Sankar Marichamy

Sankar Marichamy is an expert on obligate anaerobes and a biotechnologist. Presently he is involved in the isolation of Anaerobic Alkane Oxidizers that includes ANMEs (anaerobic methanotrophs), Ethane, Propane and Butane oxidizers from various ocean deep subsurfaces. He is investigating the Anaerobic Methane Oxidation Pathway with cutting edge analytical tools and with carbon isotope enrichments in Archaea.

Arpita Bose

Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation

I am a microbiologist by training. My general interests are microbial physiology, microbial ecology, biogeochemical cycling, gene regulation, microbial metal respiration and Earth history. During my graduate work and post-doctoral research, I used genetics, biochemistry and molecular biology to understand microbial metabolism. My Master’s research at the All India Institute of Medical Sciences, New Delhi, dealt with understanding the physiological response of Mycobacterium tuberculosis to hypoxia. For my PhD research I studied methanogenesis performed by the poorly understood archaea, in the lab of Prof. William Metcalf at the University of Illinois at Urbana. During this period I took, and subsequently taught, the Microbial Diversity Summer course at the Marine Biological Laboratory. I was a Howard Hughes Medical Institute research associate for a year in the lab of Prof. Dianne Newman at the Massachusetts Institute of Technology, where I studied photoferrotrophy performed by purple non sulfur bacteria. I thereafter moved to the Girguis lab, where I use a combinatorial approach to study microbial metabolism at the environmental level. My projects focus on hydrocarbon oxidation and metal respiration. I hope to answer important questions about the prevalence of microbes that perform these metabolisms in nature as well as understand the molecular mechanisms underlying these microbial processes. In my free time I like to cook, sketch, paint, travel, hike, play with dogs and hang out with my husband, Josh.

Mark Nielsen

www.people.fas.harvard.edu/~mnielsen

I am an interdisciplinary earth scientist with experience and interests in geology, oceanography, hydrology, microbiology and engineering.  During my PhD I designed, deployed and studied sediment microbial fuel cells.  A major thrust of my postdoctoral research is to test the hypothesis that oceanic hydrothermal vents are natural analogs of fuel cells.  I am also interested in the forces that drive advective exchange between the oceanic lithosphere and overlying water, and the chemical fluxes in these advective systems (e.g., how does fluid chemistry from a seep or vent vary with time, what controls the variability and what is the magnitude of the potential energy flux from the seafloor to the overlying ocean?).  

My interest in oceanography is fueled by my passion for sailing. Outside of work, I can be found spending time with my family (Steph, Scarlett and Zephyr), enjoying the outdoors, cooking, or playing ice hockey.

Pengfei Song

I come from a diverse background of chemical engineering, biochemistry, microbiology and molecular biology. I am interested in understanding the molecular mechanisms of different biological processes.

Prior to joining the Girguis Lab, I received three years of postdoctoral training in human cancer biochemistry and molecular biology, which was heavily involved in identification and investigation of novel proteins in cancer cell regulation. In the Girguis Lab, I apply modern technologies, such as metagenomics, proteomics, microarray, mutagenesis, Q-PCR and confocal microscopy to identify the functional genes responsible for power production in bacteria of the microbial fuel cells (MFCs). With collaboration from chemists and geologists in the group, I attempt to link environmental data with cellular processes to unveil the role of microbes in the circle of life.

Charles Vidoudez

I have a multidisciplinary background in plant biochemistry, biotechnology, chemical ecology, metabolomics and mass spectrometry. The major aim of my postdoc is to combine all theses disciplines to better understand the deep-sea ecosystems.

I recently finished my PhD in developing new analytical methods to explore the interactions and dynamics of microalgae. In particular I used mass spectrometry to decipher the metabolome of diatoms. In the lab I use and further develop in situ mass spectrometers. These instruments are a highlight of this lab and allow direct in situ characterization of the gases dissolved in the seawater, especially at hydrothermal vent sites. The direct and virtually unlimited amount of sampling allowed by the in situ mass spectrometer is helping us to understand the geological and biological processes that produce and use these gases.

My general interest in science is to better understand the dynamics and the interaction of the aquatic ecosystems. I also have a passion for electronics, new technologies and methods, all of which are useful in helping me use and develop new instruments for my science.

