Former Lab Members
Peter R. Girguis
Professor of Organismic & Evolutionary Biology - Harvard University
Adjunct Research Engineer - Monterey Bay Aquarium Research Institute
His research resides at the crossroads of microbial ecology, physiology, and biogeochemistry, and as such is highly interdisciplinary. He uses the appropriate combinations of molecular biology (e.g., genomics, transcriptomics, proteomics, qPCR, mutagenesis), as well as physiological and geochemical techniques (gas chromatography, in situ and laboratory mass spectrometry, in situ and laboratory isotope analyses, x-ray diffraction, atomic spectroscopy) to examine the relationship between microbial diversity/physiology and biogeochemical cycles. Due to the limitations of existing in situ measurement and incubation technologies, he and his lab have develop novel instruments and samplers that enable them to better study microbial-geochemical relationships. This includes high-pressure systems to mimic natural environments, in situ geochemical sensors, in situ microbial fuel cells as experimental apparatus and power sources, and novel in situ preservation technologies.
He received his B.Sc. from UCLA, where he also worked with Drs. David Chapman and William Hamner. He received his Ph.D. from the University of California Santa Barbara, where he worked with Dr. James Childress on the physiological and biochemical adaptation of deep-sea hydrothermal vent tubeworms and their microbial symbionts to the vent environment. He did postdoctoral research at the Monterey Bay Aquarium Research Institute with Dr. Edward Delong on the growth and population dynamics of anaerobic methanotrophs.
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.
Hello, I’m Vicky! I am an environmental microbiologist by training. In general, I enjoy combining different avenues of science (geochemistry, microbiology, molecular biology, ecology, etc.) to the study of one environment in hopes of understanding how that ecosystem functions as a whole. My work has focused on examining the biogeochemical processes that occur in marine sediments and the complex interactions that are established between animals, sediment, and microbes in the benthic realm. Specifically, I am interested in sulfur, carbon, and nitrogen cycling, and how these cycles are linked in shallow and deep-sea environments. Environments I have focused on in the past include intertidal mud flats, methane seeps, hydrothermal vents, oxygen minimum zones, and Arctic sediments. During my Ph.D., I worked on Animal-Sediment-Microbe interactions in coastal lagoons and at methane seeps, with an emphasis on the impact of bioturbation on geochemical microniche formation, sulfate reduction, and N2-fixaiton in marine sediments. From there, I went on to study nitrogen fixation, and its linkage to sulfate reduction, in marine oxygen minimum zone sediments, as well as methane hydrate dissolution and methane emissions in Arctic waters. Recently, I joined the Girguis lab to examine the use of acetogens, possibly isolated from marine sediments, in bioreactor systems for the potential production of biodiesel.
I did my undergraduate studies at the University of California at Berkeley, majoring in Integrative Biology and Geology – Marine Science. I did my graduate work at the University of Southern California (USC) in the Biological Sciences Department in the laboratory of Prof. Wiebke Ziebis. After defending, I went on to do an Alexander von Humboldt Post-Doctoral Research Fellowship at GEOMAR (Kiel, Germany) in the Marine Biogeochemistry Division in the laboratory of Prof. Tina Treude. Following this fellowship, I joined the Girguis lab to work on projects related to MFCs and nutrient cycling in the deep ocean.
When not at work, I immensely enjoy traveling, dancing, playing musical instruments, camping, and scuba diving. I also enjoy more relaxing activities such as reading, cooking, drawing, photography, and playing with my cat.
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 metal respiration, microbial extracellular electron transfer and hydrocarbon oxidation. 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, and play with dogs. I am also an avid orchid collector.
- Bose A, Vidoudez C, Parra EA, Gardel EJ, Girguis PR (2012). Microbial photoelectroautotrophy by Rhodopseudomonas palustris TIE-1. (Submitted)
- Bose A, Hoarfrost A, Skutnik J, Girguis PR, Newman DK. A whole genome approach to understand ferrous iron acquisition in the photoferrotrophic model organism Rhodopseudomonas palustrisTIE-1. (In submission)
- Bose A, Metcalf WW. An archaeal-specific family of DNA-binding proteins regulates expression of methanol methyltransferase operons in Methanosarcina acetivorans C2A. (In submission)
- Bose A, Rogers D, Adams MM, Delaney J, Girguis, PR. Anaerobic short chain alkane degradation in Gulf of Mexico sediments is linked to sulfate reduction. (Manuscript in preparation)
- Bose A, Newman DK. (2011) Regulation of the phototrophic iron oxidation (pio) genes in Rhodopseudomonas palustris TIE-1 is mediated by the global regulator, FixK. Mol Microbiol. 79(1):63-75.
