Graduate Students

[ Postdoctoral Scholars | Graduate Students | Alumni ]

	Harriet Alexander Graduate Student in Dyhrman’s lab Columbia University Research interest: Alexander is interested in the physiological ecology of eukaryotic phytoplankton and their role in the marine biogeochemical cycle. Her current research is motivated by the question: Do different species of diatoms partition their nitrogen and phosphorus niche space? To address this question, she is using eukaryotic (meta)transcriptomics, which enable the examination of species-specific changes in transcription. Through a combination of culture- and field-based experiments, Alexander hopes to better understand diatom nutrient physiology and how that physiology changes in response to a changing environment. Keywords: metatranscriptomics, biogeochemistry, diatoms halexand@mit.edu
	Lydia Baker Ph.D. Student in Kemp’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Baker is interested in the dynamics of diatom-bacterial interactions in the open ocean, especially at the cell-to-cell level. She plans to compare diatom-bacteria associations between the Northern and Southern Pacific and will be initiating mixed cultures for later study. Additional research directions include the study of potential causes of their association as well as the influence their interaction may have on bloom formation. Keywords: diatoms, bacteria, symbiosis, community dynamics bakerlyd@hawaii.edu sites.google.com/site/cmorelbaker/
	Rene Boiteau Ph.D. Student in the Repeta and Boyle labs MIT-WHOI Joint Program in Chemical Oceanography Research interest: Boiteau is interested in the interactions between trace metals and microbial communities in the ocean. His goal is to understand how microbes access trace metals that are bound by strong organic ligands in regions where these metals are scarce. Boiteau is developing a method for extracting dissolved organic compounds from seawater, separating them by liquid chromatography, and measuring their trace metal content by mass spectrometry. He will use this methods to identify specific natural ligands in seawater and to screen cultured marine organisms for ligand production. Keywords: trace metals, organic ligands, liquid chromatography, mass spectrometry rboiteau@mit.edu sites.google.com/site/cmoreboiteau/home
	Jessica A. Bryant Ph.D. Student in DeLong’s lab Massachusetts Institute of Technology (MIT) Research interest: Bryant is broadly interested in understanding how aspects of the marine environment shape marine microbial diversity. She is currently investigating seasonal variation in marine microbial assemblages within surface and mesopelagic layers of the oligotrophic open ocean. Keywords: microbial ecology, phylodiversity, metagenomics, community ecology jbryant@mit.edu
	John Casey Graduate student in Karl’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Casey is broadly interested in ecological stoichiometry and the roles of individual microbial taxa in controlling the magnitude and direction of the flow of carbon in oligotrophic waters. His current research focuses on the metabolic linkages of phytoplankton and bacterial respiratory pathways through a combination of cell sorting, stable and radioisotope tracers, and metabolite profiling techniques. Keywords: flow cytometry, cellular elemental stoichiometry, photorespiration, microbial metabolism, biological carbon pump, new production jrcasey@hawaii.edu sites.google.com/site/cmorecasey/
	Andres Cubillos-Ruiz Graduate Student in Chisholm’s lab Massachusetts Institute of Technology (MIT) Research interest: Cubillos-Ruiz’s main interest is in understanding the role of secondary metabolites in planktonic marine microbial communities. His research uses a combination of metagenomics and molecular biology methods to study the diversity, evolution and biological function of prochlorosins, a unique type of cyclic peptide secondary metabolites produced by strains of Prochlorococcus and Synechococcus. Keywords: Prochlorococcus, secondary metabolites, metagenomics cubillos@mit.edu
	Kyle Frischkorn Graduate Student in Dyhrman’s lab Columbia University and the Lamont-Doherty Earth Observatory Research interest: By virtue of living in an aqueous environment, marine microbes are connected. At the smallest spatial scale, microbes can be intimately associated with one another through direct symbiotic relationships. More broadly, the biogeochemical cycles driven by marine microbes inextricably link patches of organisms across wide spatial scales. Frischkorn is interested in using genomics-enabled approaches to study how communities of phytoplankton interact with each other, with other species, and with their predators, as well as ultimately how these interactions influence the biogeochemistry of the oceans. Keywords: phytoplankton, molecular ecology, genomics, transcriptomics, biogeochemistry kylef@ldeo.columbia.edu
	Katya Frois-Moniz Graduate Student in Chisholm’s lab Massachusetts Institute of Technology (MIT) Research interest: Cyanophages (viruses that infect cyanobacteria) play a key role in the community composition, activity, and evolution of their hosts – which, themselves, are critical components of marine ecosystems and major contributors to global biogeochemical cycles. Frois-Moniz's research aims to develop a better understanding of the cyanophage infection process by characterizing host transcriptional responses and infection outcomes during infection by different types of cyanophages, as well as under different environmental conditions. Keywords: viral ecology, cyanophage, cyanobacteria, transcriptomics kmoniz@mit.edu
