Guest Scientists

Guest, October 2007-February 2008

In April 2007 I completed my diploma thesis in human genetics on the nuclear topology of ultra-conserved non-coding sequences (UCS) in embryos of mouse and chicken models, at the Ludwig-Maximilians-University in Munich, Germany. Previously, I applied the techniques of RNA in situ hybridization (RNAISH), DNA-FISH, M-FISH and fluorescence-, as well as confocal laser scanning microscopy. Due to my passion for diving, I discovered my strong interest in marine sciences. Since June 2007 I am a member of the research group of Dr. Christian Wild, GeoBio-Center LMU Munich, working on warm-water coral exudates. During my internship at the MPI I will be assisting Sandra Schoettner with her PhD thesis project concerning microbial ecology of cold-water coral ecosystems. Under the supervision of Dr. Alban Ramette I will extract DNA from deep-sea corals, learn ARISA, cloning, sequencing and CARD-FISH.

Visiting student January 2008

I am a master student at the University of Bergen in Norway. The aim of my thesis is to describe the associated microbes involved in the sulfur cycle of the cold-water sponge Geodia barretti. I am using culture-independent methods as DGGE, 16SrRNA sequencing and functional gene analysis. During my visit in Bremen, I aim to develop specific oligonucleotide probes for my target microbes and apply them on sponge tissue sections (FISH and Clone-FISH).

Masters Student, Universidad Nacional Autonoma de Mexico (UNAM) Laboratory of Dr. Elva Escobar - Mexico City, Mexico
October – December 2007

Gerardo Ramon is completing a masters thesis at the National Autonomous University of Mexico (UNAM) as a student of Professor Elva Escobar. His thesis topic concerns the study of the ecology of the holothurian Chiridota heheva, found in the asphalt volcano habitat of the southern Gulf of Mexico, at approximately 3000 meter depth. While his academic interest is in describing the habitat, the diet, and the patterns of distribution of this holothurian species, his work as a guest of the Habitat Group concerned elucidating the microbial communities of various locales within the asphalt volcano area using a DNA fingerprinting technique (ARISA) and the creation of 16S rRNA-based clone libraries. While in Bremen, Gerardo Ramon also cooperated with members of Prof. Gerhard Bohrmann’s laboratory, at the University of Bremen.
(gerardolunavyahoo.com.mx)

Internship July – September 2007

Ich studiere Angewandte Naturwissenschaften an der TU Bergakademie Freiberg im 6.Semester. Im Moment vertiefe ich die naturwissenschaftlichen Grundlagen der Biotechnologie. In meiner Freizeit gehe ich sehr gerne tauchen und interessiere mich somit sehr für die Unterwasserwelt. Im August und September 2007 absolviere ich ein Praktikum in der Habitat Gruppe unter der Betreuung von Friederike Hoffmann.

Visiting scientist July 2007

I am a PhD student at the University of Bergen in Norway. I work with procaryotes associated to the seaweed Laminaria hyperborea along the Norwegian coast using culture independent methods. During my visit in Bremen in July 2007 I aim to adapt the CARD-FISH method to visualize bacteria on the surface of seaweeds in collaboration with Friederike Hoffmann.

Undergraduate student, Jacobs University Bremen - January 2007

Majoring in Biochemistry and Cell Biology, I joined the Habitat group for one of my guided research laboratory rotations in January 2007. Under the supervision of Dr. Alban Ramette I worked on the purification of microbial DNA from deep sea sediment samples. The aim of the project was to improve the yield and further minimize the contamination of the DNA extracts. I learned new PCR techniques and got to experience what marine molecular ecology work is like. I did not have any previous lab exposure to marine microbiology, making this work particularly interesting for me.

Undergraduate student, Jacobs University Bremen - January 2007

I am an Undergraduate student at Jacobs University Bremen, Germany from Nepal majoring in Biology. My interests in Microbiology and Astrobiology were fostered further by my internship during the Winter break at the Habitat group of Professor Antje Boetius. Under the guidance of Viola Beier, I learnt various techniques like DNA extraction from sediments, DNA insert ligation into a vector and bacterial transformation. I will graduate from Jacobs University Bremen in June 2008. I am going to DTU (Technical University Denmark) this summer for an internship on biofilms under the guidance of Professor Søren Molin.

When I was a senior student at Jacobs University Bremen (2005-2006), I had an internship in Prof. Dr Antje Boetius’ Lab under the guidance of Dr. Alban Ramette. Our focus was to optimize the ARISA (automated ribosomal intergenic spacer analysis) protocol by comparing some of the parameters used in the protocol. ARISA is a culture independent method that allows rapid, easy and precise investigation of microbial diversity at the intraspecific level. Along with testing the ARISA parameters, we also investigated the reproducibility of the results and the capability of ARISA in detecting the similarities between bacterial communities from different samples. This hands-on research experience at the MPI stimulated my interest in microbiology further and I decided to continue working with microbes post college graduation. Currently I am doing my master’s in biology at University of San Francisco in Prof. Dr Juliet V. Spencer’s lab and my master’s project is about immunomodulation by rhesus cytomegalovirus .