Erika A. Parra

erikaparra.com

As a microsystems engineer turned bioelectrochemical scientist, my interests range over many disciplines. Specifically, I’m interested in the development of visualization techniques and quantitative platforms to illuminate bacterial interactions with surfaces. For my PhD at UC Berkeley, I developed a microfluidic microbial fuel cell for single cell analysis of extracellular electron transfer. Now at the Girguis lab, I study electrically stimulated microbial metabolism for biofuel production. However, my interests span over other areas such as sustainable built environments, excellent design, and cultural paradoxes. In my spare time, I enjoy traveling, long distance running, sailing, and anything Japanese. However, I’m always getting into new things and am willing to try just about anything once! For more info, please check out my personal website at erikaparra.com.

Dan Rogers

Profile forthcoming...

Melissa Adams

I am interested in the ecophysiology of microorganisms that mediate geochemical cycling in marine sediments, where there is limited diffusion of dissolved ions and volatile compounds. My research interests also extend to studies of microbial adaptation and acclimation responses to environmental perturbations, such as changes in nutrient availability. In the Girguis Lab, I plan to pursue a combination of in situ and ex situ studies focused on hydrocarbon metabolism at deep sea vents and seeps, focusing on the enigmatic anaerobic oxidation of methane. Currently, I am constructing “mud hotels” or artificial seep systems that will allow us to better understand the key microbes, functional genes, and molecular mechanisms underlying these globally important biogeochemical processes.

Select Publications

• Adams, M.M., M.R. Gómez-García, A.R. Grossman, and D. Bhaya (2008) Phosphorus deprivation responses and phosphonate utilization in a thermophilic Synechococcus sp. from microbial mats. Journal of Bacteriology 190(24): 8171-8184.
• Tamone S.L., M.M. Adams, and J.M. Dutton (2005) Effect of eyestalk-ablation on circulating ecdysteroids in hemolymph of snow crabs, Chionoecetes opilio: physiological evidence for terminal molt. Integrative and Comparative Biology 45:166–171.

Roxie Beinart

I am interested in the non-antagonistic interactions between microbes and metazoans, particularly the influence of the symbiont on the niche of the host animal.  Often, the niche of the host organism is expanded by its partnership with a symbiont through the addition of novel physiological capabilities.  However, not all symbionts are “equal”; there can be functional differences among closely related symbionts (e.g., differences in rate) or even fundamental physiological differences among lineages (e.g., distinct physiological capacities).  I am currently comparing the metabolic capacities (i.e., variations in rate, substrate use and pathway) of the bacterial symbionts within and between invertebrate host species at hydrothermal vents in the Lau Basin.  I am integrating experimental physiological studies of these symbioses with molecular characterization and in situ environmental data in order to understand how symbiont physiology drives the distribution of their mollusk hosts in the chemical gradients found at vents.

Geoff Dilly

My research couples the fields of physiology and biochemical adaptation to understand thermotolerance at hydrothermal vents.  I am interested in identifying the thermal boundaries of metazoan life (both the limitations an organism faces under heat stress and the mechanisms by which the organism can acclimate or adapt to its environment).  To this end, I study the marine polychaete Paralvinella sulfincola, a vent endemic with the largest experimentally verified thermal range known in the animal kingdom (5 - >50°C) as compared to its closely related congener, Paralvinella palmiformis, whose range in thermotolerance is limited to <40°C. 

Animals are collected live from vents, placed into shipboard high-pressure respirometry systems, and subjected to a wide range of thermal and temporal conditions.  Oxygen consumption is measured over time to determine physiological responses to thermal stress.  Subsequent biochemical investigations of the organisms have included building an Expressed Sequence Tag (EST) library with the DoE-JGI and proteomics using a MS/MS.  Further investigations of gene expression will be conducted using RT-qPCR. 

Kiana Frank

First and foremost, bacteria rule!  It is surmised that approximately ½ of the life on our planet is microbial and, as we are a planet comprised of 2/3 water, it seems to follow that aquatic microbiology is a pretty exciting field to be in.   Growing up on an island, I’ve always been interested in aquatic microbial ecology and, armed with a background in molecular genetics, I’ve settled in the Girguis Lab to start some exciting microbial adventures.  In this lab, I have been given the opportunity to dive deeper and explore the unique microbial communities that occur in the deepest and darkest environs, on and far below the seafloor.   I am interested in studying microbial community compositions, with respect to both phylogeny and functional gene capacity, in these extreme environments (e.g., hydrothermal vents, deep subsurface biosphere, etc.) over varying time, depth, and geochemical and temperature gradients.   New technologies and sampling advancements in the field (some being developed in this lab) allow me to design in situ experiments to probe the metabolic potential of these communities (contributing to common themes in this lab which explore the role of deep ocean microbes in biogeochemical cycling), gather insights about the origins of life on Earth and how life might exist on other planets, and prompt fresh ideas about the limits of life.

