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Alumni:
Former Post-docs in New C-MORE PositionsFormer Post-docs ElsewhereFormer Graduate Students ]

Former Postdoctoral Scholars in New C-MORE Positions

Photo of Daniela Böttjer.

Daniela Böttjer

  • Formerly Post-doc in Church’s lab
  • University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Böttjer is primary interested in studying the sensitivity of N2-fixation to perturbations in seawater carbon chemistry. Her work will investigate the responses and consequences of changes in seawater pCO2 on the growth and community structure of naturally-occurring assemblages of N2-fixers and place these experimental approaches into the context of monthly time-series estimates on N2-fixing bacterial dynamics at station ALOHA.
  • Keywords: biogeochemical cycling, nitrogen fixation, ocean acidification
  • dbottjer@hawaii.edu
  • sites.google.com/site/cmorebottjer/
Photo of Nicole Goebel.

Nicole Goebel

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Current position: Research Scientist in Zehr's lab, University of California, Santa Cruz (UCSC)
  • Research interest: Goebel’s research focuses on the the temporal and spatial variability of the community structure of marine phytoplankton communities. Statistical and numerical modeling approaches have been used in order to assess the relative contributions of three known diazotrophs (Trichodesmium, Group B, and Group A) to nitrogen fixation at Station ALOHA, and are currently used to predict the predominant primary producers within the California Current. She has also carried out growth measurements of Trichodesmium and Crocosphaera cultures in order to constrain parameterizations of modeled growth rates.
  • Keywords: modeling, nitrogen fixation
  • ngoebel@pmc.ucsc.edu
Photo of Irina Shilova.

Irina Shilova

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Current position: Assistant Project Scientist in Zehr’s lab, University of California, Santa Cruz (UCSC)
  • Research interest: Cyanobacteria: picocyanobacteria and diazotrophs. Gene expression in cyanobacteria under various environmental conditions and during a diel cycle. Application of high-density microarrays to study microbial community gene expression.
  • Keywords: cyanobacteria, gene expression, stress responses, diel cycle, microarrays
  • iirina@ucsc.edu
Photo of Angelicque White.

Angelicque White

  • Formerly a graduate student and postdoctoral scholar at Oregon State University (OSU)
  • Current position: Assistant Professor at Oregon State University (OSU)
  • Research interest: White’s primary research interests involve understanding how specific organisms acquire the elements necessary for growth and how different nutrient sources impact primary productivity and particle export. She is also working on the development of stochastic, optimization models which can allow for more realistic simulations of the taxonomic and biogeochemical diversity of the phytoplankton community in the upper water column of the North Pacific.
  • Keywords: nitrogen fixation, phosphorus, model development, cyanobacterial diversity, cyanobacterial physiology, Trichodesmium
  • awhite@coas.oregonstate.edu
Photo of Sam Wilson.

Sam Wilson

  • Formerly a post-doc in Karl’s lab at University of Hawai‘i at Manoa (UH Manoa)
  • Current position: Assistant Researcher, C-MORE, at University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Wilson’s research focuses on the cycling of trace gases in the upper ocean and examines why reduced gases such as methane, nitrous oxide, and hydrogen are supersaturated in surface seawater. To investigate this phenomenon, monthly measurements of dissolved gases are made at Stn ALOHA as part of the HOT program. Complimentary laboratory work with cultures of key cyanobacteria species including nitrogen-fixing micro-organisms provides species-specific production rates that are compared with the microbial community composition at Stn ALOHA. Current work focuses on the production of hydrogen and carbon monoxide by Trichodesmium and Crocosphaera cultures.
  • Keywords: reduced gases, cyanobacteria
  • stwilson@hawaii.edu
  • www.samtwilson.com

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Former Postdoctoral Scholars in New Positions Elsewhere

Photo of Kate Achilles.

