THE ECOLOGICAL IMPORTANCE OF DEEP CHLOROPHYLL MAXIMA IN THE LAURENTIAN GREAT LAKES A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Anne Scofield August 2018 © 2018 Anne Scofield THE ECOLOGICAL IMPORTANCE OF DEEP CHLOROPHYLL MAXIMA IN THE LAURENTIAN GREAT LAKES Anne Scofield, Ph. D. Cornell University 2018 Deep chlorophyll maxima (DCM) are common in stratified lakes and oceans, and phytoplankton growth in DCM can contribute significantly to total ecosystem production. Understanding the drivers of DCM formation is important for interpreting their ecological importance. The overall objective of this research was to assess the food web implications of DCM across a productivity gradient, using the Laurentian Great Lakes as a case study. First, I investigated the driving mechanisms of DCM formation and dissipation in Lake Ontario during April–September 2013 using in situ profile data and phytoplankton community structure. Results indicate that in situ growth was important for DCM formation in early- to mid-summer but settling and photoadaptation contributed to maintenance of the DCM late in the stratified season. Second, I expanded my analysis to all five of the Great Lakes using a time series generated by the US Environmental Protection Agency (EPA) long-term monitoring program in August from 1996-2017. The cross-lake comparison showed that DCM were closely aligned with deep biomass maxima (DBM) and dissolved oxygen saturation maxima (DOmax) in meso-oligotrophic waters (eastern Lake Erie and Lake Ontario), suggesting that DCM are productive features. In oligotrophic to ultra-oligotrophic waters (Lakes Michigan, Huron, Superior), however, DCM were deeper than the DBM and DOmax, indicating that photoadaptation was of considerable importance. Across lakes, euphotic depth was a significant predictor of both DCM depth and chlorophyll concentration, with greater water clarity associated with deeper and weaker DCM. Lastly, I investigated how DCM formation affects zooplankton diel vertical migration (DVM) by comparing the diel movements of different zooplankton size groups across three transects in southern Lake Michigan during summer 2015. Using taxonomy data from stratified net tows to inform our interpretation of laser optical plankton (LOPC) data, I concluded that phytoplankton distributions are an important determinant of zooplankton weighted mean depth. Trade-offs between optimal temperature, access to food resources, and predator avoidance contributed to differences in DVM among zooplankton size groups and regions of the lake. Overall, DCM production likely contributes significantly to phytoplankton biomass in oligotrophic lakes, causing selection pressure toward cold-adapted zooplankton that can effectively utilize DCM resources. BIOGRAPHICAL SKETCH Anne Scofield was born in Austin, TX and resided there until attending Stanford University. She completed her B.S. in Earth Systems with a concentration in Energy Sciences & Technology and a minor in Geological and Environmental Sciences. While at Stanford, she completed her first undergraduate research project through participation in the Stanford@SEA program – after which she decided to pursue marine science for her future studies. Her experience at Sea Education Association (SEA) inspired her to stay at Stanford University to complete a co-terminal M.S. degree in Earth Systems, during which she studied at Hopkins Marine Station in Monterey Bay, California. After her time at Stanford University, Annie went to work for Sea Education Association (SEA), where she taught oceanography and marine biology to undergraduate students through hands-on science at sea. When she was ready to go back to graduate school, serendipity landed her at Cornell University where she had the opportunity to work in the Laurentian Great Lakes. She was skeptical (at first) about making the switch to fresh water, but the research was intriguing, so she made the leap. The Great Lakes proved to be an exciting system study, and she thoroughly enjoyed her time doing research aboard the R/V Lake Guardian, at the Cornell Biological Field Station, and at Cornell University in Ithaca, NY. Annie is looking forward to starting a post-doctoral research position at Purdue University in the fall, where she will continue working in the Great Lakes system. iii I dedicate this dissertation to my parents and grandparents, who have always encouraged me to pursue my dreams, whatever they may be. Thank you for your love and support. Frank & Patricia Scofield William & Dorothy Bonham Frank & Alice Scofield iv ACKNOWLEDGMENTS This dissertation research was funded by the Great Lakes Fisheries Commission (2013_RUD_44029) and the Great Lakes Restoration Initiative, through grants from the USGS-Great Lakes Science Center (G13AC00064) and the U.S. Environmental Protection Agency (U.S. EPA) Cooperative Agreement to Cornell University (GL 00E01184-0). The research described in this dissertation has not been subjected to U.S. EPA review. Any opinions expressed in this publication are those of the authors and