- Bose A, Kopf S, Newman DK. (2010) From geocycles to genomes and back. In Stolz JF and Oremland, RS (ed.), Microbial metal and metalloid metabolism. ASM press, Washington, D.C. (Book Chapter)
- Bose A, Kulkarni G, Metcalf WW. (2009) Regulation of putative methyl-sulfide methyltransferases in Methanosarcina acetivorans C2A. Mol Microbiol. 74(1):227-38.
- Opulencia RO, Bose A, Metcalf WW. (2009) Physiology and post-transcriptional regulation of methanol:coenzyme M methyltransferase isozymes in Methanosarcina acetivorans C2A. J Bacteriol. 191(22):6928-35.
- Bose A, Pritchett MA, Metcalf WW. (2008) Genetic analysis of the methanol specific methyltransferase 2 genes of Methanosarcina acetivorans C2A. J Bacteriol. 190(11):4017-26.
- Bose A, Metcalf WW. (2008) Distinct regulators control the expression of methanol methyltransferase isozymes in Methanosarcina acetivorans C2A. Mol Microbiol. 67(3):649–61.
- Bose A, Pritchett MA, Rother M, Metcalf WW. (2006) Differential regulation of the three methanol methyltransferase isozymes in Methanosarcina acetivorans C2A. J Bacteriol. 88(20):7274-83.
- Sharma D*, Bose A*, Shakila H, Das TK, Tyagi JS, Ramanathan VD. (2006) Expression of mycobacterial cell division protein, FtsZ, and dormancy proteins, DevR and Acr, within lung granulomas throughout guinea pig infection. FEMS Immunol Med Microbiol. 48(3):329-36. (*DS and AB contributed equally to this work)
- Rother M, Boccazzi P, Bose A, Pritchett MA, Metcalf WW. (2005) Methanol-dependent gene expression demonstrates that methyl-coenzyme M reductase is essential in Methanosarcina acetivorans C2A and allows isolation of mutants with defects in regulation of the methanol utilization pathway. J Bacteriol. 187(16):5552-59.
I am interested in chemical transformations across redox boundaries in aquatic environments, with a particular interest in submicron particles and their role in global elemental fluxes.
During my PhD I studied iron and sulfur dynamics in marine systems. This work included synthesis of pyrite nanoparticles in order to study their formation and oxidation. I also spent time at sea researching hydrothermal vent chemistry, including the prevalence of pyrite nanoparticles in hydrothermal emissions.
During my postdoctoral research, I will be furthering my research of mineral formation and dissolution to include the role of microbes in these processes. I am especially interested in the deep ocean, including hydrothermal vents and the basaltic crust.
- Gartman A., Yücel, M and G.W. Luther, III. An Introduction to the Major Chemical Components Released from Hydrothermal Vents. In Press, Earth Systems and Environmental Sciences.
- Gartman A., A.J. Findlay, and G.W. Luther, III. 2014. Nanoparticulate pyrite and other nanoparticles are a widespread component of hydrothermal vent black smoker emissions. Chemical Geology, 366, 32-41.