	Carla Gimpel PhD Student in DeLong’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Gimpel is interested in the marine microbial ecology of the Southern Ocean. By focusing on the Antarctic Peninsula, an area that has experienced some of the greatest effects of climate change, Gimpel is trying to help broaden our knowledge of the diversity and metabolic dynamics of microbial communities in this habitat. The shifts that affect bacterioplankton communities during winter (sea ice) and summer, in addition to heavy physicochemical selection pressures, make this understudied system highly attractive. Keywords: bacterioplankton, Southern Ocean, microbial ecology cgimpel@hawaii.edu
	Rosie Gradoville Graduate Student in Letelier’s lab Oregon State University (OSU) Research interest: Gradoville is interested in the effects of climate change on ocean nutrient cycling, particularly the effects of increased carbon dioxide concentrations on phytoplankton carbon and nitrogen fixation rates. She is using laboratory cultures and field samples to investigate whether several species of nitrogen-fixing cyanobacteria show signs of carbon limitation. Keywords: phytoplankton ecology, nitrogen fixation, climate change rgradoville@coas.oregonstate.edu
	Nick Hawco Ph.D. Student in Saito’s lab Woods Hole Oceanographic Institution (WHOI) Hawco studies metalloenzymes in oceanic phytoplankton, focusing on how — and to what purpose — trace-metals like Cobalt, Iron, and Zinc are allocated in the cell. Using global and quantitative proteomic methods, he intends to characterize metal containing proteins and identify controls that they impose on upper-ocean community composition and interaction, as well as macronutrient speciation and cycling. Keywords: trace-metals, proteomics, phytoplankton, cyanobacteria, metabolic pathways nhawco@whoi.edu
	Philip Heller Graduate student in Zehr’s lab University of California, Santa Cruz (UCSC) Research interest: Heller studies patterns of diel gene expression in cyanobacteria. He is developing machine-learning techniques for analyzing and comparing global expression studies. He plans to extend the technique toward community metatranscript analysis. His ultimate goal is to understand how expression rhythms influence community function. Phil is returning to graduate school after a career as a software developer and educator. He is the author of several books on the Java programming language. Keywords: cyanobacteria, machine-learning, metatranscript analysis pheller@soe.ucsc.edu
	Sean Jungbluth Graduate student in Rappé’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Jungbluth studies the deep subsurface biosphere of aging oceanic basement rock. In conjunction with the Integrated Ocean Drilling Program, he has been using seafloor instrumentation platforms called Circulation Obviation Retrofit Kits (CORKs) to sample fracture water percolating deep within the basaltic rock of the Juan de Fuca ridge flank. Using a variety of molecular tools and techniques, Jungbluth intends to probe the diversity of life and elucidate the functional underpinnings of this remote and extreme biosphere. Keywords: subsurface, biogeochemistry, microbial diversity, cultivation, metagenomics, metatranscriptomics seanpj@hawaii.edu sites.google.com/site/cmorejungbluth/
	Elaine Luo Ph.D. Student in DeLong’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Marine viruses are the most abundant yet understudied biological entities known in the ocean. The study of marine viruses has been historically hindered by their small size, but direct filtration coupled with advances in metagenomics enable high-throughput analysis of the abundance and diversity of viruses through extensive temporal and spatial scales. Luo\92s main research interest characterizes how marine viruses and their hosts change with time, depth, and environmental variability at Station ALOHA to address the following ecological questions: i) What are the most important environmental variables mediating virus-host dynamics? ii) What is the temporal and vertical variability of the viral diversity and how is it related to light intensity and hydrodynamic forces? iii) How does viral diversity co-vary with host diversity? Keywords: virus-host interactions, microbial ecology, viral diversity, metagenomics elaine.luo@hawaii.edu
	Simone B. Moos Ph.D. Student in Boyle’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Moos is generally interested in the biogeochemical cycling of trace metals and their isotopes in the ocean. Currently she studies chromium isotopes and their fractionation between redox states using single-collector and multi-collector ICP-MS. Previous work focused on the redox speciation of chromium in the tropical Atlantic Ocean using a voltammetric method. Keywords: trace metals, chromium isotopes, biogeochemistry, mass spectrometry sbmoos@mit.edu
	Jackie Mueller Graduate student in Steward’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Mueller studies marine RNA viral diversity and dynamics. She is using cultivation independent techniques to characterize the composition and structure of the RNA viral community along the Antarctic Peninsula. She is interested in identifying and describing novel viruses, and tracking specific phylotypes throughout the summer bloom in the Western Antarctic Peninsula. Mueller uses epifluorescence microscopy and molecular approaches to investigate both virus and host abundance and diversity throughout the summer bloom. Keywords: RNA viruses, protists, phytoplankton, virus-host interactions, metagenomics mueller3@hawaii.edu sites.google.com/site/cmoremueller/
