Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards

2018 Awardees

Jeff Bowman

University of California, San Diego

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Jeff Bowman is an assistant professor in the Integrative Oceanography Division at Scripps Institution of Oceanography. His research focuses on the biogeochemical role of marine microbes in the Earth system and the process by which genetic and community structures enable specific ecosystem functions. He received his Ph.D. in oceanography and astrobiology from the University of Washington, where he studied the microbial ecology of sea ice and other cold environments. Prior to joining the faculty at Scripps, he was a postdoctoral fellow at the Lamont-Doherty Earth Observatory at Columbia University. There he developed new informatics techniques for assessing the ecological function of marine microbial communities in the Palmer Long Term Ecological Research Site off the western Antarctic Peninsula.

Project: Quantifying microbial ecosystem functions via high-resolution time series

Marine microbes (collectively the single-celled members of the domains bacteria, archaea and eukarya) carry out an exhaustive array of metabolic activities with profound consequences for human and ecosystem health. Specific metabolic outcomes of marine microbes can be viewed as microbial ecosystem functions; for example, diazotrophic marine microbes carry out the critical ecosystem function of nitrogen fixation. Ecosystem functions collectively support marine ecosystem services, which are broad benefits society obtains through access to a properly functioning marine ecosystem. Microbial metabolism is correlated with taxonomy, albeit imperfectly as a result of horizontal gene transfer, genome duplications and genome streamlining. A reasonable supposition based on this correlation is that microbial ecosystem function is a result of the taxonomic and physiological state of the microbial community. In the proposed work I will test this broad hypothesis by developing a high-resolution time series of microbial community structure and predicted gene content. The time series will be guided by an intelligent sampling algorithm to capture stochastic features and will be coupled to continuous measurements of net community production (NCP, a measure of community physiology) and volatile organic compounds (VOCs, the production of which is a key ecosystem function). To integrate these data, I will employ new data analysis and modeling techniques with the goal of building predictive, mechanistic models of key microbial ecosystem functions.

Kyle Edwards

University of Hawaii

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Kyle Edwards is an assistant professor in the Department of Oceanography at the University of Hawai’i at Mānoa. His research combines theoretical and empirical approaches to the ecology and evolution of microbial communities. Particular research interests include fundamental constraints on organismal traits, how community structure and diversity emerge from these underlying rules, and the consequences for ecosystem and biogeochemical processes. Edwards received a B.A. in biological sciences with honors from the University of Chicago (2003) and a Ph.D. in population biology from the University of California, Davis (2010). Before joining the faculty at UHM he was a postdoc at the Kellogg Biological Station at Michigan State University.

Project: The evolution of ecosystem function in phytoplankton-virus communities

Marine microbes play a prominent role in ocean ecosystems and global biogeochemistry, with phytoplankton in particular accounting for about half of global primary production. When we zoom in on the organisms performing these functions, we find immense diversity, from high genetic diversity within ‘species’ to deep phylogenetic diversity across the tree of life. Interactions like competition, predation and parasitism are ubiquitous, leading to complex network dynamics. Furthermore, the short generation times of microbes means that rapid evolution is possible and probably common. There is a critical need to develop and test general theory that explains how these diverse, coevolving communities are structured, and how they drive change in ecosystem function across changing environmental conditions.

This research project will address these questions in communities of phytoplankton and their viruses. Recent work has argued that host and virus genetic diversity may be maintained by host tradeoffs between competitive ability and resistance to infection and by viral tradeoffs between breadth of host range and infection success. An important implication is that viruses may alter the ecological function and functional diversity of host populations, and these effects may vary in systemic ways across environments. Furthermore, it is commonly argued that the immense taxonomic diversity in microbial systems is also maintained by viruses and that coexistence between species may depend on tradeoffs within species that affect competitive ability. Ultimately, the effect of viruses on large-scale ecosystem processes will be derived from these population and community eco-evolutionary dynamics. This project will address these questions by combining experimental evolution, trait-based models of eco-evolutionary dynamics and long-term culture experiments with diverse phytoplankton and virus isolates.

Katherine Mackey

University of California, Irvine

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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.

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.

