Microbiological insights into ecology and taphonomy of prehistoric wetlands. By © 2018 Ashley A Klymiuk M.Sc. Systematics & Evolution, University of Alberta, 2011 B.Sc. Paleontology, University of Alberta, 2009 Submitted to the graduate degree program in Ecology & Evolutionary Biology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Chair: Benjamin Sikes Mark Holder Ari Jumpponen Leonard Krishtalka Jennifer Roberts Date Defended: 04 December 2018 ii The dissertation committee for Ashley A Klymiuk certifies that this is the approved version of the following dissertation: Microbiological insights into ecology and taphonomy of prehistoric wetlands. Chair: Benjamin Sikes Date Approved: 7 December 2018 iii Abstract In the course of this dissertation, I present investigations of the microbial constituents of fossil plants preserved at an anatomical level of detail, and detail the results of an ecological survey of root-endogenous fungi within the cosmopolitan emergent macrophyte, Typha. These studies together elucidate processes in the taphonomy of fossil plants. Biostratinomy is addressed through descriptions of saprotrophic communities within the Eocene Princeton Chert mire assemblage, and within a Carboniferous fern which previous studies had suggested contained fossilized actinobacteria. Re-investigation of the ‘actinobacteria’ suggests instead that the structures are disordered ferrous dolomites, raising implications for the contribution of sulfate- reducing bacteria to the early-diagenesis mineralization of plants preserved in carbonaceous concretions. The fossilized remains of saprotrophic and putatively endophytic fungi within roots of in-situ plants from the Princeton Chert also provide insight into early diagenesis. Some of the fungi described herein are preserved in several co-occurring developmental phases, providing evidence that early phases of silicification in this assemblage were rapid. As the Princeton Chert is not a hot-spring sinter deposit, these data conflict with prior hypotheses for the preservation of this peat-forming wetland assemblage. Understanding the microbial paleoecology of this system, and other wetland assemblages that constitute paleobotanical Konservat-lagerstätten, will provide important foundations upon which to improve hypotheses of plant-microbe interactions in the fossil record. Research into fossil plant-microbe interactions must, however, be conducted with reference to appropriate biogeochemical analogues. The concluding component of this dissertation establishes that endogenous fungi in contemporary wetland plant roots are affected by persistent inundation. Although the constituents of root- endogenous communities do not appear to change between inundated roots and those growing in iv subaerially-exposed soils, their incidence within roots does differ. These data offer clear implications for assessing the probable ecology of in-situ fossil plants that hosted endogenous microbial communities during life. v Acknowledgments My immense gratitude to the academic mentors I’ve had the privilege to work with: my advisor, Ben Sikes, who took a chance on my and probably regretted it more than once, but was nevertheless incredibly kind and positive; Ruth Stockey, who taught me valuable lessons about plant anatomy, quality control, and gave me a start in science; Gar Rothwell, whose dictum ‘When all else fails, look at the plant’ applies to so much more than botany and inspires me to think creatively about living and fossil analogues; Tom Taylor†, who illustrated gamesmanship and dedication to one’s goals; and Edith Taylor, whose kindness was only matched by her skilful editorial eye! Various members of the University community helped out with logistics or provided support during my time at KU. These include: Chris Haufler (Chair, Ecology & Evolutionary Biology); Leonard Krishtalka (Director, Biodiversity Institute); A. Townsend Peterson (Chair, Graduate Program Committee); Heather Shinogle (Microscopy and Analytical Imaging Lab); Wayne Dickerson (Geology); Dean Kettle and Scott Campbell (KU Field Station and Kansas Biological Survey); the US Army Corps of Engineers, Melvern Lake; Don Huggins (Central Plains Bioassessment Center); Rudolph Serbet (Taylor Paleobotany Lab); Aagje Ashe (Graduate Coordinator) and Dorothy Johanning (EEB Program Assistant). Over the course of many years at KU, I enjoyed the company of many labmates. In the Taylor Lab, Benni Bomfleur, Anne-Laure Decombiex, Patty Ryberg, Carla Harper and Julie Bergene offered stimulating conversation. Sikes Lab alumni Abby Glauser, Olivia Lynch, Taylor Patterson, Thomas Anneberg, and Jacob Stops are owed many thanks for assistance with research activities. I’ve enjoyed the occasional cup of coffee with current Sikes Lab members Theo