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Project results originating from DFG-funded projects must be made available to the general public in an appropriate manner. Publications must contain the following reference to the DFG funding:
„Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB1535 - Project ID 458090666"
Publications
Hasenklever, D., Boecker, J., Grankin, A., Şener, F., Axmann, I.M., & Behle, A. (2026). A Spectrum of Possibilities: A Systematic Evaluation of Fluorescent Proteins in Cyanobacteria. bioRxiv
Müsgens, A., Wilke, L., & Blank, L.M. (2026). Itaconic acid production from acetate by Ustilago maydis: A step towards land-free biotechnology. bioRxiv
Mesny, F., Wolf, V., Lopez-Moral, A., Kraege, A., Punt, W., Liu, S., Zhu, J., Park, J., Sato, Y., & Thomma, B. (2026). Plant-associated fungi co-opt ancient antimicrobials for host manipulation. Sci Adv
Krüger, A., Paik, S. H., Bund, M., Pesch, M., Krueger, S., Lückel, B., Papadopoulos, A., Hassan, T., Wiechert, J., Weber, U., Avellan, R., Smits, S., Bott, M., Kovács, A., Westhoff, P., Matuszyńska, A., Kohlheyer, D., Drepper, T., & Frunzke, J. (2026). Context-dependent siderophore exploitability shapes microbial community structure. bioRxiv
Paik, S. H., Paik, G. H., Kruse, L., Horbach, T., Hilgers, F., Weiler, A., Pesch, M., Witting, L., Bund, M., Kohlheyer, D., & Drepper, T. (2026). A Multichromatic UV-RGB Optogenetic Toolbox for control of gene expression in Pseudomonas putida. bioRxiv
Ernst, L., Gätgens, C., Rackow, B., Pozhydaieva, N., Gaaloul, E., Krüger, A., Seiffarth, J., Bund, M., Joisten-Rosenthal, V., Kohlheyer, D., Usadel, B., Harms, A., Höfer, K., & Frunzke, J. (2026). DNA-intercalating antiphage molecules trigger abortive infection through ‘mutual destruction’ and synergize with bacterial immunity. PNAS
Papadopoulos, A., Kaiser, C.F., Schlumpberger, P., Eßer, J., Reiners, J., Gertzen, C.G.W., Grossmann, G., & Smits, S. H. J. (2026). ATPLyzer – An advanced ratiometric multi-colour biosensor for long-term monitoring of ATP dynamics. bioRxiv (accepted in Advanced Sensor Research)
Hammond, M., Chmelová, L., van Geelen-Kuenzel, N.A., Maurya, A.K., Ferreira, E.R., Puente, V., Cadena, L.R., Záhonová, K., Dowle, A., Mottram, J.C., Nowack, E.C.M., Lukeš, J., & Yurchenko, V. (2026) Subcellular proteomics reveals a blueprint for endosymbiont integration in trypanosomatid Angomonas deanei. Nat Commun
Witting, L., Stirba, F.P., Nohr, J., Ivanova, E., Kolkhof, P., Kohlheyer, D., Wiegard, A., & Axmann, I.M. (2026). Live-cell imaging enables reporter-free monitoring of the circadian rhythm in individual Synechocystis cells. bioRxiv
Papadopoulos, A., Anlauf, M. T., Reiners, J., Paik, S.H., Krüger, A., Luckel, B., Bott, M., Drepper, T., Frunzke, J., Gohlke, H., Weidtkamp-Peters, S., Smits, S.H.J., & Gertzen, C.G.W. (2026). A Novel Biosensor for Ferrous Iron Developed via CoBiSe: A Computational Method for Rapid Biosensor Design. ACS Sens
Hofer, J.M., Schulze, T., Witting, L., Laker, B., Krueger, S., Westhoff, P., Kohlheyer, D., Weber, A.P.M., & Eisenhut, M. (2026). Glycogen deficiency impairs diurnal energy metabolism and cell division in Synechocystis. bioRxiv
