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Faculty for Biology, Chemistry, and Earth Sciences

Experimental Biogeochemistry - Prof. Dr. Martin Obst

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List of publications

Peer reviewed


Ingino, P., Tiew, K., Obst, M.: Suitability of lectin binding studies for the characterization of redox-active microbial environmental biofilms. AMB Express, 12, No. 140 (2022).

Schaller, J., Wu, B., Amelung, W., Hu, Z., Stein, M., Lehndorff, E., Obst, M.: Silicon as a potential limiting factor for phosphorus availability in paddy soils. Scientific Reports, 12(1), No. 16329 (2022).

Pucetaite, M., Hitchcock, A., Obst, M., Persson, P., Hammer, E.: Nanoscale chemical mapping of exometabolites at fungal–mineral interfaces. Geobiology, 20(5), 650-666 (2022).

Elagami, H., Ahmadi, P., Fleckenstein, J., Frei, S., Obst, M., Agarwal, S., Gilfedder, B.: Measurement of microplastic settling velocities and implications for residence times in thermally stratified lakes. Limnology and Oceanography, 67(4), 934-945 (2022).


Gkoutselis, G., Rohrbach, S., Harjes, J., Obst, M., Brachmann, A., Horn, M., Rambold, G.: Microplastics accumulate fungal pathogens in terrestrial ecosystems. Scientific Reports, 11, No. 13214 (2021).

Marouane, B., Chen, N., Obst, M., Peiffer, S.: Competing Sorption of Se(IV) and Se(VI) on Schwertmannite. Minerals, 11(7), No. 764 (2021).

Peiffer, S., Kappler, A., Haderlein, S., Schmidt, C., Byrne, J., Kleindienst, S., Vogt, C., Richnow, H., Obst, M., Angenent, L., Bryce, C., McCammon, C., Planer-Friedrich, B.: A biogeochemical–hydrological framework for the role of redox-active compounds in aquatic systems. Nature Geoscience, 14, 264-272 (2021).


Hömberg, A., Obst, M., Knorr, K., Kalbitz, K., Schaller, J.: Increased silicon concentration in fen peat leads to a release of iron and phosphate and changes in the composition of dissolved organic matter. Geoderma, 374, No. 114422 (2020).

Tomaszewski, E., Olson, L., Obst, M., Byrne, J., Kappler, A., Muehe, E.: Complexation by cysteine and iron mineral adsorption limit cadmium mobility during metabolic activity of Geobacter sulfurreducens. Environmental Science : Processes & Impacts, 22(9), 1877-1887 (2020).

Yang, Z., Sun, T., Subdiaga, E., Obst, M., Haderlein, S., Maisch, M., Kretschmar, R., Angenent, L., Kappler, A.: Aggregation-dependent electron transfer via redox-active biochar particles stimulate microbial ferrihydrite reduction. Science of the Total Environment, 703, No. 135515 (2020).


Schaller, J., Faucherre, S., Joss, H., Obst, M., Göckede, M., Planer-Friedrich, B., Peiffer, S., Gilfedder, B., Elberling, B.: Silicon increases the phosphorus availability of Arctic soils. Scientific Reports, 9, No 449 (2019).

Picard, A., Gartman, A., Cosmidis, J., Obst, M., Vidoudez, C., Clarke, D., Girguis, P.: Authigenic metastable iron sulfide minerals preserve microbial organic carbon in anoxic environments. Chemical Geology, 530, No. 119343 (2019).


Obst, M., Ingino, P., Hitchcock, A., Prabu, V., Picard, A.: Redox-Chemistry of Environmental Biofilms Probed on the Submicron Scale by in-situ Electrochemistry Scanning Transmission (soft) X-ray Microscopy. Microscopy and Microanalysis, 24(Suppl. 2), 502-505 (2018).