Kate Achilles

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Achilles' research focuses on the diversity and abundance of diazotrophic microbes in the open ocean, denitrification in oxygen minimum zones in the water column, development of techniques for cell sorting of cyanobacteria by flow cytometry for subsequent cultivation and molecular analyses, as well as the bioavailability of iron to cyanobacteria. She is also actively working on the development of educational programs that promote awareness and interest in microbial oceanography by creating innovative curriculum modules, providing access to teacher workshops and shipboard experiences, and establishing active community outreach programs.
  • Keywords: nitrogen fixation, cyanobacteria, bioavailability of iron, denitrification, flow cytometry, education, outreach
  • kate.achilles@soest.hawaii.edu
Photo of Nilo Alvarado.

Nilo Alvarado

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Research interest: Alvarado is interested in phytoplankton ecology and harmful algal bloom species. Specifically, what ecological factors contribute to changes in toxicity levels of different phytoplankton.
  • Keywords:
  • nilo@mbari.org
Photo of Deniz Bombar.

Deniz Bombar

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Research interest: Bombar’s research focuses on the role of microbes in oceanic nitrogen cycling. He aims to understand how the distribution and activity of different nitrogen-fixing prokaryotes is regulated by environmental factors. The approach he uses combines flow-cytometric sorting of different populations of microbes, molecular methods for identification, and substrate uptake measurements using stable isotope tracers.
  • Keywords: nitrogen fixation, isotopes, microbial diversity
  • dbombar@ucsc.edu
Photo of Paulo H. R. Calil.

Paulo H. R. Calil

Photo of Alex Culley.

Alex Culley

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Current position: Assistant professor/professeur adjoint, Université Laval, Département de biochimie, de microbiologie et de bio-informatique
  • Research interest: Culley will use cultivation dependent and independent techniques to investigate marine virus diversity and dynamics. Specific objectives include the isolation and characterization of viruses that infect organisms of ecological importance, particularly from the open ocean, and the exploration of the population composition and structure of marine RNA virus communities, a very poorly characterized group of marine microbes.
  • Keywords: microbial diversity, viral ecology, marine RNA virus, picorna-like virus
  • alexander.culley@bcm.ulaval.ca
Photo of Daniela del Valle.

Daniela del Valle

  • Formerly at University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Del Valle’s research focuses on the biogeochemistry of reduced gases in the surface ocean. She is particularly interested in the metabolic fate of dimethylsulfoniopropionate (DMSP) and the factors controlling dimethylsulfide (DMS) production. She is also interested in studying the dynamics of hydrogen gas at Station ALOHA and its relation to nitrogen fixation, as well as the production of methane from methylphosphonate in the surface ocean.
  • Keywords: reduced gases in the surface ocean; DMSP-DMS production, nitrogen fixation
  • dadv@hawaii.edu
  • sites.google.com/site/cmoredelvalle/
Photo of Solange Duhamel.

Solange Duhamel

  • Formerly at the Woods Hole Oceanographic Institution (WHOI) and University of Hawai‘i at Manoa (UH Manoa)
  • Current position: Lamont Assistant Research Professor, Lamont-Doherty Earth Observatory, Columbia University
  • Research interest: Duhamel is interested in the dynamics of phosphorus biogeochemistry and bioavailability and its link with C and N cycling. She is particularly interested in prokaryotes and phytoplankton P incorporation pathways (direct incorporation from DIP or indirect incorporation from DOP) and in the algal-bacterial competition for P in P-limited areas. She develops cell-specific indicators of nutritional status such as ELF-labeling (Enzyme-Labeled Fluorescence).
  • Keywords: DIP, DOP, phosphatase, ELF, prokaryotes, phytoplankton, microscopy, flow cytometry
  • sduhamel@ldeo.columbia.edu
Photo of Jennifer Edmonds.

Jennifer Edmonds

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Edmonds is interested in how microbial community gene structure and expression influences key biogeochemical transformations of C, N, P, and S. She is currently focusing on the microbial utilization of complex dissolved organic phosphorus (DOP) compounds under conditions of P stress or starvation. Particular interest falls on the C-P lyase pathway, which may be a mechanism for aerobic methane production in the ocean water column.
  • Keywords: diversity, ecology, mRNA, methane production, DOP
  • jedmonds@hawaii.edu
Photo of Alexander Eiler.