Jodi Young

University of Washington

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Jodi Young is a Future of Ice assistant professor within the School of Oceanography at the University of Washington (UW) and a faculty member of the UW astrobiology program. Her research focuses on understanding the underlying mechanisms of photosynthesis in marine microbes. In particular, she investigates how the adaptation and function of enzymes interact with microbe physiology to constrain CO2 fixation rates in widely diverse environments and organisms. Half of Earth’s photosynthesis occurs in the oceans, greatly influencing biogeochemical cycles that form the base of marine ecosystems. Understanding the mechanics and variability of marine photosynthesis will enable more accurate predictions of the response of the marine biosphere to future change. Her research includes exploring photosynthesis in extreme environments, such as within sea ice in the polar oceans. These productive regions are experiencing rapid change and also act as an analog for life on exoplanets. Young received a B.Sc in marine sciences and biotechnology from Murdoch University, Australia (2000) and a D.Phil in Earth sciences from Oxford University (2011). During her D.Phil she studied the adaption of CO2 fixation in phytoplankton over geological timescales. From 2011–2015 she was a postdoctoral researcher at the Department of Geosciences at Princeton University, where she investigated marine photosynthesis in polar environments, taking part in a two-month field study of algal photosynthesis in Antarctica.

Project: Marine Rubiscos are the key to understanding carbon fixation in the oceans

The process of taking air (CO2) and turning it into living matter (e.g. plants and algae) is the fundamental building block for life on Earth. Almost all of this conversion is catalyzed by the world’s most abundant enzyme, Rubisco, of which half of this productivity occurs in the oceans across a diverse array of environments and organisms. Marine CO2 fixation influences not only marine ecosystems and biogeochemical cycles, but also has a major effect on global climate. However, research on Rubisco has predominately focused on terrestrial plants at 25 °C, and we only have a rudimentary understanding of Rubisco function in marine organisms and environments. This project aims to uncover the diversity of marine Rubiscos across a wide range of microbes including eukaryotic phytoplankton, bacteria and archaea. Our new understanding of Rubisco, coupled with laboratory and field measurements of CO2 fixation by phytoplankton, will enable us to understand the underlying mechanisms that constrain rates of phytoplankton photosynthesis across ocean habitats. In addition, genetic sequences of Rubisco will be used to reconstruct its evolutionary history over 3 billion years to identify how this ancient enzyme has adapted and enabled marine primary producers to thrive in diverse and changing environments.


2017 Awardees

Andrew Barton

University of California, San Diego (Scripps Institution of Oceanography)

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Andrew Barton is an Assistant Professor at the Scripps Institution of Oceanography and at the section of Ecology, Behavior and Evolution of the University of California, San Diego. His research combines observational and numerical modeling perspectives to understand the fundamental mechanisms that regulate microbial population dynamics, community structure, biogeography and biodiversity in the ocean. Barton investigates how changes in Earth’s climate, including natural variability and long-term changes driven by human activities, have the potential to alter microbial species distributions and community composition through time. He received a B.A. in Science of Earth Systems from Cornell University (2000) and a Ph.D. in Climate Physics and Chemistry from Massachusetts Institute of Technology (2011). He was an NSF International Research Postdoctoral Fellow hosted jointly between Duke University and the University of Liverpool in the United Kingdom, and later was an Associate Research Scholar at the Geophysical Fluid Dynamics Laboratory at Princeton University.

Project: Environmental and ecological drivers of marine microbial morphology

The diversity of photosynthetic marine microbes can be astonishingly high, with up to hundreds of species coexisting in a single teacup of seawater. The coexisting community exhibits tremendous variation in cell size, shape and coloniality (some species form chains of cells, for example), and this morphological variation may help sustain species diversity by providing multiple avenues for species to survive in the ocean. Far from being ecological curiosities, morphological variations impact ecosystem function by influencing the export of carbon from the ocean surface to greater depths. To date, however, we have limited understanding of what sustains this great morphological variation and its wider significance.

The proposed work is an interdisciplinary and multi-methodological research campaign to study the environmental and ecological drivers of the size and shape of phytoplankton cells and colonies. We will use high-resolution underwater images of phytoplankton cells, colonies and zooplankton from the Scripps Plankton Camera (, in combination with oceanographic and atmospheric observations, to quantify how the size, shape and aspect ratio of phytoplankton cells and colonies vary with environmental and predatory conditions. We will complement the observational program by developing novel trait-based numerical models of the plankton community that resolve varying body size, form and colony size. Our aim is to extend the lessons learned at Scripps Pier to the globe using coupled ocean circulation, biogeochemical and plankton community models, where we can quantify biogeographic patterns of morphology and their biogeochemical impacts. Thus, the goals of the proposed research are to: a) understand how environmental and ecological processes shape phytoplankton and colony morphology and b) map and predict the diversity and biogeography of morphologies over the global ocean and their significance.