Prabu, V., Obst, M., Hosseinkhannazer, H., Reynolds, M., Rosendahl, S., Wang, J., Hitchcock, A.: Instrumentation for in-situ flow electrochemical Scanning Transmission X-ray Microscopy (STXM). Review of Scientific Instruments, 89(6), No. 063702 (2018).


Zobi, F., Obst, M.: Two- and Three-dimensional Mid-Infrared Chemical Imaging. Chimia, 71(1), 32-37 (2017).

Hagemann, N., Joseph, S., Schmidt, H., Kammann, C., Harter, J., Borch, T., Young, R., Varga, K., Taherymoosavi, S., Elliott, K., McKenna, A., Albu, M., Mayrhofer, C., Obst, M., Conte, P., Dieguez-Alonso, A., Orsetti, S., Subdiaga, E., Behrens, S., Kappler, A.: Organic coating on biochar explains its nutrient retention and stimulation of soil fertility. Nature Communications, 8(1), No. 1089 (2017).

Laufer, K., Nordhoff, M., Halama, M., Martinez, R., Obst, M., Nowak, M., Stryhanyuk, H., Richnow, H., Kappler, A.: Microaerophilic Fe(II)-Oxidizing Zetaproteobacteria Isolated from Low-Fe Marine Coastal Sediments : Physiology and Composition of Their Twisted Stalks. Applied and Environmental Microbiology, 83(8), e03118-16 (2017).

Swanner, E., Bayer, T., Wu, W., Hao, L., Obst, M., Sundman, A., Byrne, J., Michel, F., Kappler, A., Schönberg, R.: Iron isotope fractionation during Fe(II) oxidation mediated by the oxygen-producing marine cyanobacterium Synechococcus PCC 7002. Environmental Science & Technology, 51(9), 4897-4906 (2017).

Nordhoff, M., Tominski, C., Halama, M., Byrne, J., Obst, M., Kleindienst, S., Behrens, S., Kappler, A.: Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS. Applied and Environmental Microbiology, 83(13), No. e00752-17 (2017).

Yanez H., J., Wang, Z., Lege, S., Obst, M., Roehler, S., Burkhardt, C., Zwiener, C.: Application and characterization of electroactive membranes based on carbon nanotubes and zerovalent iron nanoparticles. Water Research, 108, 78-85 (2017).


Schmid, G., Zeitvogel, F., Hao, L., Adaktylou, I., Eickhoff, M., Obst, M.: Submicron-Scale Heterogeneities in Nickel Sorption of Various Cell–Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria. Environmental Science & Technology, 50(1), 114-125 (2016).

Zeitvogel, F., Obst, M.: ScatterJn : An ImageJ Plugin for Scatterplot-Matrix Analysis and Classification of Spatially Resolved Analytical Microscopy Data. Journal of Open Research Software, 4(1), e5 (2016).

Zeitvogel, F., Schmid, G., Hao, L., Ingino, P., Obst, M.: ScatterJ : An ImageJ plugin for the evaluation of analytical microscopy datasets. Journal of Microscopy, 261(2), 148-156 (2016).

Grösbacher, M., Spicher, C., Bayer, A., Obst, M., Karwautz, C., Pilloni, G., Wachsmann, M., Scherb, H., Griebler, C.: Organic contamination versus mineral properties : competing selective forces shaping bacterial community assembly in aquifer sediments. Aquatic Microbial Ecology, 76(3), 243-255 (2016).

Jin, X., Wu, S., She, M., Jia, Y., Hao, L., Yin, B., Wang, L., Obst, M., Shen, Y., Zhang, Y., Li, J.: Novel Fluorescein-Based Fluorescent Probe for Detecting H2S and Its Real Applications in Blood Plasma and Biological Imaging. Analytical Chemistry, 88(22), 11253-11260 (2016).

She, M., Yang, Z., Hao, L., Wang, Z., Luo, T., Obst, M., Liu, P., Shen, Y., Zhang, S., Li, J.: A novel approach to study the structure-property relationships and applications in living systems of modular Cu2+ fluorescent probes. Scientific Reports, 6, No. 28972 (2016).

