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Dr. Florence Schubotz


Organic Geochemistry


Independent PostDoc and Lecturer


+49 421 218-65724


+49 421 218-65715



MARUM Pavillon

Dr. Florence Schubotz
I'm a research scientist funded by the Central Research Development Fund of the University of Bremen. At the MARUM I'm affiliated to the Organic Geochemistry group of Kai-Uwe Hinrichs.
I can also be reached with this email adress: [Bitte aktivieren Sie Javascript]

Photo: Harald Rehling

Research Interests

I'm a biogeochmist studying the interactions of microorganisms with their surrounding environment. The number of metabolic reactions microbes can perform are vast and so are the types of habitats they can live in. I am particularly interested in studying microbial communities that live in extreme environments, such as hot springs, cold seeps, hypersaline lakes and the oligotrophic ocean. My main line of research lies in investigating microbial physiological response to environmental change, but also how microorganisms shape and modify their surrounding environment.
To investigate the microbial ecophysiology I use the taxonomic, metabolic and physiologic information encoded in cellular membrane lipids. Together with the analyses of metabolites and other organic molecules I gain insights on the role microbes play in the flow and fate of organic matter in ecosystems.

Current Research Projects

Survival of the fittest: Unraveling the role of membrane lipids in physiological adaptations of marine bacteria
Collaborators: Tanja Bosak (MIT, USA), Otto Geiger (CCG and UNAM, Mexico)

With this project I intend to shed light into physiological response mechanisms of marine bacteria by investigating modifications of their membrane lipids under environmental stress. Cellular membrane lipids are vital components that help cells acclimate to changing environmental conditions. In the ocean, membrane lipid changes have been reported with temperature, salinity and nutrient limitation. In particular aminolipids, such as betaine and ornithine lipids, have been shown to be sensitive to environmental stress. Despite being major lipids in the ocean, their biological sources are in many cases still unknown. With my research I want to exploit the vast potential these compounds harbor as ecological markers. My goal is to combine targeted genetic and lipid-based techniques to identify sources and functions of aminolipids and other polar lipids in the marine environment.
Asphalt volcanism in the southern Gulf of Mexico: Biotic and abiotic processes involved in oil degradation
Collaborators: Gerhard Bohrmann (Uni-Bremen, Germany), Gunter Wegener (MPI Bremen, Germany), Chris Reddy (WHOI, USA), Elva Escobar (UNAM, Mexico)

Oil pollution and the persistence of hydrocarbons in the marine environment is of high ecological significance and greatly depends on the composition of the respective oil. Naturally occuring hydrocarbon seeps provide a unique chance to study long-term compositional changes of oil in the marine evironment and its effects on ecosystems. Deposits of heavy oil and asphalt in the southern Gulf of Mexico forms the basis of a natural ecosystem with a thriving cold seep community including tube worms, mussels, sea cucumbers and crabs. With this project I seek to unfold postdepositional mechanisms involved in the biotic and abiotic degradation of heavy oils and test the efficient recycling of petroleum compounds by microorganisms. Insights into these processes can aid future mitigations of oil spills.

Photo: Stephanie von Neuhoff

Photo: Patrizia Geprägs

Seafloor image: Copyright MARUM

Photo: Christian Rohleder

Life in extreme environments: Adaptations and microbial community dynamics in hot springs and shallow hydrothermal vents
Collaborators: Roger Summons (MIT, USA), Everett Shock (ASU, USA), Eric Boyd (MSU, USA), Jan Amend (USC, USA), Anke Meyerdierks (MPI Bremen, Germany)

The terrestrial hot springs of Yellowstone National Park and the shallow marine hydrothermal vents in northen Sicily serve as comparative models for non-marine and marine environments for conditions that might have prevailed throughout Earth‟s history and thus may provide windows into the early evolution of life on Earth. Both systems contain microbial communities that are adapted to extreme conditions at the limit of life, such as extremely high temperatures, strong variations in pH and other extreme geochemical gradients. We are using a combination of intact polar membrane lipid analysis and molecular biological tools to characterize physiological adaptations and metabolic capacities of microbial communities in these two distinct environments.