Ph.D. Student, University of Aveiro, Aveiro, Portugal
January – February 2006

I am a Ph.D. student at the University of Aveiro, Portugal where I am working in the laboratories of Maria A. Cunha and Luis M. Pinheiro. Within the framework of the CRUP-ICCI/DAAD Portuguese/German joint research program “Geosphere/Biosphere coupling processes in the Gulf of Cadiz” – (A-15/04; Boetius, Pinheiro), I analysed lipid biomarkers in sediments from submarine mud volcanoes in the Gulf of Cadiz. The aim of this work was to investigate microbial communities related to past and present methane seepage. The work was carried out in Microbial Habitat Group of Antje Boetius and was supervised by Helge Niemann, who gave me an introduction in the theoretical and technical background of lipid analysis and helped me with interpretation of the results.

Ph.D. student, University of Georgia, Department of Marine Sciences, Athens, GA, USA
December 2005 - March 2006

I am a Ph.D. student at the University of Georgia, Athens, GA, USA, working with Dr. Samantha Joye in the Department of Marine Sciences. The central theme of my research is understanding the microbial communities which perform anaerobic oxidation of methane, sulfate reduction and methanogenesis in gassy and/or oily sediments from methane seeps (in the Gulf of Mexico) and the deep biosphere (under Hydrate Ridge). I am using an interdisciplinary approach to do this, combining geochemical analyses, radiotracer measurements of microbial activity, computer modeling, lipid biomarker characterization, and molecular ecological techniques. Supported by a National Science Foundation Graduate Research Fellowship, I have made repeat visits to Bremen to make use of the state-of-the-art technology and expertise in the fields of molecular ecology and lipid biomarkers. My sincerest thanks go to Prof. Antje Boetius, my gracious host; Dr. Katrin Knittel, Tina Loesekann and Viola Beier of the MPI Department of Molecular Ecology for teaching me to FISH and in other aspects of molecular ecology; and Dr. Kai-Uwe Hinrichs, Dr. Marcus Elvert and Julius Lipp of the Research Center Ocean Margins for assistance with lipid biomarker analysis.

Professor of Oceanography, University of Hawaii at Manoa, USA
October 2005 – January 2006

My collaborations at the Max Planck Institute focus on (1) microbial processes on large organic falls (whale, wood and kelp falls) and (2) temperature-substrate limitation of microbial metabolism in high latitude sediments.
It is know well known that whale falls create sulfide-rich reducing habitats at the deep-sea floor, but the rates of sulfate reduction and microbial anaerobic metabolism on lipid-rich whale bones remained poorly known. In collaboration with Antje Boetius, Hans Roy and Frank Wenzhöfer, we are conducting laboratory studies of sulfur, methane and oxygen cycling in microbial assemblages on minke whale bones. We are also using ROV and submersible based photographic surveys to map the development of microbial mats and reducing conditions on whale falls at the deep-sea floor. These studies will provide key insights into the quality and scales of reducing habitats afforded by sunken whales and other large organic falls in deep-sea ecosystems. While at MPI, I also plan to develop collaborative studies with Antje Boetius to test the hypothesis that at very low seawater temperatures, microbial exoenzymes become less efficient, yielding a requirement by heterotrophic bacterial communities for higher concentrations of organic substrates to maintain particular rates of community metabolism and organic-matter oxidation. This hypothesis is supported by our recent studies of Antarctic sediments and merits rigorous testing. If it is correct, climate warming in high latitudes might significantly decrease the carbon storage capacity of shelf sediments and reduce food availability for detritivores, which key components of Antarctic benthic food webs.

PhD student, Renard Center for Marine Geology / Lab. of Microbial Ecology and Technology, Gent University, Belgium.
September – November 2005

Within the framework of the EURODOM European project, my thesis aim at studying the microbial ecology and biogeochemistry of carbonate mounds along the European margins. The rationale underlying this research is that these original deep-sea structures, often covered with cold-water corals, might be related to localized hydrocarbon seepage, including methane.
Under the supervision of Prof. Antje Boetius and Dr. Helge Niemann at the Habitat group, and thanks to an excellent cooperation with the technical staff, I learned how to measure turnover rates of anoxic methane oxidation (AOM) and Sulfate Reduction (SR) using radiotracer techniques. These techniques will be key tools to understand the carbonate mound’s genesis and stabilization processes. During my stay, I have also been introduced to several molecular methods in marine microbiology such as cell counting in sediment and FISH/Card-FISH cell staining.
And last, but not least, I could fully benefit from the expertise developed at the MPI through numerous helpful discussions with the staff from the different groups.
My warmest thanks to all of them!

