Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards

2016 Awardees

andrewalverson copy

Andrew Alverson

University of Arkansas

Website | aja(replace this with the @ sign)

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

Website  | ottox(replace this with the @ sign)

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

 Website  | klloyd(replace this with the @ sign)

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

Website  | jwal(replace this with the @ sign)

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

Website | baileyj(replace this with the @ sign)

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

Website | tbosak(replace this with the @ sign)

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

Website | alyson.santoro(replace this with the @ sign)

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

Website | frank.stewart(replace this with the @ sign)

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.