Emily Gardell

I am interested in how microorganisms interact with materials as electron acceptors, specifically in microbial fuel cells.  What is the intersection between microbial physiology and ecology with microbial fuel cell performance?  To answer this question, I am working with a salt marsh sediment microbial fuel cell containing multiple anodes to study how switching between the anodes changes the power production by the fuel cell and the microbial ecology at each anode.  My background lies in physics and chemistry with a particular emphasis on materials science.  I am excited to bring some of these perspectives as I learn more about microorganisms and to conduct research that bridges materials science and microbiology.  I think combining these two fields is an interesting way to better understand how microbial fuel cells function.

Li Liao

I am a visiting PhD student from Zhejiang University supported by a Chinese government scholarship. My research is mainly focused on microorganisms that live in extreme environments, such as extremely high salinity environments and the deep sea. I started my scientific journey by exploring the functional genes and proteins of haloarchaea through cloning and expression of key enzymes (e.g., alcohol dehydrogenase and malate dehydrogenase) in various metabolic pathways. I discovered a novel agarase from a previously unknown marine Vibrio strain. Through homology-based cloning, I amplified the gene directly from its genome. This agarase was characterized and found to belong to GH50 family and has potential industrial applications. My interest in marine ecology evolved from the study on microbial diversities in gas hydrate-bearing sediments of the northern slope in South China and polymetallic deposits in the Pacific Ocean. My project at Harvard will be focused on the understanding of tube worm symbionts and free-living counterparts in deep-sea hydrothermal vents. I will try to answer the following questions: a) What is the impact of symbiosis on free-living bacterial diversity? b) What is the relationship of diversity between symbionts and free-living bacteria?

Heather Olins

I am interested in deep-sea microbial ecology, specifically in extreme environments (e.g., hydrothermal vents).  I am working to constrain rates of microbially mediated metabolic processes that occur in vent chimney walls through the use of flow-through bioreactors (aka artificial vents) in the lab.  I hope to be able to extend these experiments into the field.  I am interested in how these types of reactions may influence broader marine biogeochemical cycles.  I am particularly interested in the role that vent ecosystems may play in the carbon cycle.  I am also interested in the insights that high-temperature microbial life can bring to the search for life elsewhere in our solar system.  I come from a geology/environmental science background, and I am fascinated by environmental overlap of geology and biology.  It is my long-term goal to increase our understanding of how biological and geological process interact in the deep sea.

Jon Sanders

I fell in love with the natural world at the edge of a pond. Born and raised in Iowa, I spent as much of my childhood as I could get away with bothering the various frogs, fish, and reptiles that lived just outside my back door. 

Just after my ninth birthday, my family moved to California; it wasn't long before I saw the ocean for the first time, and not long after that I'd decided to become a marine biologist. I've pretty much stuck with that plan ever since. As an undergraduate at Stanford, I spent as much time as I could get away with bothering the various limpets, crabs, and anemones at the Hopkins Marine Station in Monterey. 

My interest in symbiosis and cooperation began as an undergraduate research project with Professor Stephen Palumbi on the phylogeography of symbiotic dinoflagellates in an intertidal anemone. Peering at this ubiquitous partnership (one which I'd been gleefully poking at since the fourth grade) through the lens of molecular ecology revealed mysteries I couldn't have imagined on my own, and which challenged my rudimentary understanding of evolution. Soon after, classes I took in anthropology and economics illustrated to me the importance that issues of cooperation have in human societies as well. 

In addition to research, I'm passionate about communicating science to others and have worked and volunteered in science outreach and education since my first year of college. When I'm not engaged in either of the above activities, I enjoy adventures in the outdoors, photography, cooking, and music. 

Research Interests

When organisms enter into cooperative partnerships with other species, it changes the adaptive landscape experienced by each partner: sulfur-oxidizing bacterial symbionts allow deep-sea snails to exploit a novel source of energy, while their hosts provide a stable and oxidant-rich habitat for the bacteria; rainforest trees grow specialized living chambers and food resources for their ant partners, which in turn defend the plant from herbivores. In these mutualistic symbioses, each partner's interaction with the environment is largely mediated through its relationship with another species. 