Gauger, T., Byrne, J., Konhauser, K., Obst, M., Crowe, S., Kappler, A.: Influence of organics and silica on Fe(II) oxidation rates and cell–mineral aggregate formation by the green-sulfur Fe(II)-oxidizing bacterium Chlorobium ferrooxidans KoFox – Implications for Fe(II) oxidation in ancient oceans. Earth and Planetary Science Letters, 443, 81-89 (2016).

Hao, L., Guo, Y., Byrne, J., Zeitvogel, F., Schmid, G., Ingino, P., Li, J., Neu, T., Swanner, E., Kappler, A., Obst, M.: Binding of heavy metal ions in aggregates of microbial cells, EPS and biogenic iron minerals measured in-situ using metal- and glycoconjugates-specific fluorophores. Geochimica et Cosmochimica Acta, 180, 66-96 (2016).


Jin, X., Hao, L., She, M., Obst, M., Kappler, A., Yin, B., Liu, P., Li, J., Wang, L., Shi, Z.: Visualizing tributyltin (TBT) in bacterial aggregates by specific rhodamine-based fluorescent probes. Analytica Chimica Acta, 853, 514-520 (2015).

Quaroni, L., Obst, M., Nowak, M., Zobi, F.: Three-dimensional mid-infrared tomographic imaging of endogenous and exogenous molecules in a single intact cell with subcellular resolution. Angewandte Chemie International Edition, 54(1), 318-322 (2015).

Yang, Z., She, M., Yin, B., Hao, L., Obst, M., Liu, P., Li, J.: Solvent-dependent turn-on probe for dual monitoring of Ag+ and Zn2+ in living biological samples. Analytica Chimica Acta, 868, 53-59 (2015).

Swanner, E., Wu, W., Hao, L., Wüstner, M., Obst, M., Moran, D., McIlvin, M., Saito, M., Kappler, A.: Physiology, Fe(II) oxidation, and Fe mineral formation by a marine planktonic cyanobacterium grown under ferruginous conditions. Frontiers in Earth Science, 3, 1-21 (2015).

Han, Z., Sani, B., Mrozik, W., Obst, M., Beckingham, B., Karapanagioti, H., Werner, D.: Magnetite impregnation effects on the sorbent properties of activated carbons and biochars. Water Research, 70, 394-403 (2015).

Picard, A., Obst, M., Schmid, G., Zeitvogel, F., Kappler, A.: Limited influence of Si on the preservation of Fe mineral-encrusted microbial cells during experimental diagenesis. Geobiology, 14(3), 276-292 (2015).

Picard, A., Kappler, A., Schmid, G., Quaroni, L., Obst, M.: Experimental diagenesis of organo-mineral structures formed by microaerophilic Fe(II)-oxidizing bacteria. Nature Communications, 6, No. 6277 (2015).


Schmid, G., Zeitvogel, F., Hao, L., Ingino, P., Kuerner, W., Dynes, J., Karunakaran, C., Wang, J., Lu, Y., Ayers, T., Schietinger, C., Hitchcock, A., Obst, M.: Synchrotron-Based Chemical Nano-Tomography of Microbial Cell-Mineral Aggregates in their Natural, Hydrated State. Microscopy and Microanalysis, 20(2), 531-536 (2014).

Klueglein, N., Zeitvogel, F., Stierhof, Y., Floetenmeyer, M., Konhauser, K., Kappler, A., Obst, M.: Potential Role of Nitrite for Abiotic Fe(II) Oxidation and Cell Encrustation during Nitrate Reduction by Denitrifying Bacteria. Applied and Environmental Microbiology, 80(3), 1051-1061 (2014).