Alexander Eiler

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Eiler is interested in the life strategies of marine microbes. He will perform laboratory experiments to study the physiological and evolutionary responses of abundant groups of marine bacteria to environmental stimuli. Additionally, Eiler will pursuit to identify the key players in marine microbial communities of the North Pacific Subtropical Gyre by linking distribution patterns of bacterial groups to ecosystem functions. Guided by this statistical approach some directed efforts will be applied to isolate and characterize the identified key-microbes.
  • Keywords: diversity, genomics, ecology, picoplankton, phylogeny, mRNA, 16S rRNA
  • eiler@hawaii.edu
Photo of Rachel A Foster.

Rachel A. Foster

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Current position: Scientist, Biogeochemistry Group, Max-Planck-Institut for Marine Microbiology
  • Research interest: Foster’s research focuses on the diversity and distribution of planktonic symbioses. In particular she is most interested in diatom hosts, which harbor symbiotic cyanobacteria or cyanobionts. Diatoms with associated diazotrophs, DDAs, have been reported from all major subtropical and tropical seas, yet very little is known about the intricacies of the relationships. She is currently working on developing and applying new methodology to reveal if fixed nitrogen by the cyanobiont is in fact transferred to the host diatom. Results from Foster’s research will be directly applicable to the modeling of nitrogen exchange between host and symbiont and vice versa.
  • Keywords: symbioses, nitrogen, diatoms, Richelia
  • rfoster@mpi-bremen.de
Photo of Jana Grote.

Jana Grote

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Grote is interested in the isolation, cultivation and genomics of marine bacteria. Her work is focused on the planktonic marine microbial lineage SAR11, one of the most abundant microorganisms in the ocean. Several different SAR11 subclades have been isolated from various marine sites and their genomes have been sequenced. Comparative analysis of these genomes together with physiological experiments with the isolated strains will allow elucidation of their ecological role and help to develop SAR11 as a model group of marine heterotrophic bacteria.
  • Keywords: isolation, cultivation, SAR11, genomics, metabolism, microbial diversity, molecular ecology
  • jgrote@hawaii.edu
Photo of Lionel Guidi.

Lionel Guidi

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Current position: UPMC Post-doctoral Scholar: Laboratoire d’Océanographie de Villefranche sur Mer
  • Research interest: Guidi is primarily interested in studying the biological, chemical and physical processes that transfer the Particulate Organic Carbon (POC) from the euphotic (0-100 m) layer to the mesopelagic (100-1000 m) zone in the open ocean by studying the spacial and temporal evolution of the particle size distribution in the water column using in-situand remote optical and imaging instrumentation.
  • Keywords: particle size, carbon export, carbon sequestration, imagery, data analysis
  • lionelg@hawaii.edu
Photo of Megan Huggett.

Megan Huggett

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Current position: At the Edith Cowan University, Perth, Australia
  • Research interest: Hugget is interested in larval settlement and recruitment, establishment of healthy coral-microbial relationships and the evolution and ecology of marine bacterioplankton. She is currently involved with projects investigating the onset of microbial associations in corals across the Pacific Ocean; genome sequencing and annotation of several marine bacteria and isolation and cultivation of previously uncultivated bacteria associated with corals.
  • Keywords: coral, microbial diversity
  • m.huggett@ecu.edu.au
Photo of Annette Hynes.

Annette Hynes

Photo of Libusha Kelly.

Libusha Kelly

  • Formerly at the Massachusetts Institute of Technology (MIT)
  • Research interest: A key challenge in biology is improving our understanding of the interactions between members of a heterogeneous population of organisms in a complex environment and determining the mechanisms that make this biological system stable to perturbation. In Kelly’s postdoctoral work in Sallie Chisholm’s lab, she is characterizing how genetic exchange between bacteria and viruses influences the ability of bacteria to adapt to different environments.
  • Keywords: metagenomics, cyanophage, cyanobacteria, systems biology, ecology
  • libusha@mit.edu
Photo of Yawei Luo.