Laker, B., Thomas, M., Weber, W., Viehoever, P., Meierhenrich, A., Klages, L.J., Busche, T., Niehaus, K., Brautigam, A., & Eisenhut, M. (2026) Tuning into xanthan: A conserved yet flexible polysaccharide utilization system in Microbacterium. bioRxiv
Müsgens, A., Wilke, L., & Blank, L.M. (2026) Itaconic acid production from acetate by Ustilago maydis: A step towards land-free biotechnology. bioRxiv
Prior, M.J., Weidauer, D., Locci, F., Liao, J.Y., Kuwata, K., Deng, C., Ye, H.B., Cai, Q., Bezrutczyk, M., Zhao, C., Jonika, M.C., Pilot, G., Jin, H., Parker, J.E., Frommer, W.B., & Kim J.Y. (2026). The Arabidopsis neutral amino acid transporter UmamiT20 confers Botrytis cinerea susceptibility. J Exp Bot
Kaplunova, V., Alioui, H., Griguschies, T., Müller, L., Joisten-Rosenthal, V., Lautwein, T., Metzger, S., Durán, P. & Loo, E. (2026). Artificial soil (ArtSoil): Recreating soil conditions in synthetic plant growth media. Plant J
Theune, M., Fritsche, R., Küppers, N., Böhm, M., Kolkhof, P., Paul, F., Popa, O., Oldenburg, E., Wiegard, A., Axmann, I.M., & Gutekunst, K. (2026). Easy-to-use whole-genome sequencing workflows and standardized practices to uncover hidden genetic variation in SynechocystisPCC 6803 wild-type and knock-out strains. bioRxiv
Prockl, Z., Neubacher, U., & Rovenich, H. (2026). The model alga Chlamydomonas reinhardtii forms mutualistic interactions with Verticillium fungi. bioRxiv
Erdrich, S. H., Župunski, M., Schurr, U., Grossmann, G., Frunzke, J., & Arsova, B. (2026). Phage biocontrol reduces the burden on plant immunity through suppression of bacterial virulence. Cell Reports
Zöllner, N., Long, J., Song, C., Sharkey, J., Wudick, M.M., Loo, E.P.I., Sadoine, M., Applegate, V., Hoppner, A., Smits, S.H.J., Yang B. & Frommer W.B. (2026) A critical role of sux cistron-mediated sucrose uptake for virulence of the rice blight pathogen Xanthomonas oryzae pv. oryzae. PNAS Nexus
Ishikawa Y., Zöllner N., Paradies S. & Frommer W.B. (2026) Evidence for rapid hydrolysis of shoot-derived sucrose using an ultrasensitive ratiometricmatryoshka-type MGlucoMetersensor. Plant J
Ernst, P., Vanselow, J., Denter, M., Li, W., Witting, L., Gätgens, J, Pauly, M., Kohlheyer, D., Urlacher, V.B., Feldbrügge, M., & Julia Frunzke (2026). Systematic evaluation of Cyanidioschyzon merolae across photobioreactor systems: Linking reactor design to biomass production and biochemical composition. bioRxiv
Joistin-Rosenthal, V., Kelly, C., Hüttenbräucker, L., Robertz, S., Feldbrügge, M., Pauly, M., Thomma, B., Altegoer, F., & Usadel, B. (2026). A chromosome-scale super-pangenome of the lichen genus Peltigera reveals genome architecture and expanded interaction repertoires shared across pathogenic and mutualistic fungi. bioRxiv
Hassen, T., Dwivedi, S., Schuster, S., & Matuszyńska, A. (2026) Cooperation, privatization and cheating in microbial exoenzyme synthesis: theoretical analysis in view of biotechnological applications. bioRxiv
Tang, K., Mueller, M.D., Huesemann, L., Rybecky, A., Heucken, N., Postma, J., van Wijlick, L., Doehlemann, G., Feldbruegge M., & Zurbriggen, M.D. (2026). LUstiGE, Light responsive Ustilago maydis Gene Expression: Optogenetic control of morphogenesis and pathogenesis in the corn fungal pathogen Ustilago maydis. bioRxiv