Eickhoff, M., Obst, M., Schröder, C., Hitchcock, A., Tyliszczak, T., Martinez, R., Robbins, L., Konhauser, K., Kappler, A.: Nickel partitioning in biogenic and abiogenic ferrihydrite : The influence of silica and implications for ancient environments. Geochimica et Cosmochimica Acta, 140, 65-79 (2014).

Wu, W., Swanner, E., Hao, L., Zeitvogel, F., Obst, M., Pan, Y., Kappler, A.: Characterization of the physiology and cell–mineral interactions of the marine anoxygenic phototrophic Fe(II) oxidizer Rhodovulum iodosum – implications for Precambrian Fe(II) oxidation. FEMS Microbiology Ecology, 88(3), 503-515 (2014).

Schmid, G., Zeitvogel, F., Hao, L., Ingino, P., Floetenmeyer, M., Stierhof, Y., Schroeppel, B., Burkhardt, C., Kappler, A., Obst, M.: 3-D analysis of bacterial cell-(iron)mineral aggregates formed during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1 using complementary microscopy tomography approaches. Geobiology, 12(4), 340-361 (2014).


Jin, X., Hao, L., Hu, Y., She, M., Shi, Y., Obst, M., Li, J., Shi, Z.: Two novel fluorescein-based fluorescent probes for hypochlorite and its real applications in tap water and biological imaging. Sensors and Actuators B: Chemical, 186, 56-60 (2013).

Yang, Z., Hao, L., Yin, B., She, M., Obst, M., Kappler, A., Li, J.: Six-Membered Spirocycle Triggered Probe for Visualizing Hg2+ in Living Cells and Bacteria–EPS–Mineral Aggregates. Organic Letters, 15(17), 4334-4337 (2013).

Muehe, E., Adaktylou, I., Obst, M., Zeitvogel, F., Behrens, S., Planer-Friedrich, B., Krämer, U., Kappler, A.: Organic carbon and reducing conditions lead to cadmium immobilization by secondary Fe mineral formation in a pH-neutral soil. Environmental Science & Technology, 47(23), 13430-13439 (2013).

Hao, L., Li, J., Kappler, A., Obst, M.: Mapping of Heavy Metal Ion Sorption to Cell-Extracellular Polymeric Substance-Mineral Aggregates by Using Metal-Selective Fluorescent Probes and Confocal Laser Scanning Microscopy. Applied and Environmental Microbiology, 79(21), 6524-6534 (2013).

Klueglein, N., Lösekann-Behrens, T., Obst, M., Behrens, S., Appel, E., Kappler, A.: Magnetite Formation by the Novel Fe(III)-reducing Geothrix fermentans Strain HradG1 Isolated from a Hydrocarbon-Contaminated Sediment with Increased Magnetic Susceptibility. Geomicrobiology Journal, 30(10), 863-873 (2013).

Joens, M., Huynh, C., Kasuboski, J., Ferranti, D., Sigal, Y., Zeitvogel, F., Obst, M., Burkhardt, C., Curran, K., Chalasani, S., Stern, L., Goetze, B., Fitzpatrick, J.: Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution. Scientific Reports, 3, No. 3514 (2013).

Muehe, E., Obst, M., Hitchcock, A., Tyliszczak, T., Behrens, S., Schröder, C., Byrne, J., Michel, F., Krämer, U., Kappler, A.: Fate of Cd during Microbial Fe(III) Mineral Reduction by a Novel and Cd-Tolerant Geobacter Species. Environmental Science & Technology, 47(24), 14099-14109 (2013).

Shimizu, M., Zhou, J., Schröder, C., Obst, M., Kappler, A., Borch, T.: Dissimilatory Reduction and Transformation of Ferrihydrite-Humic Acid Coprecipitates. Environmental Science & Technology, 47(23), 13375-13384 (2013).