Curriculum Vitae

2014-presentResearch Assistant and Lecturer, University of Bremen & MARUM
2013-2014Research Associate, MIT, USA
2011-2013Research Fellow (Feodor-Lynen Fellowship, Alexander von Humboldt Society), MIT, USA
2009-2010PostDoc, MARUM & University of Bremen
2009PhD, University of Bremen
2006-2009 PhD candidate, Advisor K-U Hinrichs
2007-2009 Member of international graduate school GLOMAR
2005M.Sc., University of Bremen
2002Vordiplom, Carl-von-Ossietzly University Oldenburg
2002-2003 ERASMUS at Universidad the Las Palmas de Gran Canaria, Spain

Publications (peer-reviewed)

2016Sahling, H., Rubin Blum, M., Borowski, C., Escobar-Briones, E., Gaytán-Caballero, A., Hsu, C.-W., Loher, M., McDonald, I., Marcon, Y., Pape, T., Römer, M., Schubotz, F., Smrzka, D., Wegener, G., Bohrmann, G. (2016) Seafloor observations at Campeche Knolls, southern Gulf of Mexico: coexistance of asphalt deposits, oil seepage and gas venting. Biogeosciences Discussion Article doi:10.5194/bg-2016-101
Bosak, T., Schubotz F., Santiago-Torio, A., Kuehl, J., Carlson, H.K., Summons, R.E., Arkin, A.P., Deutschbauer, A.M. (2016) System-wide adaptations of Desulfovibrio alaskensis G20 to phosphate-limited conditions. PLoS ONE 11(12): e0168719. doi.org/10.1371/journal.pone.0168719
2015Klein, F., Humphris, S.E., Guo W., Schubotz, F., Schwarzenbach, E.M., Orsi, E.D. (2015) Fluid Mixing and the deep biosphere of a fossil Lost City-type hydrothermal system at the Iberia Margin. Proceedings of the National Academy of Sciences, 112:12036-12041. doi:10.1073/pnas.1504674112
Segarra, K.E.A., Schubotz, F., Samarkin, V., Yoshinaga, M.Y., Hinrichs, K.-U., Joye, S.B. (2015) Anaerobic oxidation of methane reduces methane fluxes from freshwater wetlands. Nature Communications, 6:7477. doi:10.1038/ncomms8477
Escobedo-Hinojosa, W.I., Vences-Guzmán, M.A., Schubotz, F., Sandoval-Calderón, M., Summons, R.E., López-Lara, I.M., Geiger, O., Sohlenkamp, C. (2015) OlsG (Sinac_1600) is an ornithine lipid N-methyltransferase from the planctomycete Singulisphaera acidiphila. Journal of Biological Chemistry, 290:15102-15111. doi: 10.1074/jbc.M115.639575
Schubotz, F., Hays, L.E., Meyer-Dombard, D.R., Gillespie, A., Shock, E., Summons, R. (2015) Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs. Frontiers in Microbiology, 6:42. doi:10.3389/fmicb.2015.00042
2014Biller, S., Schubotz, F., Roggensack, S., Thompson, A., Summons, R., Chisholm, S.W. (2014) Bacterial vesicles in marine ecosystems. Science 343, 183-186
Xie, S., Liu, X.-L., Schubotz, F., Wakeham, S.G., Hinrichs, K.-U. (2014) Distribution of glycerol ether lipids in the oxygen minimum zone of the Eastern Tropical North Pacific Ocean. Organic Geochemistry 71, 60-71.
2013Edgcomb V.P., Bernhard J.M., Beaudoin D., Pruss S., Welander P.V., Schubotz F., Mehay S., Gillespie A.L., Summons R.E. (2013) Molecular indicators of microbial diversity in oolitic sands of Highborne Cay, Bahamas. Geobiology 11, 234-251.
Raggi, L., Schubotz, F., Hinrichs, K.-U., Dubilier, N., Petersen, J.M. Bacterial symbionts of Bathymodiolus mussels and Escarpia tubeworms from Chapopote, an asphalt seep in the southern Gulf of Mexico. (2013) Environmental Microbiology 15, 1969-1987.