Erin Bertrand

Dalhousie University

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Erin Bertrand is an Assistant Professor and NSERC Tier II Canada Research Chair in Marine Microbial Proteomics in the Biology Department at Dalhousie University, Halifax, Nova Scotia. Erin received a B.S. with honors in Chemistry and Environmental Studies from Bates College in 2005. She went on to complete her Ph.D. in Chemical Oceanography in the MIT/WHOI Joint Program, where she was awarded the Fye Award for Excellence in Chemical Oceanography research, 2010–2015. From 2012 to 2015, Erin was a U.S. National Science Foundation Office of Polar Programs Postdoctoral Fellow at the J. Craig Venter Institute and Scripps Institution of Oceanography. Her research aims are focused on understanding how microbes influence ocean biogeochemistry. She is particularly interested in the molecular basis of microbial micronutritional requirements and what the consequences of those requirements are for global carbon, nitrogen and sulfur cycling. Her group employs a range of quantitative mass spectrometry–based techniques, paired with field and laboratory experiments, to ask these questions.

Project: Quantifying the impact of rising temperatures on microbial micronutrient demand

Marine primary productivity, conducted largely by phytoplankton, forms the base of marine food webs and is a major factor in determining the relationship between the ocean and atmospheric CO2 concentrations. Temperature, nutrient and light availability are key drivers of phytoplankton growth. Questions regarding how these variables interactively influence photosynthetic microbes remain and are a major source of uncertainty in efforts to predict future changes in marine primary productivity. Along with macronutrients like nitrogen, phosphorus, and silica, phytoplankton also require a suite of micronutrients including iron, zinc, and cobalamin (vitamin B12). In vast regions of the surface ocean, phytoplankton growth is limited by the availability of these micronutrients. Given the extent of this limitation as well as the fact that micronutrient availability is projected to change regionally in the coming decades, understanding the ramifications of simultaneous alterations in micronutrient availability and temperature for phytoplankton growth is imperative. Available evidence suggests that micronutrient demand may decrease in the face of elevated temperatures; however predictions from cellular models are not always reflected in observations and so major uncertainties remain. This research program aims to identify, quantify and contextualize interactions between micronutrient demand and temperature in marine microbes. This research program will use a combination of quantitative field, laboratory and metabolic modeling approaches to (1) enhance our understanding of the role of micronutrients in a changing ocean, (2) offer empirical data for evaluating fundamental questions about the relationships between matter and energy balance in microbial ecology, and (3) provide clarity to global modeling efforts seeking to predict changes to primary productivity in the future ocean.

andrewalverson copyAnne Dekas

Stanford University

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Anne Dekas is an Assistant Professor at Stanford University in the Earth System Science Department, studying the microbiology and biogeochemistry of the deep sea. She is broadly interested in how microbial life affects the chemistry and climate of the planet, today and throughout time. Her research combines tools from molecular biology and isotope geochemistry to identify and quantify microbial metabolic capabilities, activity and interactions, with a focus on understanding uncultured microorganisms in deep-sea water and sediment. Before joining the faculty at Stanford, she was a Lawrence Postdoctoral Fellow at Lawrence Livermore National Laboratory in the Chemical Sciences Division, where she investigated the carbon metabolic flexibility of pelagic marine archaea. She received a Ph.D. in Geobiology from the California Institute of Technology for her research on nitrogen fixation, methane oxidation and sulfate reduction at deep-sea methane seeps. She received an A.B. in Earth and Planetary Sciences from Harvard University on the Biogeochemistry track. Originally interested in space sciences, Dekas performed research at three NASA centers (Jet Propulsion Laboratory, Ames Research Center and Goddard Space Flight Center) before beginning her Ph.D., and she continues to be interested in the survival strategies of life in extreme environments.