Hilhorst, J., van Schooneveld, M., Wang, J., de Smit, E., Tyliszczak, T., Raabe, J., Hitchcock, A., Obst, M., de Groot, F., Pethukov, A.: Three-Dimensional Structure and Defects in Colloidal Photonic Crystals Revealed by Tomographic Scanning Transmission X-ray Microscopy. Langmuir, 28(7), 3614-3620 (2012).

Behrens, S., Kappler, A., Obst, M.: Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM). Environmental Microbiology, 14(11), 2851-2869 (2012).

Pantke, C., Obst, M., Benzerara, K., Morin, G., Ona-Nguema, G., Dippon, U., Kappler, A.: Green Rust Formation during Fe(II) Oxidation by the Nitrate-Reducing Acidovorax sp. Strain BoFeN1. Environmental Science & Technology, 46(3), 1439-1446 (2012).

Hitchcock, A., Obst, M., Wang, J., Lu, Y., Tyliszczak, T.: Advances in the detection of as in environmental samples using low energy X-ray fluorescence in a scanning transmission X-ray microscope : arsenic immobilization by an Fe(II)-oxidizing freshwater bacteria. Environmental Science & Technology, 46(5), 2821-2829 (2012).


Benzerara, K., Menguy, N., Obst, M., Stolarski, J., Mazur, M., Tyliszczak, T., Brown Jr., G., Meibom, A.: Study of the crystallographic architecture of corals at the nanoscale by scanning transmission X-ray microscopy and transmission electron microscopy. Ultramicroscopy, 111(8), 1268-1275 (2011).

Obst, M., Grathwohl, P., Kappler, A., Eibl, O., Peranio, N., Gocht, T.: Quantitative High-Resolution Mapping of Phenanthrene Sorption to Black Carbon Particles. Environmental Science & Technology, 45(17), 7314-7322 (2011).


Lam, K., Hitchcock, A., Obst, M., Lawrence, J., Swerhone, G., Leppard, G., Tyliszczak, T., Karunakaran, C., Wang, J., Kaznatcheev, K., Bazylinski, D., Lins, U.: Characterizing magnetism of individual magnetosomes by X-ray magnetic circular dichroism in a scanning transmission X-ray microscope. Chemical Geology, 270(1-4), 110-116 (2010).


Hitchcock, A., Dynes, J., Lawrence, J., Obst, M., Swerhone, G., Korber, D., Leppard, G.: Soft X-ray spectromicroscopy of nickel sorption in a natural river biofilm. Geobiology, 7(4), 432-453 (2009).

Obst, M., Wang, J., Hitchcock, A.: Soft X-ray spectro-tomography study of cyanobacterial biomineral nucleation. Geobiology, 7(5), 577-591 (2009).

Obst, M., Dynes, J., Lawrence, J., Swerhone, G., Benzerara, K., Karunakaran, C., Kaznatcheev, K., Tyliszczak, T., Hitchcock, A.: Precipitation of amorphous CaCO3 (aragonite-like) by cyanobacteria: A STXM study of the influence of EPS on the nucleation process. Geochimica et Cosmochimica Acta, 73(14), 4180-4198 (2009).

Hanhan, S., Smith, A., Obst, M., Hitchcock, A.: Optimization of analysis of soft X-ray spectromicroscopy at the Ca 2p edge. Journal of Electron Spectroscopy and Related Phenomena, 173(1), 44-49 (2009).

Norlund, K., Southam, G., Tyliszczak, T., Hu, Y., Karunakaran, C., Obst, M., Hitchcock, A., Warren, L.: Microbial architecture of environmental sulfur processes: a novel syntrophic sulfur-metabolizing consortia. Environmental Science & Technology, 43(23), 8781-8786 (2009).

Miot, J., Benzerara, K., Morin, G., Kappler, A., Bernard, S., Obst, M., Férard, C., Skouri-Panet, F., Guigner, J., Posth, N., Galvez, M., Brown Jr., G., Guyot, F.: Iron biomineralization by anaerobic neutrophilic iron-oxidizing bacteria. Geochimica et Cosmochimica Acta, 73(3), 696-711 (2009).