van Aalst, M., Lahlou, A., Hassan, T., Gaultier, W., Colliaux, D., & Matuszyńska A. (2026). Web-based collaborative model development in interdisciplinary consortia: Design principles and practical guidance. PLOS
Peltz, N., Armbruster, L., Stephens, C., Joisten-Rosenthal, V., Thomsen, T., Yan, A. W., Dunken, N., Granado, R., Kopriva, S., de Meaux, J., Langen, G., Koprivova, A., Usadel, B., & Zuccaro, A. (2025). A fungal root endophyte functionally complements host immunity and mitigates natural immune variation in Arabidopsis. bioRxiv
Altin, S., Simões, T., Behrendt, C., Anton, V., Domke, D., Voltzke, K. M., Kumar, R., Nolte, H., Hermanns, T., Brocke-Ahmadinejad, N., Bendrin, K., Zimmermann, M., Büttner, R., Ventura, N., Krüger, M., Dohmen, R. J., Hofmann, K., Hoppe, T., Reichert, A. S., & Escobar-Henriques, M. (2025). Ubiquitin precursor with C-terminal extension promotes proteostasis and longevity. Mol Cell
Redzich, L., Ma, Z., Schepler-Luu, V,. Loo, E.I.P., & Frommer, W.B. (2025). Differentiation of Xanthomonas oryzae pv. oryzae in vitro and during rice leaf infection. bioRxiv
DOI | ARC
Redzich, L., Arra, Y., Loo, E.I.P., & Frommer, W.B. (2025). Restricted transmission of Xanthomonas oryzae pv. oryzae from rice roots to shoots detected by a rapid root infection system. bioRxiv
DOI | ARC
Bollé, S., Koc, E., Saiardi, A., Juhran, L., Walla, E., Fleig, U., & Alcázar-Román A. (2025). Inorganic Polyphosphate Modulates Chromosome Transmission Fidelity in the Fission Yeast Schizosaccharomyces pombe. Biomolecules
Alcázar-Román, A.R., & Fleig, U. (2025). An In Vivo Yeast-Based Activity Assay for the PPIP5K Family.
In: Saiardi, A., Fiedler, D., Jessen, H.J. (eds) Inositol Pyrophosphates. Methods in Molecular Biology, vol 2972. Humana, New York, NY.
Dali, S., Schultz, M., Köster, M., Kamel, M., Busch, M., Steinchen, W., Haensch, S., Papadopoulos, A., Reiners, J., Smits, S. H. J., Kedrov, A., Altegoer, F., & Schipper, K. (2025). Specific phosphoinositide interaction of Jps1 is a key feature during unconventional secretion in Ustilago maydis. J Biol Chem
Witting, L., Seiffarth, J., Stute, B., Schulze, T., Hofer, J.M., Noh, K., Eisenhut, M., Weber, A.P.M., von Lieres, E., & Kohlheyer, D. (2025). A microfluidic system for the cultivation of cyanobacteria with precise light intensity and CO(2) control: enabling growth data acquisition at single-cell resolution. Lab Chip
Mager, M., Becker, L., Schulten, N., Fraune, S., & Axmann, I. M. (2025). Oligonucleotide library assisted sequence mining reveals promoter sequences with distinct temporal expression dynamics for applications in Curvibacter sp. AEP1-3. Synthetic Biology
Loo, E.P.I., Szurek, B., Arra, Y., Stiebner, M., Buchholzer, M., Devanna, B.N., Cruz, C.M.V., & Frommer, W.B. (2025). Closing the Information Gap Between the Field and Scientific Literature for Improved Disease Management, with a Focus on Rice and Bacterial Blight. APS
Berwanger, L.C. Thumm, N., Stirba, F.P., Gholamipoorfard, R., Pawlowski, A., Kolkhof, P., Volke, J., Kollmann, M., Wiegard, A., & Axmann, I.M. (2025). Self-sustained rhythmic behavior of Synechocystis sp. PCC 6803 under continuous light conditions in the absence of light–dark entrainment. PNAS NEXUS