Project: Quantifying microbial activity in the deep sea using NanoSIMS

The deep sea, also known as the dark ocean, is one of the largest habitats for microbial life on the planet: it covers nearly two thirds of the Earth’s surface and harbors approximately 55 percent of all marine microorganisms. Although severely understudied relative to the photic zone, the activity of deep microbial life plays an important role in marine biogeochemical cycling. In particular, recent evidence has shown the importance of chemoautotrophic Thaumarchaea, a phylum of archaea comprising about 20 percent of all marine microbes, in the cycling of nitrous oxide and carbon dioxide, both greenhouse gases. Our knowledge of the diversity and distribution of microorganisms in the deep sea has expanded in recent years with the development of next generation sequencing (i.e., “-omics”) methodologies. However, our understanding of microbial activity in the deep sea, including its phylogenetic and physicochemical controls, is still lacking. Closing this gap in our knowledge will increase our understanding of greenhouse gas cycling in the marine environment, and will better equip us to predict the activity of deep-sea microorganisms in a changing climate. This project will develop and utilize new methods to use nanoscale secondary ion mass spectrometry (NanoSIMS) — a tool to measure the isotopic composition of individual, uncultured cells — to quantify and characterize microbial activity in deep ocean waters. Combined with metagenomic and metatranscriptomic analyses, this work will link geochemical and molecular datasets, and specifically address the role of Thaumarchaea in deep-sea biogeochemical cycling.

Naomi M. Levine

University of Southern California

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Naomi Levine is a Gabilan Assistant Professor of Biological Sciences and Earth Sciences at the University of Southern California. She received her B.A. in Geosciences from Princeton University and her Ph.D. in Chemical Oceanography from the MIT-WHOI Joint Program. Naomi’s interest in the interactions between fluctuating environments and ecosystem dynamics led her to join Paul Moorcroft’s lab at Harvard University as a NOAA Climate and Global Change Postdoctoral Fellow. In 2013, Naomi joined the faculty at USC, where she holds joint appointments in Marine and Environmental Biology, Molecular and Computational Biology, and Earth Sciences. Her research focuses on understanding the interactions between climate and marine microbial ecosystem composition and function. The Levine lab is developing novel modeling approaches that explicitly represent the response of dynamic microbial communities to a variable and changing environment. Naomi is the recipient of an Alfred P. Sloan Foundation Research Fellowship in Ocean Sciences.

Project: The role of marine microbial plasticity in evolution and biogeochemistry

Marine microbes are the engines of global biogeochemical cycling in the oceans. They are responsible for approximately half of all photosynthesis on the planet and drive the ‘biological pump,’ which transfers organic carbon from the surface to the deep ocean. Therefore, it is important to determine how marine microbes will adapt and evolve to a changing climate in order to understand and predict how the global carbon cycle may change, and predict pivotal feedback responses that might impact future climate states. This work focuses on developing a mechanistic understanding of how marine microbes respond to environmental fluctuations, and exploring how these individual-scale responses can result in large-scale ecosystem shifts and ecosystem-climate feedback loops. Untangling the complex interactions between climate and biology requires pioneering interdisciplinary approaches. The research will integrate ecological and evolutionary theory, and biological, chemical, and physical observations with innovative numerical ecosystem models, to gain new insight into the relationship between plasticity and evolution in marine microbial ecosystems.


2016 Awardees

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Andrew Alverson

University of Arkansas

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Andrew Alverson is an evolutionary biologist whose research combines phylogenetic, experimental, and evolutionary genomic approaches to identify the ecological and genomic factors driving the diversification of diatoms. He received his B.S. in Biology from Grand Valley State University in 1997, an M.S. from Iowa State University in 2000, and a Ph.D. from The University of Texas at Austin in 2006. For his Ph.D. research, Andrew studied the patterns and consequences of marine–freshwater transitions by diatoms, a diverse lineage of microalgae that produce some 20% of the earth’s oxygen. From there he went on to Indiana University where he worked on the evolution of mitochondrial genome size in flowering plants with funding from a NIH NRSA Postdoctoral Fellowship. Andrew became an Assistant Professor in the Department of Biological Sciences at the University of Arkansas in 2011.

