ECIMMEE Project: Toward a conceptual understanding of nutrients and toxicants in microbiomes
Every natural environment on the planet – from the human body to the vast expanses of the open ocean – are inhabited by microbial communities. These microbiomes are complex systems in which different populations of microbes compete, cooperate and coexist. The dizzying pace with which new microbiome-probing technologies like metagenomics, transcriptomics and proteomics have exploded in recent years is staggering, and has led to major advances in our understanding of how microbiomes mediate infectious disease, make useful products and respond to climate change in the environment.
Along with these cutting edge molecular approaches, microbiome research is drawing more and more on traditional ecological theories to shed light on how microbial interactions give rise to distinct microbiome communities and how these, in turn, shape the environments they inhabit. Resource ratio theory is one example; it describes how competition for shared resources affects species coexistence. The theory provides a mathematical framework to predict microbial competition and is the cornerstone behind many ecosystem models in a range of environments. While competition for a shared limiting resource is at the heart of the theory, toxicity is not represented even though toxicity from certain resources is known to occur. Good examples are metal micronutrients, which are beneficial at low concentrations but can be toxic at high levels. At present there is no mechanistic framework to model how toxicity affects microbiome composition or activity.
Our understanding of competition and the effects of toxicants on microbial competition would be improved if toxicity could be mechanistically represented in competition models like resource ratio theory. This project aims to develop a new framework to predict how resource toxicity affects microbial competition. The project has three overarching aims: (1) generate mathematical equations to describe microbial growth responses to nutrients/toxicants and use them to predict competitive outcomes; (2) test these predictions via competition experiments in the lab and field; (3) explore the implications on a global scale in a global biogeochemical ecosystem model to demonstrate the utility of the toxicity framework across the entire marine microbiome. Together, these aims will allow us to identify areas of the ocean in which toxicity shapes microbial competition through both natural and anthropogenic processes.
Marine phytoplankton do half of all photosynthesis on Earth and directly influence global biogeochemical cycles and climate, yet how they will respond to future global change is unknown. As an oceanographer who takes an integrative Earth system approach to research, Kate Mackey addresses this knowledge gap by studying the biogeochemical activity of phytoplankton over a range of scales, from the cellular level up to global biogeographical distributions of species and strains. She uses culture studies to characterize biochemical processes on a mechanistic level, and fieldwork to verify lab findings, identify the range of responses from natural populations and determine their implications in nature. Mackey is the Clare Boothe Luce Assistant Professor of Earth System Science at the University of California, Irvine. She leads a large, dynamic lab of talented graduate and undergraduate students who work together and share a passion for research, teaching, science outreach and promoting diversity in academia. Mackey was named a Sloan Research Fellow in ocean sciences in 2017 and was a recipient of the inaugural Marion Milligan Mason Award for Women in the Chemical Sciences by the American Association for the Advancement of Science (AAAS) in 2015. Mackey completed postdoctoral research at the Woods Hole Oceanographic Institution and the Marine Biological Laboratory in Cape Cod Massachusetts, where she was a National Science Foundation Postdoctoral Fellow. She received her M.S. and Ph.D. in environmental engineering from Stanford University in 2004 and 2010, respectively, and held graduate research fellowships from both the National Science Foundation and the Department of Energy. She earned two B.S. degrees in biological engineering and plant science in 2002 at the University of Maryland at College Park.