Dr. Martin Taubert

2012 02 19 - 39 Martin

Phone: +49 (0)3641 9-494 59










Our knowledge about Earth’s microbiome is rapidly expanding through extensive metagenomics studies, providing hypotheses about the microbial activities present. The elucidation of the functions of the immense microbial diversity unveiled poses the current critical challenge in microbial ecology and will allow us to understand how microorganisms fulfill their roles as ecosystem engineers. My research combines different *omics and single cell based analyses with stable isotope probing, a metabolic labeling approach with heavy isotopes such as 13C, 15N, or 2H. This approach allows me to elucidate carbon fluxes in microbial communities, identify key players in the biogeochemical cycles, and characterize the function of specific taxonomic groups.

Carbon fluxes in the subsurface

The subsurface is naturally overlooked in our everyday life. Nevertheless, man-made changes propagate into the subsurface and affect its poorly understood, but highly important functions, such as carbon storage and groundwater regeneration. Microbial life in groundwater can be driven by organic carbon transported from the surface or produced locally via CO2 fixation. My research aims to elucidate how primary production by chemolitho- and chemoorganoautotrophs influences the microbial food web in the groundwater, including the abundant but largely uncharacterized candidate phyla. I hypothesize that carbon fixed by primary production plays a critical role in sustaining the groundwater core microbiome, and hence for the ecosystem functions this unique environment provides.

Functional biodiversity of aquatic methylotrophs

One carbon (C1) compounds play important roles in biogeochemical cycles and can influence climate processes in the atmosphere. Microorganisms able to degrade these compounds, and thus modulate their emission from aquatic ecosystems. First pathways for breakdown of various C1 compounds have long been elucidated, and key genes were used as markers to assess these processes in the environment. Recent research has revealed the presence of alternative pathways so far overlooked. These novel pathways appear much more widespread in the environment, and potentially link to other metabolic functions, requiring a reassessment of the environmental impact of C1 metabolism.




23. Taubert M., Stöckel S., Geesink P., Girnus S., Jehmlich N., von Bergen M., Rösch P., Popp J., and Küsel K. 2018. Tracking active groundwater microbes with D2O labelling to understand their ecosystem function. Environmental Microbiology 20(1):369-384.

22. Howat A.M., Vollmers J., Taubert M., Grob C., Dixon J.L., Todd J.D., Chen Y., Kaster A.K., and Murrell J.C. 2018. Comparative genomics and mutational analysis reveals a novel XoxF-utilizing methylotroph in the Roseobacter group isolated from the marine environment. Frontiers in Microbiology 9:766.



21. Taubert M., Grob C., Howat A.M., Burns O.J., Pratscher J., Jehmlich N., von Bergen M., Richnow H.H., Chen Y., and Murrell J.C. 2017. Methylamine as a nitrogen source for microorganisms from a coastal marine environment. Environmental Microbiology 19(6):2246-2257.

20. Jameson E., Taubert M., Coyotzi S., Chen Y., Eyice Ö., Schäfer H., Murrell J.C., Neufeld J.D., Dumont M.G. 2017. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods in Molecular Biology. 1539. Metagenomics: Methods and Protocols:57-74.



19. Taubert M., Grob C., Howat A.M., Burns O.J., Chen Y., Neufeld J.D., Murrell J.C. 2016. Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies. In: Martin F., Uroz S. (eds) Microbial Environmental Genomics (MEG). Methods in Molecular Biology, vol 1399. Humana Press, New York, NY. DOI: 10.1007/978-1-4939-3369-3_14.



18. Grob C., Taubert M., Howat A.M., Burns O.J., Chen Y., Neufeld J.D., Murrell J.C. 2015. Generating Enriched Metagenomes from Active Microorganisms with DNA Stable Isotope Probing. In: McGenity T., Timmis K., Nogales B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. DOI: 10.1007/8623_2015_81.

17. Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Dixon, J.L., Richnow, H.H., Jehmlich, N., von Bergen, M., Chen, Y., Murrell, J.C. 2015. Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environmental Microbiology. 17(10):4007–4018. DOI: 10.1111/1462-2920.12935.

16. Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Dixon, J.L., Chen, Y., Murrell, J.C. 2015. XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments. Environmental Microbiology. 17(10): 3937–3948. DOI: 10.1111/1462-2920.12896.

15. Sachsenberg, T., Herbst, F.A., Taubert, M., Kermer, R., Jehmlich, N., von Bergen, M., Seifert, J., Kohlbacher, O. 2015. MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics. Journal of Proteome Research. 14(2):619-627.



14. Bozinovski, D., Taubert, M., Kleinsteuber, S., Richnow, H.H., von Bergen, M., Vogt, C., Seifert, J. 2014. Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in m-xylene degradation pathway and metabolic activity of proteobacteria. Systematic and Applied Microbiology. 37(7):488-501.