Project: The Genomic Basis of Microbial Adaptation to New and Changing Environments

Although evolutionary biology is a historical science, it provides a powerful means of looking forward as well—offering predictions on issues ranging from the spread of human disease to adaptation of species to global climate change. Increased atmospheric carbon and global warming are having profound impacts on the world’s oceans. Changing precipitation patterns and melting polar ice caps are freshening large regions of the ocean, resulting in changes in water stratification, convection, and nutrient availability. Although these changes are predicted to have important impacts on the phytoplankton communities in these areas, relatively few data are available to predict how phytoplankton—which produce 40% of the earth’s oxygen and form the base of marine food webs—will respond to a rapidly changing ocean. Laboratory experiments have shown that microbial eukaryotes can adapt quickly to environmental change in vitro, but it’s not always clear how these results extrapolate to natural systems. This project leverages a natural evolutionary experiment, the colonization of low-salinity habitats in the Baltic Sea by an ancestrally marine diatom, Skeletonema marinoi, to determine the mechanisms and rate of adaptation to environmental stress across ecological and evolutionary timescales. Comparative and population genomic data, together with experimental transcriptomic data, will be combined to determine the tempo and mode of environmental adaptation of S. marinoi populations spanning the North–Baltic Sea salinity cline. Data from a related species, Skeletonema potamos, which has independently adapted to freshwaters, will show whether there is more than one adaptive solution to managing salinity stress, providing general insights into the adaptive potential of phytoplankton to a rapidly changing ocean.

Otto Cordero

Otto Cordero

Massachusetts Institute of Technology

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Otto X. Cordero received a B.S. in Computer and Electrical Engineering from the Polytechnic University of Ecuador, an MSc in Artificial Intelligence from Utrecht University, and a PhD in Theoretical Biology also from Utrecht University. His main research focus is the ecology and evolution of natural microbial collectives. The Cordero lab is interested in understanding how social and ecological interactions at micro-scales impact the global productivity, stability and evolutionary dynamics of microbial ecosystems.

Project: Systems Ecology of Particle-Attached Microbial Communities in the Ocean

Bacteria play an essential role in the oceans by digesting particles of organic matter that would otherwise sink to the ocean floor and remove essential nutrients from the marine food web. At the micro-scale, particle degradation is carried out, not by a single species, but by a multi-species collective (i.e. a community) that grows attached to particle surfaces. Within these particle-attached communities there is a multitude of bacteria-bacteria interactions that can control the function and dynamics of the community, ultimately affecting the global ecosystem process. By and large, the nature of these interactions and their impact on community dynamics and ecosystem function remain unknown. This gap in our understanding of microbial ecology ultimately hampers the development of mechanistic models that explain how ecological function emerges from interactions within hyper-diverse microbial collectives. This Simons Early Career Investigator Award will support the development of a systems ecology approach to the study of particle-attached communities in the ocean. Within this research program we will learn the general structure of ecological interaction networks on particles, and the classes of interactions that dominate the particle-attached community. We will learn for instance whether interactions are primarily exploitative, competitive or mutualistic, and how these different types of interactions impact the degradation dynamics. Overall, through this project we will establish the link between micro-scale community ecology to macro-scale ecosystem function in the ocean.

Karen Lloyd

Karen Lloyd

The University of Tennessee

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Karen Lloyd is from Beaufort, North Carolina, and graduated from Swarthmore College with a degree in Biochemistry. She completed an MS and PhD in Marine Sciences at the University of North Carolina, and a postdoc at the Center for Geomicrobiology at Aarhus University, Denmark. She is currently an Assistant Professor at the University of Tennessee, where her research group studies the vast majority of marine subseafloor microorganisms that have never been grown in a laboratory, and are therefore mostly uncharacterized. Lloyd was awarded the Holger Hannasch Award from the Woods Hole Oceanographic Institution (2012), and the Alfred P. Sloan Fellowship (2015), and is an editor at mSystems.