do not necessarily reflect the views or policies of the U.S. EPA. Any use of trade, product or firm names is for descriptive purposes only and does not imply endorsement by the U.S. EPA or USGS. I also acknowledge that Chapter 1 of this dissertation was previously published in the Journal of Great Lakes Research, published by Elsevier. I am incredibly grateful to the mentors, staff, and other graduate students who have provided both technical and moral support throughout my years working on this dissertation research. I have truly enjoyed working with my committee chair Dr. Lars Rudstam, who has a contagious enthusiasm for the work that he does has provided endless feedback and support during my graduate studies. He has been a wonderful advisor and I am grateful for his advice, patience, and the freedom he gave me to explore my scientific interests. I also have enjoyed our travels for conferences and the community he fosters at the Cornell Biological Field Station. I also extend a thank you to my other special committee members, Drs. Patrick Sullivan, Nelson Hairston, and Brian Weidel, who have provided valuable insights, feedback, and encouragement over the past few years. I appreciate that you all made time to chat and brainstorm about my work even when you were incredibly busy with other obligations. I also thank Dr. Jim Watkins for his input and contributions. I also grateful to the captains and crews of the R/V Lake Guardian and R/V Kaho, the technicians, graduate students, and staff at Cornell University, EPA GLNPO and v USGS that contributed to the data presented in this dissertation. This research would not have been possible without your efforts. Beyond the logical support, my friends at CBFS and my fellow Cornell graduate students have made my time here so much more meaningful through friendship and camaraderie – it has been a fantastic time! A huge thank you to my parents and my extended family – all of whom have been amazingly supportive of me throughout this process in good times and bad. I am grateful to them all for believing in me, cheering me on, and taking such an interest in what I do. It means the world to me. vi TABLE OF CONTENTS Biographical Sketch iii Dedication iv Acknowledgements v Preface viii The deep chlorophyll layer in Lake Ontario: extent, mechanisms Chapter 1 1 of formation, and abiotic predictors Testing theory of deep chlorophyll maxima formation Chapter 2 across a productivity gradient: a case study in the Laurentian 14 Great Lakes Variability in zooplankton diel vertical migrations Chapter 3 in Southern Lake Michigan 66 vii PREFACE Deep chlorophyll maxima (DCM) are common features in stratified lakes and oceans, and phytoplankton growth in DCM often contributes significantly to total system primary production. The primary mechanisms contributing to the formation of a DCM include growth of phytoplankton at depth due to increased nutrient availability, settling of phytoplankton cells at the thermocline, and photoadaptation (increased cell chlorophyll:carbon) of phytoplankton cells exposed to low-light environments (Camacho, 2006; Cullen, 1982). Understanding the drivers of DCM formation is needed to interpret its ecological importance as a food resource. The overall objective of this research was to improve our ability to assess the food web implications of various chlorophyll distributions observed across a productivity gradient, using the Laurentian Great Lakes as a case study. Motivation for this dissertation was initially driven by the need to better understand the importance of DCM in Lake Ontario. Lake Ontario has undergone significant changes in nutrient concentrations, water clarity, and epilimnetic chlorophyll over the past several decades, due to the combined effects of reduced nutrient loading since the 1972 Great Lakes Water Quality Agreement (GLWQA) and impacts of invasive dreissenid mussels (Dove, 2009; Holeck et al., 2015; Mills et al., 2003; Rudstam et al., 2017). Spring total phosphorus has decreased from over 20 μg/L in the late 1960s to between 7 and 10 μg/L as of the mid-1990s (Dove and Chapra, 2015; Holeck et al., 2015), while lake-wide average euphotic depth has increased by over 50% during that time (Binding et al., 2015). Concerns about increasing oligotrophy and potential consequences for higher trophic levels in Lake Ontario prompted an interest in studying viii whether the observed decreases in epilimnetic production might be offset by increased production in DCM. Although there was previous work describing the occurrence of the DCM during offshore Lake Ontario in summer (Watkins et al., 2015), the relative importance of various DCM-forming mechanisms had not thoroughly been assessed. To understand the potential bottom-up effects of the observed changes in Lake Ontario, we needed a more thorough understanding of DCM dynamics. To address these concerns, I investigated the driving mechanisms of DCM formation and dissipation in Lake Ontario during April–September 2013 using in situ profile data and phytoplankton community structure (Chapter 1).