13. Siegert, M., Taubert, M., Seifert, J., von Bergen-Tomm, M., Basen, M., Bastida, F., Gehre, M., Richnow, H.H., Krüger, M. 2013. The nitrogen cycle in anaerobic methanotrophic mats of the Black Sea is linked to sulfate reduction and biomass decomposition. FEMS Microbial Ecology. 86(2):231-45.

12. Herbst, F.A., Taubert, M., Jehmlich, N., Behr, T., Schmidt, F., von Bergen, M., Seifert, J. 2013. Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation. Molecular & Cellular Proteomics. 12(8):2060-9.

11. von Bergen, M., Jehmlich, N., Taubert, M., Vogt, C., Bastida, F., Herbst, F.A., Schmidt, F., Richnow, H.H., Seifert, J. 2013. Insights from quantitative metaproteomics and protein stable isotope probing (protein-SIP) into microbial ecology. ISME Journal. 7(10):1877-85.

10. Taubert, M., von Bergen, M., Seifert, J. 2013. Limitations in Detection of 15N Incorporation by Mass Spectrometry in Protein-based stable isotope probing (protein-SIP). Analytical and Bioanalytical Chemistry. 405(12):3989-96.



9. Taubert, M., Vogt, C., Wubet, T., Kleinsteuber, S., Tarkka, M.T., Harms, H., Buscot, F., Richnow, H.H., von Bergen, M., Seifert, J. 2012. Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium. ISME Journal. 6(12):2291-301.

8. Kermer, R., Hedrich, S., Taubert, M., Baumann, S., Schlömann, M., Johnson, D.B., von Bergen, M., Seifert, J. 2012. Elucidation of carbon transfer in a mixed culture of Acidiphilium cryptum and Acidithiobacillus ferrooxidans using protein-based stable isotope probing. Journal of integrated OMICS. 2(1):37-45. DOI: 10.5584/jiomics.v2012i2012.85.

7. Seifert, J., Taubert, M., Jehmlich, N., Schmidt, F., Völker, U., Vogt, C., Richnow, H.H., von Bergen, M. 2012. Protein-based stable isotope probing in functional Metaproteomics. Mass Spectrometry Reviews. 31(6):683-97.



6. Taubert, M., Baumann, S., von Bergen, M., Seifert, J. 2011. Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP). Analytical and Bioanalytical Chemistry. 401(6):1975-82.

5. Taubert, M., Jehmlich, N., Vogt, C., Richnow, H.H., Schmidt, F., von Bergen, M., Seifert, J. 2011. Time resolved protein-based stable isotope probing (Protein-SIP) analysis allows quantification of induced proteins in substrate shift experiments. Proteomics. 11(11):2265-74.

4. Jehmlich, N., Seifert, J., Taubert, M., Schmidt, F., Vogt, C., Richnow, H.H., von Bergen, M. 2011. Protein Stable Isotope Probing. In: Murrell JC, Whiteley AS (eds) Stable isotope probing and related technologies. ASM Press, Washington.



3. Jehmlich, N., Schmidt, F., Taubert, M., Seifert, J., Bastida, F., von Bergen, M., Richnow, H.H., Vogt, C. 2010. Protein stable-isotope probing (Protein-SIP). Nature Protocols. 5(12):1957-1966.



2. Wischgoll, S., Taubert, M., Peters, F., Jehmlich, N., von Bergen, M., Boll, M. 2009. Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria. Journal of Bacteriology. 191(13):4401-9.

1. Jehmlich, N., Schmidt, F., Taubert, M., Seifert, J., von Bergen, M., Richnow H.H., Vogt, C. 2009. Comparison of methods for simultaneous identification of bacterial species and determination of metabolic activity by protein-based stable isotope probing (Protein-SIP) experiments. Rapid Communications in Mass Spectrometry. 23:1871-1878.


Since 2015         Senior researcher, Aquatic Geomicrobiology, Friedrich Schiller University Jena

2012-2015          Senior research associate, School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom

Juni 2012            Dissertation in microbial ecology (Dr. rer. nat., magna cum laude), University of Leipzig; supervisor: Prof. Dr. Matthias Boll

2012                     Postdoctoral researcher, Dept. of Proteomics, Helmholtz Centre for Environmental Research – UFZ, Leipzig

Jul./Aug. 2010     Research internship as DAAD scholarship holder, School of Biological Sciences, University of Aberdeen, United Kingdom

2008-2011           Ph.D. studies in microbial ecology, Dept. of Proteomics, Helmholtz Centre for Environmental Research – UFZ Leipzig

2003-2008           Diploma studies in Biochemistry, Leipzig University; thesis supervisor: Prof. Dr. Matthias Boll

Dr. Nico Jehmlich (Helmholtz Centre – UFZ Leipzig)

Prof. J. Colin Murrell (University of East Anglia)

Prof. Dr. Georg Pohnert (Friedrich Schiller University Jena)

Prof. Dr. Jürgen Popp (Friedrich Schiller University Jena)