Project: The role of uncultured microbes in the Arctic marine sediment carbon cycle

The Arctic is experiencing disproportionately large effects of global climate change and melting glaciers will likely deposit large amounts of organic carbon into Arctic coastal marine zones. Once this organic carbon is deposited on the seafloor, microbes quickly use up all the available oxygen, leaving the rest of the carbon cycle to anaerobic microbes. Little is known about the responses of the sedimentary microbial populations to this increasing organic carbon deposition. If anaerobic microorganisms living in the upper meter of Arctic marine sediments adapt quickly to the increase in organic matter, much of this organic matter will be remineralized back to CO2, driving a positive feedback on warming. On the other hand, if these populations cannot keep up with the influx of organic matter, organic matter burial rates will increase, driving a negative feedback on warming. Much of the microbial communities in Arctic sediments are unrelated to cultured microbes, so their potential role in organic matter remineralization is unknown. These types of organisms have been termed Microbial Dark Matter (MDM) since they are ubiquitous, enigmatic, and comprise some of the deepest evolutionary branches of life. I propose to use novel genetic, metabolic, and quantitative techniques to incorporate these MDM communities into models of carbon degradation in Arctic marine sediments in Svalbard, Norway.

Jacob Waldbauer

Jacob Waldbauer

The University of Chicago

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Jacob Waldbauer is a Neubauer Family assistant professor in the Department of the Geophysical Sciences at the University of Chicago. His research combines field observations and laboratory experiments to explore the metabolic basis of biogeochemical fluxes, how microbial community response to environmental perturbations shapes biogeochemical feedbacks, and the molecular fossil record of past life and environments. His laboratory develops novel molecular analytical techniques, particularly using high-resolution mass spectrometry, to address outstanding questions in biogeoscience. He received a B.A. in Physics and Astronomy from Dartmouth College and a Ph.D. in Chemical Oceanography from the MIT/WHOI Joint Program, and was a Stanback/Beckman Postdoctoral Fellow at Caltech. He is the recipient of an Alfred P. Sloan Foundation Research Fellowship in Ocean Sciences and of the Cozzarelli Prize from the National Academy of Sciences.

Project: Forging the Missing Link: A Protein-Level View of Marine Microbial Ecology

Proteomic analysis — the identification of proteins in complex biological samples, and the quantification of protein-level gene expression — can enable quantitative, mechanistic connections between large-scale measurements of the chemical state of the oceans and of the genomic diversity in marine microbial ecosystems. In this project, we will use proteomics to gain new insights into two key aspects of marine microbial biogeochemistry: nitrogen limitation and anoxygenic phototrophy. Nitrogen availability is one of the most globally significant ecological pressures shaping the physiology and evolution of marine microbes, limiting primary production throughout much of the tropical and subtropical surface ocean. Since typically more than 80% of a cell’s nitrogen is in protein, N limitation is fundamentally a constraint on protein production, yet many questions remain about the molecular basis of this phenomenon in protein-level gene expression. Proteomic analysis can lend new insight into marine N limitation by quantification of community proteome abundance scales across spatial and temporal biogeochemical gradients. And while significant contributions of anoxygenic phototrophy to the metabolic energy budget of marine microbial communities (e.g., ATP production by proteorhodopsin-based phototrophy) have been hypothesized based on the abundance and diversity of sequences for these genes in marine metagenomic and metatranscriptomic datasets, testing this hypothesis has proven challenging. Measurement of the protein machinery that enables these metabolisms is a direct means to quantify their role in energy transduction. High-resolution proteomic measurements can also identify the primary organisms responsible for different modes of anoxygenic phototrophy in a range of oceanic habitats.


2015 Awardees

Jake Bailey

Jake Bailey

University of Minnesota, Twin Cities

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Bailey is an interdisciplinary scientist who combines approaches from microbiology and the earth sciences to investigate interactions between the biosphere and geosphere, as well as to study the ecologies and physiologies of microorganisms that are involved in geobiological processes. Bailey is an assistant professor in the Department of Earth Sciences at the University of Minnesota, Twin Cities. He received his Ph.D. at the University of Southern California prior to receiving an Agouron Institute Geobiology Fellowship to support his postdoctoral research at Caltech. Bailey is an Alfred P. Sloan Foundation Research Fellow, University of Minnesota McKnight Land Grant Professor, and recipient of a National Science Foundation CAREER grant.

