Martin Obst: Publications

Peer reviewed


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).

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 (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, (2020).


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 (2019).

Schaller, J., Faucherre, S., Joss, H., Obst, M., Goeckede, M., Planer-Friedrich, B., Peiffer, S., Gilfedder, B., Elberling, B.: Silicon increases the phosphorus availability of Arctic soils. Scientific Reports, 9 (2019).


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) (2018).

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).


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).

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) (2017).

Swanner, E., Bayer, T., Wu, W., Hao, L., Obst, M., Sundman, A., Byrne, J., Michel, M., 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).

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).

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).

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


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).

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).

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).

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).

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).

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).

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).

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).


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).

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).

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).

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).

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).

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).

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).


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).

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).

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., 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).


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).

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).

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).

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).

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).

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).

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).

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).


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).

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).

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).

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).


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).


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

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).

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).

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).

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).

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

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).


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).

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 : nano micro, 4(12), 2279-2285 (2008).


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).

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).


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., 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).

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).


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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