Yawei Luo

  • Formerly at the Woods Hole Oceanographic Institution (WHOI)
  • Research interest: Luo’s research focuses on microbial ecosystem modeling in the open ocean, particularly diazotrophic bacteria, heterotrophic bacteria and dissolved organic matter (DOM) dynamics. Luo uses data assimilation methods to combine observations and modeling through optimizing model parameters. Luo also models the decadal trends observed in the Hawaii Ocean Time-series (HOT).
  • Keywords: ecosystem modeling, data assimulation, heterotrophic bacteria, dissolved organic matter, diazotroph
  • yluo@whoi.edu
Photo of Rex Malmstrom.

Rex Malmstrom

  • Formerly at the Massachusetts Institute of Technology (MIT)
  • Research interest: Malmstrom is interested in the dynamics of marine cyanobacterial populations. Currently, he is investigating seasonal changes in the abundance of various subgroups of Prochlorococcus, an abundant clade of marine cyanobacteria, in the North Pacific and North Atlantic oceans. In addition, he is exploring new technologies for targeted gene expression studies of natural Prochlorococcus populations.
  • Keywords: Prochlorococcus, genomics, transcriptomics, whole genome amplification
  • rexrm@mit.edu
Photo of Sandra Martinez-Garcia.

Sandra Martinez-Garcia

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Martinez-Garcia’s research focuses on the role of marine microbial communities on the biogeochemical fluxes through planktonic food webs. In particular, she is interested in understanding and predicting the effects that the anthropogenic changes in matter inputs into the ocean exert on the microbial heterotrophic and autotrophic metabolisms. She is also interested in studying carbon cycling at Station ALOHA, specifically through bacterial and community respiration rates.
  • Keywords: biogeochemistry, nitrogen cycle, food-web structure, primary and secondary production, microbial respiration, metabolic balance
  • sandramg@hawaii.edu
  • sites.google.com/site/cmoremartinezgarcia/
Photo of Vanessa Michelou.

Vanessa Michelou

  • Formerly at University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Michelou’s research interests lie in understanding the forces that shape bacterial community structures and dynamics, microbial diversity, and the roles of microbes in biogeochemical fluxes. She wants to integrate genomic analysis with an understanding of the functional properties that connect microbial and abiotic ecosystem processes. Combining molecular biology with oceanographic tools and ecological concepts will refine our understanding of relationships between community diversity and ecosystem function. Michelou is currently a postdoctoral fellow in Mike Rappe’s lab. Her work at C-MORE will address specific hypotheses regarding the physiological characteristics of bacterial isolates derived from their whole genome sequences. Some of her projects will be to examine the growth of bacterial isolates possessing the genetic potential for phototrophy, in both light and dark incubations, in order to measure parameters that would be of primary interest to biological oceanographers.
  • Keywords: microbial diversity, biogeochemical cycling, dissolved organic nutrients, photoheterotrophy, isolation, cultivation, microscopy, flow cytometry
  • michelou@hawaii.edu
  • sites.google.com/site/cmoremichelou/
Photo of Pia Moisander.

Pia Moisander

  • Current position: Assistant Professor at the University of Massachusetts Dartmouth
  • Research interest: Investigates the ecology of microbial communities in marine and freshwater environments. She focuses on the ecology of microbial communities that play important roles in the nitrogen cycle, such as nitrogen-fixing micro-organisms, many of which are bloom-forming, toxin-producing cyanobacteria. She uses functional genes in investigations of diversity and activity of these microbes that carry out important elemental transformations in biogeochemical cycles and are of interest from the ecosystem health perspective.
  • Keywords: estuarine, coastal, cyanobacteria, nifH-gene, sequencing, functional gene
  • pmoisander@umassd.edu
Photo of Mar Nieto-Cid.