Samir, S Doello, S., Enkerlin, A.M., Zimmer, E., Haffner, M., Müller, T., Dengler, L., Lambidis, S.P., Sivabalasarma, S., Albers, S.V. & Selim, K.A. (2025). The second messenger c-di-AMP controls natural competence via ComFB signaling protein. Cell Discov
Samir, S., Elshereef, A.A., Alva, V., & Selim K.A. (2025). ComFB, a widespread family of c-di-NMP receptor proteins. PNAS
Kraege, A., Chavarro-Carrero, E., Schnell, E., Heilmann-Heimbach, S., Becker, K., Köhrer, K., Huettel, B., Sargheini, N., Schiffer, P., Waldvogel, A.M., Thomma, B.P.H.J., & Rovenich, H. (2025). High quality genome assembly and annotation (v1) of the eukaryotic freshwater microalga Coccomyxa elongata SAG 216-3b. G3
Mendoza-Rojas, G., Nakonz, P., Lu, M., Postma, J., Shtakser, N., Heinen, M., Patel, M., Arguello-Miranda, O., Billerbeck, S., & Altegoer, F., (2025). A co-evolved peptide-GPCR system senses host entry to drive fungal infection. bioRxiv
Seiffarth, J., Kasahara, K., Bund, M., Lückel, B., Paul, R.D., Pesch, M., Witting, L., Bott, M., Kohlheyer, D., & Nöh, K. (2025). acia-workflows: Automated Single-cell Imaging Analysis for Scalable and Deep Learning-based Live-cell Imaging Analysis Workflows. arXiv
Shang, X., Bartels, N., Weck, J.M., Suppmann, S., Basquin, J., Thaventhiran, G., Heuer-Jungemann, A., & Monzel, C. (2025). High yield purification of an isoleucine zipper-modified CD95 ligand for efficient cell apoptosis initiation and with biotin or DNA-oligomer binding domain to probe ligand functionalization effects. BMC Biotechnol
Stephens, T. G., Van Etten, J., McDermott, T., Christian, W., Chaverra, M., Gurney, J., Lee, Y., Kim, H., Cho, C. H., Chovancek, E., Westhoff, P., Otte, A., Northen, T. R., Bowen, B. P., Louie, K. B., Barry, K., Grigoriev, I. V., Mock, T., Liu, S. L., Miyagishima, S. Y., Yoshinaga, M., Weber, A. P. M., Yoon, H. S., & Bhattacharya, D. (2024). Temporal dynamics in a red alga dominated geothermal feature in Yellowstone National Park. ISME Commun, 4, ycae151
Sorensen, M. E. S., Stiller, M. L., Kröninger, L., & Nowack, E. C. M. (2024). Protein import into bacterial endosymbionts and evolving organelles. Febs Journal.
Beyer, H. M., Kumar, S., Nieke, M., Diehl, C. M. C., Tang, K., Shumka, S., Koh, C. S., Fleck, C., Davies, J. A., Khammash, M., & Zurbriggen, M. D. (2024). Genetically-stable engineered optogenetic gene switches modulate spatial cell morphogenesis in two- and three-dimensional tissue cultures. Nat Commun
Laker, B., Schulze, T., Reis, M., Bormann, S. M., Radke, G., Klages, L. J., Busche, T., Wobbe, L., Bräutigam, A., & Eisenhut, M. (2024). Circularly assembled genome sequences of Asticcacaulis sp. strain MM231 and Brevundimonas subvibrioides MM232, isolated from a pond at Bielefeld University campus. Microbiol Resour Announc.
Mostafa, F., Krüger, A., Nies, T., Frunzke, J., Schipper, K., & Matuszyńska, A. (2024). Microbial markets: socio-economic perspective in studying microbial communities. microLife.
Kever, L., Zhang, Q., Hardy, A., Westhoff, P., Yu, Y., & Frunzke, J. (2024). Resistance against aminoglycoside antibiotics via drug or target modification enables community-wide antiphage defense. microLife.