Schubotz F., Meyer-Dombard D.R., Bradley A.S., Fredricks H.F., Hinrichs K.-U., Shock E.L., Summons R.E. (2013) Spatial and temporal variability of biomarkers and microbial diversity reveal metabolic and community flexibility in streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park. Geobiology 11, 549-569.
2012Bühring, S.I., Schubotz, F., Harms, C., Lipp, J.S., Amils, R. and Hinrichs, K.-U. (2012) Lipid signatures of acidophilic microbial communities in an extreme, acidic environment: Río Tinto, Spain. Organic Geochemistry 47, 66-77.
Kellermann, M.Y., Schubotz, F., Elvert, M., Lipp, J.S., Birgel D., Prieto Mollar, X., Dubilier N., Hinrichs, K.-U. (2012) Symbiont-host relationships in chemosynthetic mussels: A comprehensive lipid biomarker study. Organic Geochemistry 43, 112-124.
Wakeham, S.G., Turich, C., Schubotz, F., Podlaska, A., Li, X.N., Varela, R., Astor, Y., Sáenz, J.P., Rush, D., Sinninghe Damsté, J.S., Summons, R.E., Scranton, M.I., Taylor, G.T. and Hinrichs, K.-U. (2012) Biomarkers, Chemistry and Microbiology Show Chemoautotrophy in a Multilayer Chemocline in the Cariaco Basin. Deep Sea Research I 63, 133-156.
2011Schubotz, F., Lipp, J.S., Elvert and Hinrichs K.-U. (2011) Stable carbon isotopic composition of intact polar lipids reveal complex carbon flow patterns among hydrocarbon degrading microbial communities at the Chapopote asphalt volcano. Geochimica et Cosmochimica Acta 75, 4377-4398.
Schubotz, F., Lipp, J.S., Elvert, M., Kasten, S., Prieto-Mollar, X., Zabel, M., Bohrmann, G. and Hinrichs K.-U. (2011) Petroleum degradation and associated microbial signatures at the Chapopote asphalt volcano, Southern Gulf of Mexico. Geochimica et Cosmochimica Acta 75, 4399-4415.
Yoshinaga M.Y., Kellermann M.Y, Rossel P.E., Schubotz F., Lipp J.S., Hinrichs, K.-U. (2011) Systematic fragmentation patterns of archaeal intact polar lipids by high-performance liquid chromatography/electrospray ionization ion-trap mass spectrometry. Rapid Communications in Mass Spectrometry 25, 1-12.
2010Borin, S., Ventura, S., Tambone, F., Mapelli, F., Schubotz, F., Brusetti, L., Scaglia, B., D’Acqui, L., Solheim, B., Turicchia, S., Hinrichs, K.-U., Baldi, F., Adani, F. and Daffonchio, D. (2010) Rock weathering creates oases of life in a high arctic desert. Environmental Microbiology 2, 293-303.
Lichtschlag, A., Felden, J., Wenzhöfer, F., Schubotz, F., Ertefai, T., Boetius, A. and deBeer, D. (2010) Methane and sulfide fluxes in permanent anoxia: in situ studies at the Dvurechenskii mud volcano (Sorokin Through, Black Sea). Geochimica et Cosmochimica Acta 74, 5002-5018.
Rethemeyer, J., Schubotz, F., Talbot, H.M., Cooke, M.P., Hinrichs, K.-U. and Mollenhauer, G. (2010) Distribution of polar membrane lipids in permafrost soils and sediments of a small Arctic catchment. Organic Geochemistry 41, 1130-1145. 

2009Schubotz, F., Wakeham, S.G., Lipp, J.S., Fredricks, H.F. and Hinrichs, K.-U. (2009) Detection of microbial biomass by intact polar membrane lipid analysis in the water column and surface sediments of the Black Sea. Environmental Microbiology 11(10), 2720-2734. 

2008Strapoc, D., Picardal, F.W., Turich, C., Schaperdoth, I., Macalady, J.L., Lipp, J.S., Lin, Y.-S., Ertefai, T.F., Schubotz, F., Hinrichs, K.-U., Mastalerz, M. and Schimmelmann, A. (2008) An analysis of the methane-producing microbial community in a coal bed of the Illinois Basin. Applied and Environmental Microbiology 74(8), 2424-2432.