	Nicole Pereira Graduate Student in Zehr’s lab University of California, Santa Cruz (UCSC) Research interest: Pereira studies marine microbiology and is interested in nutrient limitation in nitrogen-fixing cyanobacteria. She is interested in exploring the response of Crocosphaera and UCYN-A. Keywords: qPCR, nutrient limitation, Crocosphaera napereir@ucsc.edu
	Shimi Rii Graduate student in Church’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Rii is interested in the role of gradients in controlling plankton community structure. Rii investigates the abundance and diversity of picophytoeukaryotes (0.2–2 µm), using the combination of flow cytometry, HPLC, and molecular approaches. Keywords: phytoplankton, nutrients, picoeukaryotes, 18S ribosomal RNA and DNA, photosynthetic pigments, flow cytometry shimi@hawaii.edu sites.google.com/site/cmoreymrii/
	Tyler Rohr Graduate student in Doney’s lab MIT-WHOI Joint Program in Biological Oceanography Research interest: Rohr is broadly interested in biogeochemical modeling and using computational methods to better understand ecosystem dynamics. In the past he has studied rainfall variability in terrestrial seasonally dry ecosystems, but has recently transitioned to an oceanic domain, working under Scott Doney in the MIT/WHOI Joint Program. Rohr’s current research focuses on using modeling techniques to better understand the controls on the magnitude and phenology of the spring phytoplankton bloom in the Southern Ocean. Specifically, he hopes to identify spatial variability in types of processes (i.e. biological vs. physical, “top-down” vs “bottom-up”) that dominate this control. Keywords: biogeochemistry, modeling, ecosystem dynamics, Southern Ocean trohr@whoi.edu sites.google.com/site/cmorerohr/
	Cristina Schultz Graduate student in Doney’s lab MIT-WHOI Joint Program in Biological Oceanography Research interest: Schultz has experience with both atmospheric and ocean dynamics, focused on ocean-atmosphere interfaces and air-sea gas exchange. She is currently working with regional ocean biogeochemical modeling, and the different ways that the ecosystem responds to climate variability. Keywords: biogeochemical cycles, carbon exchange, ocean modeling cschultz@whoi.edu
	Chris Schvarcz Graduate student in Steward’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Schvarcz is interested in the ecology of viruses infecting marine protists (particularly eukaryotic phytoplankton), as well as the “giant” viruses (> 0.2 µm) of the ocean. He uses the isolation and cultivation of novel virus-host systems, genomics, and other molecular tools to investigate the diversity of these viruses, what they infect, and how they affect the ecology of their hosts in the environment. Keywords: viruses, giant viruses, protists, phytoplankton, genomics schvarcz@hawaii.edu
	Oscar Sosa Graduate student at DeLong’s lab MIT-WHOI Joint Program in Biological Oceanography Research interest: Sosa is interested in learning how microbes transform marine dissolved organic matter (DOM) in oligotrophic ocean regions such as the subtropical gyres. He aims to identify particular microbial populations capable of utilizing high molecular weight compounds for growth and the genes and metabolic pathways involved to later investigate their abundance and distribution in the dynamic ocean. Keywords: heterotrophic bacteria, oligotrophic, high molecular weight dissolved organic matter, carbon cycle ososa@whoi.edu
	Jessica Thompson Graduate student in Chisholm’s lab With the new interdepartmental graduate program in Microbiology, Massachusetts Institute of Technology (MIT) Research interest: Thompson studies photosynthesis in the oceans; specifically she is interested in the evolution of different clades of Prochlorococcus throughout the water column and across chemically, physically and biologically distinct ocean provinces. Keywords: Photosynthesis, light, phytoplankton, Prochlorococcus jwthomps@mit.edu
	Michael Valliere Ph.D. Student in DeLong’s lab Massachusetts Institute of Technology (MIT) Research interest: Valliere is interested in using evolution to generate novel strains of bacteria for scientific study and biotechnological applications. The purpose of his research project is to characterize genotypic and phenotypic changes that occur as a heterotroph is converted to a photoheterotroph through acquisition of the proteorhodopsin photosystem (PRPS). Evolution will be used as an experimental tool to generate adaptive mutations that directly or epigenetically improve the bacterium’s ability to capture and utilize light energy. Experimental results are expected to demonstrate that the PRPS module is functional and beneficial within a model organism (such as E. coli), and will subsequently reveal how the PRPS module alters the course of adaptation by enabling light energy capture and utilization. mfv@mit.edu
	Donn A. Viviani Ph.D. Student in Church’s lab University of Hawai‘i at Manoa (UH Manoa) Research interest: Viviani investigates how open ocean primary production is partitioned between particulate and dissolved pools. He is also interested in how primary and bacterial production rates change over time, with varying nutrient concentrations, and under high pCO2 conditions that mimic ocean acidification. Keywords: microbial activity, biogeochemistry, primary and secondary production, microbial food webs viviani@hawaii.edu sites.google.com/site/cmoreviviani/