Project: Investigating the Microbiome of the Largest Known Bacteria

“Microbiome” is a term often given to the microbes associated with multicellular organisms, such as bacteria living in the human gut. While bacteria and archaea are known to live in association with other microbes, individual bacterial cells are not generally thought of as hosting a characteristic microbiome. My lab studies the largest known bacteria, Thiomargarita spp. These giant bacteria are involved in the biogeochemical cycling of carbon, sulfur, nitrogen, and phosphorus. They are also known for their involvement in the precipitation of calcium phosphate mineral deposits on the seafloor that are an important source of phosphorus for modern agriculture. Individual Thiomargarita cells can approach a millimeter in diameter, making them large enough to host extensive populations of other bacterial cells. New observations and molecular analyses suggest that smaller cells living in close association with Thiomargarita are important for the ecologies, physiologies, and biogeochemical influences of these giant bacteria. Interactions between Thiomargarita and other bacteria, as well as the biogeochemical influences they catalyze, will be investigated using a variety of interdisciplinary approaches ranging from genomics to geochemistry.

Tanja Bosak

Tanja Bosak

Massachusetts Institute of Technology

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Tanja Bosak was born in Croatia and graduated from the Zagreb University with a degree in Geophysics. After a summer of research at JPL and a short stint as a meteorologist at the Zagreb Airport, she moved to the California Institute of Technology in Pasadena, where she studied signatures of microbial processes in ancient sedimentary rocks and earned a Ph.D. in Geobiology. She spent two years at Harvard as a Microbial Initiative Postdoctoral Fellow, joined the Department of Earth, Atmospheric and Planetary Sciences at MIT in 2007 and is now an associate professor of Geobiology. Tanja’s work integrates microbiology, sedimentology and stable isotope geochemistry into experimental geobiology to ask how microbes shape sedimentary rocks, how organisms fossilize and how microbial metabolisms leave biogeochemical patterns in sediments. Her lab uses this approach to explore modern biogeochemical and sedimentological processes and interpret the record of life on the Early Earth. For this work, and her work with graduate students and undergraduates, Bosak received the Subaru Outstanding Woman in Science award by the Geological Society of America (2007), the Macelwane Medal from the American Geophysical Union (2011), the Edgerton Award for young faculty at MIT (2012) and the Undergraduate Research Opportunities for Undergraduates Mentor of the Year award by MIT (2012). Bosak is a fellow of the American Geophysical Union (2011) and one of the subject editors of Geobiology.

Project: Record of Microbial and Geochemical Co-evolution in Cyanobacterial Genomes

Cyanobacteria have the longest and most continuous fossil record of all organisms. This fossil record is used to time events in the evolution of different cyanobacterial groups, as encoded by the genomes of modern cyanobacteria, and reveal links between ecological, evolutionary and geochemical changes on Earth’s surface. However, current time-calibrated models of cyanobacterial evolution (molecular clocks) rely on a simple fossil morphology whose cyanobacterial origin and taxonomic associations have been questioned. Furthermore, most taxonomically diagnostic cyanobacterial fossils represent benthic organisms, but the sampling of modern cyanobacterial genomes is biased toward unicellular planktonic taxa.

The work proposed here will improve the sampling of the cyanobacterial phylum and the understanding of its evolution through three major aims:

  1. To sequence and annotate the genomes of 40-60 undersampled, but geologically and environmentally relevant cyanobacterial taxa;
  2. To reconstruct major genomic events (gene additions, duplications and losses) in cyanobacterial history;
  3. To correlate these data with major events in Earth history and correlate events in cyanobacterial evolution with the evolution of other organismal groups which may lack a fossil record.

Sequencing efforts will use pure cultures from existing collections, or sorted cells/filaments from enrichment cultures and field samples. Modern homologs of the most taxonomically diagnostic and oldest unambiguous cyanobacterial fossils are not well represented in culture collections, so these samples will be obtained in the field. The newly sequenced genomes will be used to re-estimate divergence times using a relaxed molecular clock and new calibration points will be provided. Based on this analysis, genome reconciliation will be performed. The new cyanobacterial molecular clock will be used to correlate major gene acquisitions, losses and duplications with known events in Earth history or to hypothesize currently unknown events based on genomic data.

Alyson Santoro

Alyson Santoro

University of California, Santa Barbara

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Alyson Santoro is an assistant professor in the Department of Ecology, Evolution, and Marine Biology at the University of California, Santa Barbara. She received a B.A. from Dartmouth College in Ecology and Evolutionary Biology and an M.S. and Ph.D. from Stanford University in Environmental Engineering and Science. She was the recipient of the Woods Hole Oceanographic Institution Postdoctoral Scholar Fellowship for her research in nitrogen isotope geochemistry. Her research combines sea-going and laboratory investigations of marine microbes, with an emphasis on marine archaea and their role in the nitrogen cycle. She is the recipient of a Sloan Foundation Early Career Fellowship in Ocean Sciences.