Mar Nieto-Cid

  • Formerly at the Woods Hole Oceanographic Institution (WHOI)
  • Research interest: In general, Nieto-Cid is interested in the composition and fractionation of dissolved organic matter (DOM) and its role in biogeochemical cycles. Specifically, she is working on the influence of DOM fractionation on microbial consortia. She is also involved in the characterization of natural iron binding organic ligands to provide a better understanding of iron speciation in seawater and to help to integrate studies of siderophores from pure culture with microbial iron acquisition in iron limited environments.
  • Keywords: dissolved organic matter, biogeochemical cycles, trace metal organic ligands
  • mnietocid@whoi.edu
Photo of Abigail Noble.

Abigail Noble

  • Formerly at the Massachusetts Institute of Technology (MIT)
  • Current position: Environmental Chemist at Gradient
  • Research interest: Noble’s research revolves around the study of trace metals in seawater that act as metal micronutrients to phytoplankton (Co, Fe, Mn) and as anthropogenic tracers (Pb and Pb isotopes). Most of the Pb that exists in the ocean was originally derived from an anthropogenic source, with the most notable offender being the usage of alkyl leaded gasoline. High temperature industrial processes also contribute to the atmospheric source of anthropogenic Pb to the surface ocean. Sources of Pb can be traced by examining the stable isotope composition of environmental samples as different Pb ores have evolved over geologic time to have distinct compositions. Co, Fe, and Mn are hybrid-type metals that are incorporated into proteins and enzymes that participate in important biological functions such as carbon, nitrogen, and light acquisition. These metals are found in vanishingly low concentrations in the open ocean, and can limit or co-limit phytoplankton growth. Studying the distributions of these metals across strong biogeochemical gradients can help constrain the potential sources and sinks of these micronutrients in the global ocean and improve our understanding of the controls on global ocean productivity
  • Keywords: biogeochemical cycling, trace metals, cobalt, lead
  • anoble@mit.edu
Photo of Sophie Rabouille.

Sophie Rabouille

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Research interest: Rabouille is interested in the influence of plankton dynamics on nutrients fluxes. She develops models of phytoplankton growth to investigate changes in metabolic activities in response to forcing conditions of the environment. In particular, she focused on the effect of metabolic constraints on nitrogen fixation in planktonic cyanobacteria; she followed their activity in relation to fluctuations of environmental variables such as irradiance and oxygen concentration. Based on the analysis of the HOT database, she also modeled the vertical segregation of high- and low-light adapted ecotypes of Prochlorococcus sp. in the North Pacific Subtropical Gyre. She is currently working on a new ecosystem model to analyze plankton diversity and dynamics in the California Current system.
  • Keywords: plankton dynamics, light response curves, nitrogen fixation, nutrient fluxes, modeling
  • srabouille@pmc.ucsc.edu
Photo of Julie Robidart.

Julie Robidart

    Formerly at the University of California, Santa Cruz (UCSC)
  • Current position: Molecular Biologist: Environmental Biosensors, at the National Oceanography Centre, Southampton (UK)
  • Research interest: Robidart’s research involves biogeochemical investigations of marine microbial cycles using in situ instrumentation. She is currently developing primer and probe sets for genes coding for key enzymes, to be deployed on the quantitative PCR module of the Environmental Sample Processor, in the Monterey Bay. Data collected by the ESP will give detailed information about how microbial communities respond to, and change, environmental conditions over time and space.
  • Keywords: in situ instrumentation, biogeochemical cycling
  • j.robidart@noc.ac.uk
Photo of Sebastien Rodrigue.

Sébastien Rodrigue

  • Formerly at the Massachusetts Institute of Technology (MIT)
  • Current position: Assistant professor/professeur adjoint at Université de Sherbrooke, Département de biologie
  • Research interest: My work focuses on cultivation-independent methods to study microbial populations and sequence genomes from single-cells. I am also involved in systems and synthetic biology of minimal genomes.
  • Keywords: genome diversity, gene expression, single-cell approaches
  • sebastien.rodrigue@usherbrooke.ca
Photo of Ty Samo.