Michaels, Paige Hansen, Jacob Hopkins, Tatiana Semenova-Neslon and Tom McKenna. vi Theo in particular helped out the first time I had to be on academic leave owing to family medical crises. Other friends who have assisted in that regard (including invaluable trips to the airport!), and who have dispensed kindness in moments when it was sorely needed, include Stephen Baca, Sally Chang, Crystal Maier, Marianna Simões, Kaila Colyott, Boryana Koseva, Kathy Denning, Spencer Mattingly, Matt Jones, Jackie Garcia, and Haley Burrill. When my mother was in grade school, she acquired the paperback Search for a Living Fossil, a narrative account of the discovery of the [first] living coelacanth, Latimeria chalumnae Smith, off the Comoros Islands. It opens with Marjorie Courtenay-Latimer poking about the docks for ichthyological specimens – female, outsider, scientist, and intensely curious. Plenty of people who come to paleontology cite Jurassic Park, or seeing dinosaurs in museums. I trace my own enthusiasm to a much-battered, age-worn green and purple schoolbook. Coming to KU was coming full circle, in a sense: Leaning over the coelacanth tank in the BI, and marvelling as JLB Smith himself might have, was the culmination of years of enthusiastic reading in pop science paleontology and geology. And in terms of reading, another serendipitous moment presented itself, when I had the opportunity to learn molecular phylogenetics from Mark Holder, whose analysis placing the Indonesian coelacanth was the first scientific paper I’d ever read. I can still hardly believe that one of my science heroes agreed to serve on my committee. I am also exceedingly grateful to Jennifer Roberts, whose geomicrobiology course filled an important gap in my knowledge and changed the way I conceptualized permineralization. Ari Jumpponen provided valuable critical feedback in the course of my research, and Leonard Krishtalka has been an enthusiastic supporter who constantly encouraged me to think big and conceptualize the ‘story’ in my work. vii My most sincere thanks and love to my mother – who not only hung onto a random book that happened to spark my imagination at the age of seven, but who encouraged me to hold onto those dreams. I’m thankful especially for all that we’ve been through together in the past three years. Or the past 15, whichever way you want to do the cancer math. I learned important life lessons, which I think will be of more use to me than a PhD, honestly. My immense gratitude to Dr Adrian Fairey, Dr Tim Wollin, and all the residents who have worked with the Alberta Urological Institute, the wonderful nurses and nephrology team at the Home Hemodialysis Program (Northern Alberta Renal Program), the brave and inspiring women of Sorrentino's Compassion House, and to all of Mum's friends up in Manning, who have been such a support to me, too. Finally, my most sincere thanks to my ‘book club’ and friends: Beth Bray, Theresa Cullen, Siobhan Davis, Jasmine DeGroot, Tatiana Hansbury†, Johanna Krüger, Karin Lach, Libby Weber, Jordan Wozniak and countless others. I appreciate every one of you, and having had you as sounding boards, moral support, and a shoulder to lean on, albeit at a distance. I don’t know why you put up with me, but I do know that Seneca wrote to Lucilius, insisting that he feared no hardship, harm, or loss of self, for he’d been writ immortal in the kind regard of friends. Last, but certainly not least, heartfelt thanks to Warren Cardinal-McTeague, who suffered my friendship a great many years, and gleefully tortured porgs with me. …It’s a long story. viii Table of Contents Chapter 1: Introduction ................................................................................................................... 1 References ................................................................................................................................... 8 Chapter 2: Reinvestigating Carboniferous ‘actinomycetes’ — authigenic formation of biomimetic carbonates provides insight into early diagenesis of permineralized plants .............. 24 Abstract ..................................................................................................................................... 24 Introduction ............................................................................................................................... 25 Materials and Methods .............................................................................................................. 28 Results ....................................................................................................................................... 30 Discussion ................................................................................................................................