy Jegla Associate Professor of Biology Paul Medvedev Assistant Professor of Computer Science and Engineering Assistant Professor of Biochemistry and Molecular Biology Stephen W. Schaeffer Professor of Biology Associate Department Head of Graduate Education * Signatures are on file in the graduate school ! ii! Abstract The ubiquity of symbiotic associations that exist in nature demonstrates the importance mutualism plays in the life history of virtually all metazoans. Even closely related species of hosts can associated with different species or genera of symbionts, with varying degrees of specificity. The co-evolutionary implications of these associations underline the genetic and molecular innovations that are a result of symbiosis. This is highlighted in the symbiosis between insects and Buchnera, as well as the bob-tail squid and Vibrio fischeri, where symbiont specific organs have evolved to facilitate the symbiosis. Genomic evolution can also be observed in bacteria as dramatic reductions in gene content, indicating evolution can act on both host and symbiont. Despite the importance and prevalence of symbiosis in nature, we still lack an understanding of how symbiosis is established and maintained for many of the associations. In particular, the mechanisms behind symbiosis-mediated developmental transitions that are found in some invertebrate symbiosis remain unsolved. Here, I utilize the Cassiopea xamachana model system to understand how symbionts can play a role in host life history transitions, and the mechanisms controlling these developmental events. I use next-generation sequencing techniques to determine how both host and symbiont genetics resulted in the evolution of larval and polyp metamorphosis. I also utilize the newly sequenced Cassiopea genome to explore genes that may have facilitated the evolution of symbiosis with Symbiodinium. The work presented in these chapters also showcase the effort put forth in developing the Cassiopea system as a model to understand various fields of organismal biology, particular in cnidarian-Symbiodinium symbiosis. ! iii! Table of Contents List of Figures!......................................................................................................................!vi! List of Tables!........................................................................................................................!x! Acknowledgment!..............................................................................................................!xi! ! Chapter!1!8!Introduction:!Symbiosis!as!a!driver!of!evolutionary!novelty!in! organismal!life!history!.....................................................................................................!1! References!....................................................................................................................................!5! ! Chapter 2: Upside-down but headed in the right direction: Review of the highly versatile Cassiopea xamachana system!...........................................................................!9! Abstract!.......................................................................................................................................!12! Introduction!................................................................................................................................!13! Evolution and Phylogenetics!...................................................................................................!14! Life History!.................................................................................................................................!16! Bud Morphogenesis!...............................................................................................................................!17! Settlement and Metamorphosis!..........................................................................................................!18! Cassiopea-Symbiodinium Symbiosis!..............................................................................................!20! Nutritional Requirements!........................................................................................................!22! Behavior!......................................................................................................................................!24! Fluid Dynamics!.......................................................................................................................................!24! Quiescence!................................................................................................................................................!26! Cassiopea in the Environment!................................................................................................!27! Bioinvasion and Blooms!......................................................................................................................!27! Environmental Monitoring and Ecotoxicology!............................................................................!28! Other Laboratory Applications!.............................................................................................!30! Toxinology and cnidome!.....................................................................................................................!30! Cassiopea Virology!................................................................................................................................!31! Cassiopea as a Laboratory Resource!.....................................................................................!32! Conclusions!.................................................................................................................................!34! References!...................................................................................................................................!36! ! Chapter 3: Is larval settlement predictable? Genomic insights of settlement and metamorphosis inducing bacteria of Cassiopea xamachana!...................................!70! Abstract!......................................................................................................................................!71! Introduction!................................................................................................................................!72! Materials and Methods!............................................................................................................!74! Larval Collection!....................................................................................................................................!74! Bacterial Isolation!..................................................................................................................................!75! Identification of bacterial Isolates!.....................................................................................................!75! Settlement Bioassays!.............................................................................................................................!76! 16S microbiome extraction and sequencing!..................................................................................!77! Genome Sequencing and Analysis!...................................................................................................!78! Results!..........................................................................................................................................!79! Bacterial Settlement Bioassay!............................................................................................................!79! Settlement Substrate Microbiome!.....................................................................................................!79! Bacterial Genome Analysis!.................................................................................................................!80! Discussion!....................................................................................................................................!82! References!...................................................................................................................................!89! ! iv! Chapter 4: Modulation of gene expression driven by symbiosis: Strobilation mechanism in the upside-down jellyfish Cassiopea xamachana!...........................!108! Abstract!.....................................................................................................................................!109! Introduction!..............................................................................................................................!110! Materials and Methods!..........................................................................................................!112! Artificial Induction of Strobilation!.................................................................................................!112! RNAseq of colonization and strobilation!.....................................................................................!113!
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