- Gartman A. and G.W. Luther, III. 2013. Comparison of pyrite (FeS2) synthesis mechanisms to reproduce natural FeS2 nanoparticles found at hydrothermal vents. GCA, 120, 447-458
- Beinart, R.A., B. Faure, J.G. Sanders, S.P. Sylva, R.W. Lee, E.L. Becker, A. Gartman, G.W. Luther III, J.S. Seewald, C.R. Fisher, and P.R. Girguis. 2012. Regional- scale habitat partitioning by hydrothermal vent symbioses. Proceedings of the National Academy of Science PLUS, 109, E3241-E3250
- Luther, G.W., A. Gartman, M. Yücel, A.S. Madison, T.S. Moore, H.A. Nees, D.B. Nuzzio, A. Sen, R.A. Lutz, T.M. Shank, C.R. Fisher. 2012. Chemistry, Temperature, and Faunal Distributions at Diffuse Flow Hydrothermal Vents: Comparison of Two Geologically Distinct Ridge Systems. Oceanography, 25(1): 234-245
- Gartman A., M. Yücel, A.S. Madison, D.W. Chu, S. Ma, C. P. Janzen, E.L. Becker, A. Sen, C.R. Fisher, R.A. Beinart, P.R. Girguis, and G.W. Luther, III. 2011. Sulfide Oxidation Across Diffuse Flow Zones of Hydrothermal Vents. Aquatic Geochemistry 17, 583-601
- Yücel, M., A. Gartman, C.S. Chan, and G.W. Luther, III. 2011. Hydrothermal vents as a kinetically stable source of iron-sulphide-bearing nanoparticles to the ocean. Nature Geoscience, 4, 367-371
My research is motivated by the desire to understand the ecological function of different groups of microorganisms. I am fascinated about the vast diversity of microbes and their versatile ecophysiological lifestyles that sustain the global recycling of nutrients. I am particularly interested in the coupling of different biogeochemical cycles eg. nitrogen cycling to carbon and sulfur cycling. Further interests are the specialization and interactions within microbial communities, processes that drive population dynamics and bioenergetical aspects of microbial metabolism.
During my Ph.D. at the Max Planck Institute for Marine Microbiology in Bremen, I investigated the competition between different nitrate reducing pathways: denitrification and dissimilatory nitrate reduction to ammonium. To answer this question I combined continuous cultivation in chemostats with stable isotope labeling experiments and metagenomics and transcriptomics. For my postdoc I am interested in the metabolic capacities of microbes in deep oceanic crustal fluids. Again, a special interest lies in the biogeochemical cycling of nitrogen and sulfur.
- Kraft, B., Tegetmeyer, H.E., Sharma, R., Klotz, G., Ferdelman, T.G., Hettich, R.L., Geelhoed, J.S., and Strous, M. (2014) The environmental controls that govern the end product of bacterial nitrate respiration. Science (in press).
- Kraft, B., Tegetmeyer, H.E., Meier, D., Geelhoed, J.S., & Strous, M. (2014) Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture. Environmental microbiology (published online).
- Hanke, A., Hamann, E., Sharma, R., Geelhoed, J.S., Hargesheimer, T., Kraft, B., Meyer, V., Lenk, S., Osmers, H., Wu,R., Makinwa, K., Hettich, R. L., Banfield, J.F., Tegetmeyer, H.E., and Strous, M. (2014) Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha-and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Frontiers in Microbiology. 5: 231.
- Strous, M., Kraft, B., Bisdorf, R. and Tegetmeyer H.E. (2012) The binning of metagenomic contigs for microbial physiology of mixed cultures. Frontiers in Microbiology. 3: 410.
- Kraft, B., Engelen, B., Goldhammer, T., Lin, Y.S., Heuer, V., Cypionka, H. and Könneke, M. (2012) Members of the genus Desulfofrigus dominate sulfate-reducing enrichment cultures from sediments of the Benguela upwelling area. FEMS Microbiology Ecology. 84: 86-97.
- Kraft, B., Strous, M., and Tegetmeyer, H.E. (2011) Microbial nitrate respiration - genes, enzymes and environmental distribution. Journal of Biotechnology 155 (1) 104-117.
I am a geomicrobiologist. I am interested in understanding how microorganisms cope in extreme environments and in defining the physical limits for microbial life on Earth. I am also investigating biomineralization processes in modern and ancient environments. My research consists mainly of performing experiments in the lab using microbial cultures or environmental samples. I use a combination of spectroscopic and imaging techniques – including cutting-edge synchrotron methods – to obtain information on microbe-mineral interactions at various scales. My current project is a joint work between the Clarke Group (SEAS) and the Girguis Lab and is aimed at evaluating the potential for microorganisms to produce thin pyrite films for solar cell technology.