Project: Growth Efficiency in the Mesopelagic at Station ALOHA

Organic carbon sinking from the ocean’s surface can meet three fates in the dark waters below: it can be assimilated into biomass, respired back to carbon dioxide, or continue sinking to the seafloor. Quantifying these fates—the ocean’s biological pump—is essential to constructing a carbon and energy budget for the ocean’s interior, and predicting changes in this budget into the future. The growth efficiency of microorganisms, that is, what fraction of the carbon they consume becomes cellular biomass, is an essential parameter to developing balanced budgets of carbon storage in the ocean’s interior. I will use novel cultivation techniques to establish bacterial and archaeal culture systems for understanding carbon, nitrogen, and energy flow in the mesopelagic at Station ALOHA. Efforts will be directed at determining quantitative physiological parameters such as growth efficiencies, substrate affinities, and temperature optima that can feed directly into predictive models of microbial ecosystem structure and function. By combining laboratory experiments, in situ experimentation, and time-series measurements of material export and microbial standing stocks, the SCOPE initiative provides a unique opportunity to undertake a systematic and integrated study of microbial growth efficiency in the mesopelagic at unprecedented resolution. The ultimate goal of this work is to construct an energy budget for the mesopelagic to understand and predict the efficiency of the biological pump.

Frank Stewart

Frank Stewart

Georgia Institute of Technology

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Frank Stewart is a marine microbiologist with broad interests in the genetic and metabolic diversity of ocean bacteria. His lab uses the tools of genomics and molecular biology to understand how marine microbes respond to environmental change and to symbiotic interactions with other organisms. In particular, research in the lab explores the diversity, evolution, and function of symbioses between bacteria and marine animals. This work targets diverse interactions, including those between deep-sea invertebrates and intracellular bacteria, as well as those within multi-species microbiomes on the surfaces and in the guts of reef corals and fish. The lab employs genomic and meta-omic methods to study these associations, often in collaboration with biogeochemists and ecologists. A second major research theme in the lab seeks to understand how declines in ocean oxygen content, due in part to climate change, affect microbial diversity and elemental cycling. This work focuses on major low-oxygen water masses in the Gulf of Mexico and the eastern Pacific Ocean, and involves a combination of oceanographic sampling, community genomics, biogeochemistry, and bioinformatics.

Dr. Stewart is an assistant professor in the School of Biology at Georgia Tech. He received a B.A. in Biology from Middlebury College and a Ph.D. in Organismic and Evolutionary Biology from Harvard University. He worked as a Postdoctoral Fellow at MIT before moving to Georgia Tech in 2011. He is a recipient of a Sloan Research Fellowship in Ocean Sciences and a Faculty Early Career Development Award from NSF.

Project: Reef Fish Microbiomes: Models for Bacteria-Host Interaction in the Ocean

Animals harbor diverse and abundant microbial communities (microbiomes) that influence key aspects of host health, development, and behavior. The ecology and evolution of microbiomes remain almost completely unexplored for the largest and most diverse of the vertebrate groups, the teleost fishes. Coral reefs in particular support one of the richest assortments of fish among the major ocean ecosystems, with over 2500 species spanning a striking diversity of niches, reproductive and parental care strategies, and diet types. Reef fish microbiomes are hypothesized to harbor a wide diversity of uncharacterized bacterial lineages with potentially important roles as mediators of fish nutrition and disease prevention and as reservoirs for free-living or coral microbiome populations. The overarching goal of this project is to characterize the reef fish microbiome as a model for understanding microbe-animal interactions in the ocean. The research involves a combination of field sampling and laboratory experiments to understand the diversity of the reef fish microbiome and its relationship to host ecology and development, genomic analyses to identify key physiological properties and novel members of the microbiome, and experiments to quantify transmission routes of fish microbiomes and potential microbiome effects on fish behavior. This integrated approach will help identify connections between fish-associated and other microbial niches on reefs, as well as benefits of microbial-association, potentially including unrecognized contributions to fish immunity, digestion, and chemical signaling between individuals.

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