Ty Samo

  • Formerly at University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Samo is interested in detailing the spectrum of marine microbial growth, enzyme activity, and identity at the single cell level in coastal and open ocean habitats. Currently, he is developing microscopy and image analysis approaches to assess the contribution of individual free-living and particle-attached microbial cells to the availability and cycling of carbon and phosphorus.
  • Keywords: bacterioplankton, phytoplankton, microscopy, physiology, biogeochemistry
  • tsamo@hawaii.edu
  • sites.google.com/site/cmoresamo/
Photo of Mariona Segura-Noguera.

Mariona Segura-Noguera

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Segura Noguera is interested in plankton stoichiometry and its variations between and within key plankton groups and species. To determine plankton stoichiometry, she studies the elemental composition of plankton using single-cell methodologies (X-ray microanalysis). Because changes in plankton stoichiometry are related to environmental conditions, which determine the availability of nutrients and light, she is also interested in dissolved inorganic and organic nutrient distributions in the sea.
  • Keywords: phytoplankton, stoichiometry, single-cell microanalysis, biogeochemical cycling, dissolved inorganic nutrients, dissolved organic nutrients
  • mseguran@hawaii.edu
  • sites.google.com/site/cmoresegura/
Photo of Christine Shulse.

Christine Shulse

  • Formerly at University of Hawai‘i at Manoa (UH Manoa)
  • Research interest: Shulse is interested in understanding the factors that govern microbial community structure. At C-MORE, she is using next-generation, massively parallel tag sequencing to identify bacteria associated with corals from disparate geographic locations and across multiple stages of development.
  • Keywords: microbial diversity, molecular ecology, coral, microbial metabolism, symbioses
  • cshulse@hawaii.edu
  • sites.google.com/site/cmoreshulse/
Photo of Matthew B. Sullivan.

Matthew B. Sullivan

  • Formerly at the Massachusetts Institute of Technology (MIT)
  • Current position: Assistant Professor at the University of Arizona in Tucson; visit the Sullivan Lab web site.
  • C-MORE Participation: Sullivan used metagenomic approaches to investigate marine viral genomic diversity, as well as high-throughput virus isolations and genomic sequencing to focus on the “population genomics” of Prochlorococcus and Synechococcus viruses (cyanophages).
Photo of Anne Thompson.

Anne Thompson

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Research interest: Thompson is interested in the ecology of the uncultured nitrogen fixer, UCYN-A. Specifically, she will be working on understanding patterns of whole-genome transcription in UCYN-A under different environmental conditions in the open ocean.
  • Keywords: nitrogen fixation, transcriptomics, UCYN-A
  • awthomps@ucsc.edu
Photo of Sasha Tozzi.

Sasha Tozzi

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Current positions: Manager of Strain Validation at Aurora Algae, Inc.; Courtesy Research Associate, University of California, Santa Cruz (UCSC)
  • Research interest: Tozzi’s interests include phytoplankton ecology and photophysiology, marine primary production; environmental forcing and regulation of phytoplankton biomass and production; photosynthesis biophysics with a main interest in studies based on fluorescence bioassays. His research aims to explore the effects of temperature, nutrients and pCO2 on phytoplankton species and assemblages’ photosynthesis by using custom designed and built chemostats and Fast Repetition Fluorometers (FRRF).
  • Keywords: phytoplankton, photosynthesis, primary production, fluorescence, chemostats, instrumentation, biogeochemical cycling
  • stozzi@aurorainc.com, stozzi@ucsc.edu
Photo of Jim Tripp.

Jim Tripp

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Research interest: Tripp’s research interest is the physiology of biogeochemically important marine microbes. Prior to joining C-MORE, he determined the unusual nutrient requirements of the SAR11 representative Candidatus Pelagibacter ubique from its complete genome sequence. As a C-MORE postdoctoral scholar in the Zehr Lab, he was part of a team that identified physiological adaptations of UCYN-A cyanobacteria to efficient nitrogen fixation as revealed by their metagenome. Tripp continues to contribute to C-MORE initiatives as a Bioinformaticist with the MEGAMER facility at UC Santa Cruz. His web site can be found at here.
  • hjames.tripp@gmail.com
Photo of Elisha M. Wood-Charlson.