I come from France, where I obtained my doctoral degree in 2007 at the University of Lyon. In 2008 I moved to Germany where I have done research at the Max Planck Institute for Marine Microbiology in Bremen, and at the University of Tübingen. I joined the Girguis Lab in March 2014.
I never go anywhere without my camera… http://fotomato.tumblr.com
I am a marine microbiologist. I have always been fascinated by the question of how life on our planet works on the micro- and global scale. These questions have ultimately led me to study marine microorganisms, because they are keyplayers in the global cycling of elements.
I did both my M.Sc. and Ph.D. in the laboratory of Prof. Friedrich Widdel and as part of the MarMic program at the Max Planck Institute for Marine Microbiology in Bremen (Germany). During my Ph.D., I investigated the degradation of short-chain and cyclic alkanes by sulfate-reducing microorganisms from marine hydrocarbon seeps. I focused on the types of sulfate-reducing microorganisms capable of degrading these alkanes and the involved activation mechanisms. Over time, I became more interested in microbiological transformations of carbon compounds in deep marine sediments and how these influence the cycling of elements and the flux of energy in marine sediments. After my Ph.D., I then joined the Girguis laboratory in November 2011, because I wanted to investigate such processes coupled to different electron acceptors, as well as under in situ pressure conditions. In my research, I use interdisciplinary approaches in order to identify the microbial keyplayers and the types of transformation reactions involved in the alteration of the organic carbon pool. I use molecular biology methods (PCR, qPCR, clone libraries, CARD-FISH, stable isotopes, nanoSIMS), classical- (aerobic and anaerobic enrichment cultures, physiological- and biochemical experiments,) and innovative (high pressure incubation systems, microbial fuel cells) cultivation techniques, as well as analytical chemistry (GC-IRMS, FT-ICR-MS). I hope that I will be able to contribute to our understanding of the global carbon cycle and how it is linked to the microbial alteration of organic matter in the deep marine subsurface biosphere.
Erika A. Parra
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.
Daniel Rogers is currently a Postdoctoral Fellow in the Department of Earth and Planetary Sciences at Harvard University. Daniel is a geomicrobiologist, trained in equal parts as a microbiologist and geochemist. He is interested in the interplay of the nitrogen and sulfur cycles, and understanding the biological signatures imparted by organisms involved in these cycles in the environment. He uses modern molecular microbiological and state-of-the-art stable isotope techniques to decipher the players (who), processes (what) and rates of reaction (how fast) within the environmental context. His work spans both coastal and deep sea environments.
Daniel received his Ph.D. through the MIT- WHOI Joint Program in Chemical Oceanography where he worked with Dr. Karen Casciotti (now at Stanford). His thesis work focused on the Geomicrobiology of Nitrogen in a Coastal Aquifer: Isotopic and Molecular Methods to Examine Nitrification and Denitrification in a Coastal Groundwater. He also has earned a M.S. and B.S. from the University of Connecticut.
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.
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.
- Adams MM, Hoarfrost AL, Bose A, Joye SB, Girguis PR. Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity. Frontiers in Microbilogy (2013)
- Adams MM, Wankel SD, Johnston DT, Hansel CM, Joye SB, Girguis, PR. Anaerobic methane oxidation in metalliferous hydrothermal sediments: influence on carbon flux and decoupling from sulfate reduction. Environmental Microbiology (2012)
- Adams MM, Hoarfrost AL, Joye SB, Girguis, PR. Activity, distribution, and function of C2-C4 alkane degrading phylotypes in metalliferous, hydrothermal vent sediments. (Manuscript in preparation for Frontiers in Extreme Microbiology Special Edition)
- Bose A, Rogers D, Adams MM, Delaney J, Girguis, PR. Anaerobic short chain alkane degradation in Gulf of Mexico sediments is linked to sulfate reduction. (Manuscript in preparation)
- Adams MM, Gómez-García MR, Grossman AR, Bhaya, D. Phosphorus deprivation responses and phosphonate utilization in a thermophilic Synechococcus sp. from microbial mats. Journal of Bacteriology (2008)
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.