Miot, J., Benzerara, K., Obst, M., Kappler, A., Hegler, F., Schädler, S., Bouchez, C., Guyot, F., Morin, G.: Extracellular Iron Biomineralization by Photoautotrophic Iron-Oxidizing Bacteria. Applied and Environmental Microbiology, 75(17), 5586-5591 (2009).

Obst, M., Wehrli, B., Dittrich, M.: CaCO3 nucleation by cyanobacteria : laboratory evidence for a passive, surface-induced mechanism. Geobiology, 7(3), 324-347 (2009).


Najafi, E., Cruz, D., Obst, M., Hitchcock, A., Douhard, B., Pireux, J., Felten, A.: Polarization Dependence of the C 1s X-ray Absorption Spectra of Individual Multi-Walled Carbon Nanotubes. Small, 4(12), 2279-2285 (2008).

Hunter, R., Hitchcock, A., Dynes, J., Obst, M., Beveridge, T.: Mapping the speciation of iron in Pseudomonas aeruginosa biofilms using scanning transmission X-ray microscopy. Environmental Science & Technology, 42(23), 8766-8772 (2008).


Kaznatcheev, K., Karunakaran, C., Lanke, U., Urquhart, S., Obst, M., Hitchcock, A.: Soft X-ray spectromicroscopy beamline at the CLS : Commissioning results. Nuclear Instruments and Methods in Physics Research Section A : Accelerators, Spectrometers, Detectors and Associated Equipment, 582(1), 96-99 (2007).

Kaznacheyev, K., Karunakaran, C., He, F., Sigrist, M., Summers, T., Obst, M., Hitchcock, A.: CLS ID-10 chicane configuration : From “Simple Sharing” to extended performance with high-speed polarization switching. Nuclear Instruments and Methods in Physics Research Section A : Accelerators, Spectrometers, Detectors and Associated Equipment, 582(1), 103-106 (2007).


Obst, M., Dittrich, M., Kuehn, H.: Calcium adsorption and changes of the surface microtopography of cyanobacteria studied by AFM, CFM, and TEM with respect to biogenic calcite nucleation. Geochemistry, Geophysics, Geosystems, 7(6) (2006).


Obst, M., Gasser, P., Mavrocordatos, D., Dittrich, M.: TEM-specimen preparation of cell/mineral interfaces by Focused Ion Beam milling. American Mineralogist, 90(8-9), 1270-1277 (2005).

Obst, M., Dittrich, M.: Living under an atomic force microscope : An optimized approach for in vivo investigations on surface alterations towards biomineral nucleation on cyanobacterial cells. Geobiology, 3(3), 179-193 (2005).


Dittrich, M., Obst, M.: Are Picoplankton Responsible for Calcite Precipitation in Lakes?. Ambio, 33(8), 559-564 (2004).

Books and Book sections


Schmid, G., Obst, M., Wu, J., Hitchcock, A.: 3D chemical imaging of nanoscale biological, environmental and synthetic materials by soft X-ray STXM spectro-tomography. In: Challa S. S. R. Kumar (eds.): X-ray and neutron techniques for nanomaterials characterization. - Berlin : Springer, 2016. - 43-94.


Schmid, G., Obst, M.: 3D chemical mapping : Application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo- and environmental science. In: John Kuo (eds.): Electron Microscopy : Methods and Protocols. 3rd ed.. - Totowa, NJ : Humana Press, 2014. - 757-781.

Other publications


Zeitvogel, F., Burkhardt, C., Schroeppel, B., Schmid, G., Ingino, P., Obst, M.: Comparison of Preparation Methods of Bacterial Cell-Mineral Aggregates for SEM Imaging and Analysis Using the Model System of Acidovorax sp. BoFeN1. Geomicrobiology Journal, 34(4), 317-327 (2017).

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