Ph.D. student, University of North Carolina, Chapel Hill, USA
September 2005

I am a Ph.D. student at the University of North Carolina, Chapel Hill, working with Andreas Teske. I am investigating the anaerobic communities responsible for methane and sulfur cycling in estuarine sediments, methane seeps, and the deep oceanic subsurface. An intergral part of my research will be to quantify and obtain images of anaerobic methane-oxidizing consortia in low biomass sediments. Through a Doctoral Travel Fellowship from the University of North Carolina Center for International Studies, I was able to spend September of 2005 at the Max Planck Institute in Bremen learning how to perform catalyzed reporter deposition in situ fluorescence hybridization (CARD-FISH). I was hosted by both the Molecular Ecology Group led by Rudolf Amann and the Habitat Group led by Antje Boetius, with Katrin Knittel and Tina Loesekann providing day-to-day instruction. Thanks to the great training I received at the MPI, I plan to use CARD-FISH to analyze and quantify anaerobic methane-oxidizing communities in a North Carolina estuary, as well as those that underlie sulfide-oxidizing mats in Gulf of Mexico methane seeps.

Masters Student, Pennsylvania State University
March 2005 – September 2005

I am a Masters Degree student in Dr. Charles Fisher’s Deep-Sea Biology Lab at the Pennsylvania State University. I spent six months at the Max Planck Institute in Bremen working in the Habitat Group led by Antje Boetius. I conducted research for my Masters thesis involving interactions between hydrocarbon seep tubeworms and microbes in the surrounding sediment. These tubeworms require sulfide for energy, which is produced by sulfate reducing bacteria in the sediment. The tubeworms could be ‘farming’ microbes by releasing sulfate from their roots into the sediment. This would provide the tubeworms with a continuous supply of sulfide, allowing them to live for hundreds of years. To investigate this hypothesized relationship, I studied microbial biomass and diversity in the sediment using acridine orange cell counts, FISH and CARD FISH, and in vitro sulfate reduction rates.

Graduated student (bachelor)
July - August 2005

Through the support of the Research Center for Ocean Margins (RCOM) Summer Student Fellowship program, I spent two months at the Max Planck Institute working in the Habitat group of Antje Boetius. Under the advisement of Tina Treude, my research examined the sediment ecology at a deep-sea whale fall site off the coast of California. I measured in situ and enrichment bacterial counts as well as sulfate reduction and methanogenesis. I recently graduated from Bowdoin College in Brunswick, Maine where I
specialized in Biology with an emphasis on genetics. Next, I am headed to Boston to work as a laboratory technician in a breast cancer research lab at Massachusetts General Hospital.

Ph. D
November 2004 - March 2005

I want to continue with the challenge of exploring the biodiversity of unusual ecosystems in order to get more clues on the origin and evolution of life. I am now at the Max Planck Institute for Marine Microbiology (Bremen, Germany) where I have started to study the microbial community composition and functional diversity of a largely unexplored habitat, sunken woods in deep marine water environments, for which I have also got a Marie Curie postdoctoral fellowship starting on May 2005 at the Observatoire Oceanologique de Banyuls (France). Sunken woods are very interesting habitats from an evolutionary point of view. Degradation occurs by specific microbes and animal communities adapted to the use of woods or other high carbon content materials as substrates. It has been suggested that, at least for metazoans, these environments could act as stepping-stones for chemosynthetic communities that inhabit hydrothermal vents and cold seeps. However, nobody has studied the microbial component of sunken wood ecosystems or demonstrated the occurrence of anaerobic microbial communities in them.

Dr. Carmen Palacios @ Winter 2004-5

Professor, Department of civil and enviromental engineering, Massachusetts Institute for Technology (MIT), USA

September - December 2004

The overarching goal of our research is to develop means to predict the fates of organic chemicals in natural and engineered environments. To that end, we pursue studies of specific processes controlling compound fates. We emphasize field studies seeking to contrast modeling predictions with observations of the spatio-temporal distributions of organic compounds.

Research in the Gschwend Lab is currently focused on: (a) assessing the role of "black carbon" as a sorbent of organic compounds like PAHs and as a factor limiting those compounds' bioavailability, (b) developing and applying passive samplers suited to quantifying the chemical activities and inter-media gradients controlling transfers of organic compounds, and (c) using computational means to estimate physical chemical properties of synthetic organic compounds, thereby enabling evaluation of their environmental distributions BEFORE large quantities are produced and utilized.

As part of ESI, we are seeking to apply our knowledge of the cycling of xenobiotic organic compounds to anticipate how these substances may act as unwanted "drugs" interfering with the Earth's metabolism.

(taken from the personal web site of Prof. Geschwend at the MIT)

Link to the personal site at the MIT