My love for microbes began when I was a kid, looking at pond scum through my father's old microscope. It was, and still is, amazing to me that there's a whole world we can't see. This interest let me to major in microbiology at the University of South Florida, where I became very interested in microbial metabolism. Specifically, how microbes acquire and use energy. I only came to the Girguis lab this fall (2013), so I don’t know exactly what I’ll be working on yet. I’m very excited to be here, though, and I can’t wait to explore questions about microbial metabolism and how it effects the world around us.
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.
I am interested in how microorganisms interact with their surroundings and subsequently play a major role in our Earth’s biogeochemistry. Specifically, I study how microorganisms interact with solid-phase materials as electron acceptors and donors during metabolism. These questions can be explored using bioelectrical systems (BESs) which separate the locations of oxidation and reduction reactions and allow the anaerobic microorganisms to use an electrode either as a donor or an acceptor. These systems have several energy and environmental applications so understanding these mechanisms is an important step towards the development of these technologies.
My research examines both environmental and pure culture systems to identify limitations of BESs and discover how microbes are capable of using an electrode during metabolism. One project investigated the degree of diffusion limitation through duty cycling and how it influences overall current production. Another project explores how methane-producing microbes can use a supplied electrode as an electron donor.
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?
I am fascinated by the overlap of geology and biology that is fundamental to hydrothermal vent environments. I come from a geology/environmental science background, and I study microbial ecology within hydrothermal vent chimney walls. I am interested in better understanding the mechanisms and scale of carbon cycling at hydrothermal vents. To do this, I am working to quantify rates of carbon fixation and investigate the distribution of different carbon fixation pathways in hydrothermal vent environments. I am also interested in microbe-mineral interactions, and I am investigating the role that mineralogy plays in microbial community structure and succession in diffuse flow environments. It is my long-term goal to increase our understanding of how biological and geological processes interact in the deep sea. Additionally, I care deeply about science education and working to build scientific curiosity and understanding among Americans of all ages.
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.
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.
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.
I currently serve as the Girguis lab manager, where I can be found doing anything from ordering to lab organization to research. I am a marine scientist by training and received my M.S. from the University of South Florida. My thesis research was in the development of molecular detection assays for the neurotoxin-producing diatom genus Pseudo-nitzschia. I then worked as a technician at USF, participating in research cruises and performing toxicity assays in response to the Deepwater Horizon oil spill. In my free time, I enjoy cooking, camping, and traveling!
Research Lab Coordinator
As a Lab technician in the Girguis lab I assist in a variety of tasks; from refreshing our amazing collection of specimens from the deep to helping rebuild our mobile lab unit. I received my B.S. from UMass Boston where I majored in ecology and evolution. I plan on continuing my education in a graduate program where I hope to study symbiotic interactions between bacteria and their invertebrate hosts. I am drawn to this line of research due to its relevance to the biogeochemical cycle in the oceans as well as the paradigm shifting implications of such associations as they relate to evolution.
Outside of the lab, I enjoy sharing my enthusiasm of the natural world, great literature, philosophizing and good food with my husband and two daughters.
Currently, I am a lab tech/manager in the Girguis lab. As a new hire (August 2012), I'm still finding my way around the lab, but am excited to eventually be the guy that people goes to when they need something fixed, designed, built, or just to figure out how it works. Though my education is in Engineering Physics, I've always found myself associated with biology laboratories. Most recently I was working as the tech/manager for the ICP-MS facility in the Marine Biology department at the University of Southern California. I enjoy working with high-tech instrumentation, computers, mechanical systems, and pretty much anything, as long as I can get my hands on it and there is a manual for it. Oh yeah, I love manuals. As a tall (198 cm), red-head with a full beard, I tend to stand out just a little bit. Aside from my work, I am an avid gamer (computer, card, board, pen and paper, whatever), consider myself fairly good with computer hardware and software, and love gadgets of any kind.
Assistant Professor of Biology - Temple University
Assistant Professor of Molecular and Cell Biology - University of Connecticut
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.
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.
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.
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.
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.
MEGAMER Postdoctoral Researcher - University of California, Santa Cruz
Assistant Professor of Chemistry - Haverford College
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.