Eisenhut, M., Schulze, T., Matten, F. N. J., Sengewald, A., Böhner, P., Falk, D., Klinge, C. V., Langschwager, R., Lohoff, S., Meyer, N., Ponomarchuk, V., Punter, F., Sherlock, J., Pschik, D., Klages, L. J., Busche, T., Wobbe, L., Bräutigam, A., & Laker, B. (2024). Complete genome sequences of Chitinophaga sp. strain MM2321 and Microbacterium sp. strain MM2322, isolated from a sand sample in Harsewinkel, Germany. Microbiol Resour Announc.
Erdrich, S. H., Luthe, T., Kever, L., Roigé, B. B., Arsova, B., Davoudi, E., & Frunzke, J. (2024). Expanding the Phage Galaxy: Isolation and Characterization of Five Novel Siphoviruses Ankus, Byblos, DekoNeimoidia, Mandalore, and Naboo. Phage-Therapy Applications and Research
Hasenklever, D., Pohlentz, J. C., Berwanger, T., Kokarakis, E. J., Hassan, T., Schipper, K., Matuszyńska, A., Axmann, I. M., & Ducat, D. C. (2024). Assembly and Quantification of Co-Cultures Combining Heterotrophic Yeast with Phototrophic Sugar-Secreting Cyanobacteria. Jove-Journal of Visualized Experiments.
Levy, T., Voeltzke, K., Hruby, L., Alasad, K., Bas, Z., Snaebjornsson, M., Marciano, R., Scharov, K., Planque, M., Vriens, K., Christen, S., Funk, C. M., Hassiepen, C., Kahler, A., Heider, B., Picard, D., Lim, J. K. M., Stefanski, A., Bendrin, K., Vargas-Toscano, A., Kahlert, U. D., Stuhler, K., Remke, M., Elkabets, M., Grunewald, T. G. P., Reichert, A. S., Fendt, S. M., Schulze, A., Reifenberger, G., Rotblat, B., & Leprivier, G. (2024). mTORC1 regulates cell survival under glucose starvation through 4EBP1/2-mediated translational reprogramming of fatty acid metabolism. Nat Commun, 15, 4083.
Kuckla, D. A., Brand, J.-S., Czech, B., Asharion, A., Jüttner J. V., Novoselova, I., Neusch, A., Hagemann, P., Getzlaff, M. and Monzel, C. (2023) An efficient magnetothermal actuation setup for fast heating/cooling cycles or long-term induction heating of different magnetic nanoparticle classes. J. Phys. D: Appl. Phys. 56 (2023) 505002 (14pp)
Bitzenhofer, N. L., Höfel, C., Thies, S., Weiler, A. J., Eberlein, C., Heipieper, H. J., Batra-Safferling, R., Sundermeyer, P., Heidler, T., Sachse, C., Busche, T., Kalinowski, J., Belthle, T., Drepper, T., Jaeger, K. E., & Loeschcke, A. (2023). Exploring engineered vesiculation by Pseudomonas putida KT2440 for natural product biosynthesis. Microb Biotechnol.
Immelmann, R., Gawenda, N., Vicente Ramírez, V., & Pauly, M. (2023). Identification of a xyloglucan beta-xylopyranosyltransferase from Vaccinium corymbosum. Plan Direct, Volume 7e514.
Molinari, P. E., Krapp, A. R., Weiner, A., Beyer, H. M., Kondadi, A. K., Blomeier, T., López, M., Bustos-Sanmamed, P., Tevere, E., Weber, W., Reichert, A. S., Calcaterra, N. B., Beller, M., Carrillo, N., & Zurbriggen, M. D. (2023). NERNST: a genetically-encoded ratiometric non-destructive sensing tool to estimate NADP(H) redox status in bacterial, plant and animal systems. Nat Commun, 14, 3277.
Weiland, P., Dempwolff, F., Steinchen, W., Freibert, S. A., Tian, H., Glatter, T., Martin, R., Thomma, B., Bange, G., & Altegoer, F. (2023). Structural and functional analysis of the cerato-platanin-like protein Cpl1 suggests diverging functions in smut fungi. Mol Plant Pathol, 24, 768-787.