I am interested in how these interspecific partnerships affect the course of evolution in their constituent organisms, especially with regards to diversification and speciation. Why do some corals host many different kinds of photosynthetic symbiont across their range, while others host only one? Which conditions favor the evolution of partner specificity, and which favor generalization? When does a symbiotic partnership 'flatten' an organism's evolutionary landscape, enabling it to adapt to a broader range of environments, and when does a partnership turn into an evolutionary liability? 

My research takes an integrated approach to answering these questions, drawing hypotheses from current theoretical models, then testing them in natural systems. Because the interactions I study may be driven by factors that aren't immediately obvious to a human observer, I endeavor to understand them in a broader context, taking advantage of techniques in molecular phylogenetics, physiology, and ecology to quantify the various facets of the symbiosis.

Dan Cahoon

I'm a senior at Harvard concentrating in Chemical and Physical Biology with a secondary field in Computer Science, and joined the Girguis lab in spring 2010. Since then, I have helped with various projects, including studies on hydrothermal vents, jellyfish, and deep sea sediment. Currently, I am working on my senior thesis on how carbon uptake by microbes in deep sea sediment is affected by conductive minerals. After graduation, I hope to work in either the biotech or tech industries doing bioinformatics or computer science work for a few years, and then possibly attend graduate school.

John Skutnik

I am currently a laboratory technician in the Girguis Lab. Currently I am assisting in various tasks around the lab such as maintenance, gas system setups, mechanical designs, and I am starting to work with an osmotic sampling system project. My academic interests rest with coral reefs and how the changing environment will impact their survival and resilience. In my spare time I am an avid scuba diver along with having a passion for cooking.

Allon Hochbaum

I am currently a postdoc in Joanna Aizenberg’s lab (SEAS/CCB, Harvard) collaborating closely with the Girguis lab to explore biological charge transfer interfaces. During my PhD research I studied the thermal and electrical transport properties of quasi-1D nanowire materials for applications in electronic and thermoelectric devices. In the Girguis lab I am investigating a different type of energy conversion: transforming chemical to electrical energy through biological systems. With my background in materials chemistry and recent work in microbial biofilms, I am exploring the relationship between bacterial community structure and bioelectrochemical properties with a view towards understanding and optimizing extracellular electron transport processes. My general research interests lie at the interface of biology and inorganic materials, coaxing microorganisms to work for us through directed biochemical and inorganic reactions. My extracurricular scientific pursuits include kitchen chemistry and experimental studies of humanoid projectiles on bikes and skis. My CV can be found here.

Scott Wankel

people.fas.harvard.edu/~sdwankel

My background lies in stable isotope biogeochemistry, specifically coupled isotopic (N and O) approaches to understanding nitrate cycling. Fundamentally, I am interested in how stable isotopes can be used (both at natural abundance and tracer level) along with other novel tools for exploring and improving our understanding of biogeochemical cycling of nitrogen and carbon in aquatic environments.

Here in the Girguis Lab, I am currently focusing on development of new approaches to coupling the measurement of biogeochemical processes in situ with the molecular assessment of the microbial communities responsible for carrying out environmentally important reactions; essentially, attempting to improve the connection between more traditional biogeochemical and molecular microbiological approaches.

Specifically, through both lab-based flow-through reactor systems and 'deployable instrumentation,' my research focuses on anaerobic carbon and nitrogen metabolisms (such as NH4+ or CH4 oxidation) coupled to other redox reactions involving metals (such as Fe and Mn) in deep-sea environments such as hydrocarbon seeps and hydrothermal vents.

Shiloh

Shiloh Herren Girguis went to the doghouse in the sky on December 24th, 2010. Shiloh was the Girguis lab mascot and worked part-time as a squirrel deterrent in Medford, MA. Born in central California, his interests included exploring the edibility of detritus found in anaerobic mudflats. He was also proficient in antagonizing skunks, and continues to hold the record for most "hits" in a single night (three). He enjoyed running and placed second in Santa Barbara’s annual State Street Run (with his partner Dr. Todd Lajeunesse at Penn State University). We miss him dearly, but are very grateful for the joy he brought to our lives.