Graduate Students

[ Postdoctoral Scholars | Graduate Students | Alumni ]
 

Photo of Harriet Alexander.

Harriet Alexander

  • Graduate Student in Dyhrman’s lab
  • MIT-WHOI Joint Program in Biological Oceanography
  • 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
Photo of Lydia Baker.

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/
Photo of Jamie Becker.

Jamie W. Becker

  • Ph.D. Student in the labs of Repeta and DeLong
  • MIT-WHOI Joint Program in Biological Oceanography
  • Research interest: Becker is working to identify dissolved organic compounds present in the marine environment and determine how these compounds affect marine microbial diversity and metabolism. His primary goal is to link the production of organic compounds by major photoautotrophs to their utilization by microbial heterotrophs through the screening of organic compound libraries for microbial activity. Becker will isolate and characterize pure organic compounds for high-throughput screening from both axenic cultures as well as naturally occurring community samples in an effort to create a link between microbial substrate production and consumption.
  • Keywords: dissolved organic matter, bacterioplankton diversity, microbial metabolism, metabolic pathways, community genomics
  • jamiewb@whoi.edu
Photo of Rene Boiteau.

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
Photo of Jessica A. Bryant.

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
Photo of John Casey.

John Casey

  • Graduate student in Church’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/
Photo of Andres Cubillos-Ruiz.

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
Photo of Jessica N. Fitzsimmons.

Jessica N. Fitzsimmons

  • Ph.D. Student in Boyle’s lab
  • MIT-WHOI Joint Program in Biological Oceanography
  • Research interest: Fitzsimmons is interested in the biogeochemical cycles of trace metals in the ocean, particularly those that function as micronutrients to marine microbes. She works primarily with iron, using inductively coupled plasma mass spectrometry to study the oceanic distribution of iron and probe its sources to the ocean by analyzing the iron isotope signature of seawater. She is also interested in measuring the concentration and strength of iron-binding ligands and hopes to work towards identifying the chemical composition of specific natural ligands.
  • Keywords: trace metals, iron, biogeochemistry, mass spectrometry
  • jessfitz@mit.edu
Photo of Kyle Frischkorn.

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
Photo of Allison Fong.

Allison A. Fong

  • Ph.D. Student in Kemp’s lab
  • University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Fong studies the bacterial assemblages associated with micro-environments in the pelagic marine environment. She is interested in examining the bacterial assemblages associated with marine snow and how populations on these micro-environments interact and/or affect open-ocean microbial communities and processes. She is also interested in coordinated micro-scale processes such as cell-cell signaling and quorum sensing, and their ecological implications for how we assess the role(s) of assemblages of micro-organisms in biological and chemical processes in the ocean.
  • Keywords: aggregates, marine snow, bacterial assemblages, micro-scale, micro-environment
  • fonga@hawaii.edu
Photo of Katya Frois-Moniz.

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
Photo of Carla Gimpel.

Carla Gimpel

  • PhD Student in Rappé’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
Photo of Rosie Gradoville.

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
Photo of Nick Hawco.

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
Photo of Philip Heller.

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
Photo of Jason Hilton.

Jason Hilton

  • Graduate student in Zehr’s lab
  • University of California, Santa Cruz (UCSC)
  • Research interest: Hilton is investigating diatom-diazotroph associations, or DDAs, commonly found in open ocean environments. Using high-throughput sequencing to assemble a symbiont genome, he locates metabolic pathways which display unusual gene representation in the genome. Studies focused on the activity of these pathways can unravel host-symbiont interactions, and further our knowledge on the contribution of DDAs to open ocean nutrient cycling.
  • Keywords: cyanobacteria, diatoms, symbiosis, genomics
  • jhilton@ucsc.edu
Photo of Sean Jungbluth.

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/
Photo of Ha Na Kim.

Ha Na Kim

  • Graduate student in DeLong’s lab
  • Massachusetts Institute of Technology (MIT)
  • Research interest: Kim’s aim of the research as a whole is to answer the question of how community dynamics and gene expression of marine archaeal and bacterial nitrifiers are affected by light and dark conditions in the surface seawater and lower euphotic zone. The design of her project involves two different approaches: application of culture-independent and -dependent techniques. To study the spatial and temporal distribution of archaeal and bacterial nitrifiers in water columns exposed to light and dark conditions and along a vertical profile in Station ALOHA she will apply genomic and transcriptomics approaches.
  • Keywords: metagenomics, metatranscriptomics, community dynamics, nitrifiers, nitrogen cycling
  • hanakim@mit.edu
Photo of Sara Lincoln.

Sara Lincoln

  • Graduate Student in DeLong’s lab
  • Massachusetts Institute of Technology (MIT)
  • Research interest: Lincoln focuses on understanding the distribution and biogeochemical significance of archaea in the marine water column. Pairing mass spectrometry and metagenomic approaches, she is trying to determine whether distinct groups of marine archaea synthesize unique suites of membrane lipids that can be used to trace their activity in the modern oceans and the geologic record. She studies archaea in diverse oceanographic provinces ranging from oligotrophic ocean to coastal upwelling sites, as well as in experimental incubations probing their carbon metabolism.
    Keywords: microbial ecology, archaea, organic geochemistry, carbon flow
  • slincoln@mit.edu
Photo of Simone B. Moos.

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
Photo of Jackie Mueller.

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/
Photo of Nicole Pereira.

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
Photo of Shimi Rii.

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
Photo of Chris Schvarcz.

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
Photo of Oscar Sosa.

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
Photo of Yanmei Shi.

Yanmei Shi

  • Graduate student in DeLong’s lab
  • Massachusetts Institute of Technology (MIT)
  • Research interest: Shi’s work focuses on developing and applying community transcriptomic approaches to study microbial gene expression in situ, and how such expression profiles vary with changing environmental conditions on spatial and temporal scales. She further uses this approach to investigate microbial responses to environmental perturbations such as nutrient loading under experimental settings. Shi’s work also involves identification and characterization of noncoding RNA families that potentially play significant roles in regulating microbial gene expression in the open ocean environment.
  • Keywords: metagenomics, metatranscriptomics, community dynamics, gene expression and regulation, noncoding RNAs, perturbation experiment
  • ymshi@mit.edu
Photo of Sara Thomas.

Sara Thomas

  • Graduate student in Church’s lab
  • University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Thomas’ interests include investigating the cyanobacteria contribution to nitrogen cycling in the open ocean. She will apply molecular techniques to samples collected through the Hawai‘i Ocean Time-series and link her findings to larger scale implications.
  • Keywords: Cyanobacteria, nitrogen fixation, nitrogen cycling
  • sethomas@hawaii.edu
Photo of Jessica Thompson.

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
Photo of Michael Valliere.

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
Photo of Donn Viviani.

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/
Photo of Brenner Wai.

Brenner Wai

  • Graduate Student in Church’s lab
  • University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Wai’s research is understanding the role of archaea in ammonia oxidation and bacteria in nitrite oxidation, the two steps required in complete nitrification. Using molecular biology, he will be able to track the abundances of these groups of microorganisms based off of their functional nitrifying genes as well as quantify the expression of these important genes. The mystery of vertical and temporal variability of these globally important chemolithoautotrophs will be sleuthed by his research.
  • Key words: Nitrification, qPCR, chemolithoautotrophs
  • brenner@hawaii.edu

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