Elisha M. Wood-Charlson

  • Formerly a post-doc at University of Hawai‘i at Manoa (UH Manoa)
  • Current positions: C-MORE EDventures Program Director and Postdoctoral Scholar, Australian Institute of Marine Science
  • Research interest: Wood-Charlson is interested in host-virus interactions. Her research focuses on two main areas: 1) tracking viral population dynamics in oligotrophic oceans over space and time, and 2) understanding the impact of viral infection on important marine symbioses. The work on viral population dynamics primarily looks at cyanobacterial viruses (cyanophages) using data collected at Station ALOHA, in collaboration with Dr. Matthew Church and the HOT program, but the project will soon be expanded to include upcoming cruises in the South Pacific. The research on symbiont viruses includes work on Symbiodinium dinoflagellates, which are mutualistic symbionts found in cnidarians such as corals and sea anemones, and will also include cyanobacteria, which can occur as symbionts in diatoms.
  • Keywords: microbial diversity, viral ecology, symbioses, host-virus interactions
  • elishawc@hawaii.edu

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Former Graduate Students

Photo of Shellie Bench.

Shellie Bench

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Research interest: Bench is interested in the genetics of nitrogen fixing cyanobacterial strains and natural populations.
  • Keywords: genomics and genome organization, microbial population structure, microbial evolutionary strategies
  • shellierb@gmail.com
Photo of Erin Bertrand.

Erin Bertrand

  • Formerly at the Woods Hole Oceanographic Institution (WHOI)
  • Current Position: NSF Polar Programs Postdoctoral Fellow, J. Craig Venter Institute
  • Research interest: Bertrand’s work focus on understanding the role of micronutrient availaiblity in major marine biogeochemical processes. She uses proteomic and transcriptomic methodologies coupled with genetic manipulation techniques to understand micronutrient starvation and acquisition processes in marine microorganism
  • Keywords: proteomics,transcriptomics, diatoms, micronutrients, vitamin B12
  • ebertran@jcvi.org
Photo of Jennifer Brum.

Jennifer R. Brum

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Current position: Postdoctoral researcher in Dr. Matthew Sullivan’s Tucson Marine Phage Lab at the University of Arizona.
  • Research interest: Jennifer is currently conducting research on temperate viruses in the Southern Ocean, exploring morphological diversity of viruses along the Tara Oceans expedition transect, and developing a new method to target uncultivated marine viruses for genome sequencing.
  • jbrum@email.arizona.edu
Photo of Brian Burkhardt.

Brian Burkhardt

Photo of Jessica N. Fitzsimmons.

Jessica N. Fitzsimmons

  • Formerly at the 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 Allison Fong.

Allison A. Fong

  • Formerly at the 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 Darin Hayakawa.

Darin H. Hayakawa

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Current position: Lecturer in Biology & Microbiology, Kapi‘olani Community College & University of Hawai‘i - West O‘ahu
  • Research interest: Marine microbial biodiversity is Hayakawa’s overarching interest. His primary objective is to develop and utilize a broad array of cultivation independent methods to assess microbial community diversity and structure at Station Aloha in a time- and depth-dependent fashion. These results will guide his secondary objective: to employ directed techniques to isolate and propagate cultures of ecologically relevant target microbes from Station ALOHA.
  • Keywords: picoplankton, diversity, spatiotemporal, molecular ecology, cultivation, metabolism, genomics
  • darin@hawaii.edu
Photo of Jason Hilton.

Jason Hilton

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Current position: Data Wrangler at Stanford University (ENCODE)
  • 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 Annette M. Hynes.

Annette M. Hynes

  • Formerly in the MIT-WHOI Joint Program in Biological Oceanography
  • Research interest: Hynes is investigating the diversity of the marine nitrogen-fixing cyanobacterium Trichodesmium. She is characterizing cultured strains using pigment analysis, microscopy, and gene sequences. The gene sequences will be used to develop a quantitative method for detecting different clades of Trichodesmium in the water column for transects across the Pacific and Atlantic oceans. This data will be used to develop a stochastic competition model incorporating different types of Trichodesmium.
  • Keywords: cyanobacteria, diversity, ecosystem modeling, nitrogen fixation, Trichodesmium
  • ahynes@whoi.edu
Photo of Ha Na Kim.

