I'm a research scientist affiliated to the Organic Geochemistry group of Kai-Uwe Hinrichs.
I'm a geobiologist 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 the Earth'*s crust, 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.
Life in extreme environments: Adaptations and microbial community dynamics in hydrothermal systems, crustal rocks and the deep biosphere
Collaborators: Frieder Klein (WHOI, USA), Virginia Edgcomb (WHOI, USA), Jason Sylvan (TAMU, USA), William Orsi (LMU, Germany)
Some of the most challenging environments for life are found within deeply buried sediments and basement rocks, where temperatures and pressures are high and pore space and water availability are low. Such sites also serve as comparative models for conditions that have prevailed throughout Earth‟s history and thus may provide windows into the early evolution of life on Earth and elsewhere. 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 unique microbial habitats.
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), Gregory Ventura (SMU, Canada), 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.
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.
|2014-present||Research Assistant and Lecturer, University of Bremen & MARUM|
|2013-2014||Research Associate, MIT, USA|
|2011-2013||Research Fellow (Feodor-Lynen Fellowship, Alexander von Humboldt Society), MIT, USA|
|2009-2010||PostDoc, MARUM & University of Bremen|
|2009||PhD, University of Bremen|
2006-2009 PhD candidate, Advisor K-U Hinrichs
2007-2009 Member of international graduate school GLOMAR
|2005||M.Sc., University of Bremen|
|2002||Vordiplom, Carl-von-Ossietzly University Oldenburg|
2002-2003 ERASMUS at Universidad the Las Palmas de Gran Canaria, Spain
|2019||Zhuang G-C, Montgomery A, Song M, Liu J, Schubotz F, Teske A, Hinrichs K-U, Joye SB. Generation and utilization of volatile fatty acids and alcohols in hydrothermally altered sediments of the Guaymas Basin. In press Geophysical Research Letters. doi.org/10.1029/2018GL081284|
Imachi H, Tasumi E, Takaki Y, Hoshino T, Schubotz F, Gan S, Tu T-H, Saito Y, Yamanaka Y, Ijiri A, Matsui Y, Morono Y, Takai K, Hinrichs K-U, Inagaki F (2019) Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation. Scientific Reports, 9:2305. doi.org/10.1038/s41598-019-38754-w
|2018||Schubotz, F., Xie, S., Lipp J.S., Hinrichs, K.-U., Wakeham, S. Diversity of intact polar lipids in the oxygen minium zone of the Eastern Tropical North Pacific: Biogeochemical implications of non-phosphorus lipids (2018) Biogeosciences, 15:6481-6501. doi.org/10.5194/bg-15-6481-2018|
Hamada Y, Hirose T, Ijiri A, Yamada Y, Sanada Y, Saito S, Sakurai N, Sugihara T, Yokoyama T, Saruhashi T, Hoshino T, Kamiya N, Bowden S, Cramm M, Henkel S, Homola K, Imachi H, Kaneko M., Lagostina L, Manners H, McClelland H-L, Metcalfe K, Okutsu N, Pan D, Raudsepp MJ, Sauvage J, Schubotz F, Spivack A, Tonai S, Treude T, Tsang M-Y, Viehweger B, Wang DT, Whitaker E, Yamamoto Y, Yang K, Kinoshita M, Maeda L, Kubo Y, Morono Y, Inagaki F, Heuer VB (2018) In-situ mechanical weakness of subducting sediments beneath a plate boundary décollement in the Nankai Trough Progress in Earth and Planetary Science 5:70.
|Carr, S., Schubotz, F., Dunbar, R., Mills C., Dias, R.R., Summons, R.E., Mandernack, K. (2018) Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments. The ISME Journal 12:330-342.|
|2016||Sahling, 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|
|2015||Klein, 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|
|2014||Biller, 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.|
|2013||Edgcomb 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.|
|2012||Bühring, 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.|
|2011||Schubotz, 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.|
|2010||Borin, 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.|
|2009||Schubotz, 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.|
|2008||Strapoc, 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.|
|Schubotz, F. (2018) Membrane Homeostasis upon Nutrient (C, N, P) Limitation. In: Geiger O. (eds) Biogenesis of Fatty Acids, Lipids and Membranes. Handbook of Hydrocarbon and Lipid Microbiology. Springer Cham.|