Ha Na Kim

  • Formerly at the 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 Binglin Li.

Binglin Li

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Current position: At the Center of Coastal Margin Observation & Prediction (CMOP), a science and technology center at Oregon Heath and Science University (OHSU).
  • Research interest: Li’s interests focus on diatom bloom dynamics in the open ocean. He looks forward to examining the diversity of diatoms and the interaction between diatoms and their endosymbiotic nitrogen fixers by developing molecular methodologies.
  • Keywords: diatom, bloom, dynamics, nitrogen fixation, endosymbiosis
  • lib@ebs.ogi.edu
Photo of Sara Lincoln.

Sara Lincoln

  • Formerly at the Massachusetts Institute of Technology (MIT)
  • Current position: Postdoctoral scholar at the Pennsylvania State University
  • 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@alum.mit.edu
Photo of Ryan W. Paerl.

Ryan W. Paerl

  • Formerly at the University of California, Santa Cruz (UCSC)
  • Current position: Post-Doctoral Scholar at Scripps Institution of Oceanography
  • Research interest: Paerl is interested in learning more about the biogeography and nitrate assimilation activity of picocyanobacteria (unicellular cyanobacteria, < 2 µm in diamater). The diversity of picocyanobacteria capable of nitrate assimilation has been initially examined by PCR amplifying the narB gene (which encodes for cyanobacterial nitrate reductase). Furthermore, using narB qPCR (quantitative PCR) assays, changes in the abundance of specific nitrate assimilating populations (narB phylotypes) will be examined on spatial and temporal scales off the CA coast and in open-ocean profiles. Lastly, gene expression of the narB gene (examined by narB RT qPCR, reverse transcription qPCR) and assimilation of stable 15NO3- (examined by SIP, stable isotope probing) will be examined in order to address nitrate assimilation by different narB phylotypes.
  • Keywords: picocyanobacteria, Synechococcus, nitrogen cycling, nitrate assimilation, qPCR, SIP, narB gene
  • rpaerl@ucsc.edu
Photo of Yanmei Shi.

Yanmei Shi

  • Formerly at the 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

  • Formerly at the 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 Laure-Anne Ventouras.

Laure-Anne Ventouras

  • Formerly at the Massachusetts Institute of Technology (MIT)
  • Research interest: Ventouras’ thesis work has been focused on using culture independent techniques to study iron acquisition mechanisms by marine microbial communities. She is specifically interested in how the heterotrophic community accesses the largely unavailable iron pool in the ocean. One approach she is using to explore this interest is to perform large perturbation incubation experiments and follow the changes in gene expression of the whole microbial community in response to changing iron availabilities.
  • Keywords: metagenomics, metatranscriptomics, iron acquisition
  • lav@mit.edu
Photo of Jacob R. Waldbauer.

Jacob R. Waldbauer

  • Formerly in the MIT-WHOI Joint Program in Biological Oceanography
  • Current position: Assistant Professor at the University of Chicago
  • Research interest: Waldbauer’s work focuses on the use of molecular and isotopic techniques, especially quantitative proteomics, in studying the mechanistic underpinnings of biogeochemical processes. Topics of particular interest include circadian expression patterns in the marine water column, modes of planktonic nutrient uptake and cellular biochemical stoichiometries.
  • Keywords: proteomics, Prochlorococcus, biogeochemistry, cytometry
  • jwal@uchicago.edu
Photo of Brenner Wai.

Brenner Wai

  • Formerly at the 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
Photo of Gordon Walker.

Gordon Walker

  • Formerly at the University of Hawai‘i at Manoa (UH Manoa)
  • Current position: Oceanographer, Pacific Integrated Ocean Observing System (PacIOOS), McManus Lab
  • Research interest: Walker is investigating the abundance, diversity and dynamics of marine viruses and how they influence microplankton ecology.
  • Key words: marine viruses, viral ecology, flow cytometry
  • gwalker@hawaii.edu

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