Dr. Martin Taubert

2012 02 19 - 39 Martin

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










In our ongoing research, we aim to assess the identity of microorganisms that contribute to the modulation of release and deposition of one carbon compounds in aquatic ecosystems, and to identify the preferred metabolic pathways used as well as their association with other biogeochemical processes.

To characterise the structure and function of methylotrophic microbial communities, we are studying the diversity of functional genes involved in C1 metabolism in marine ecosystems, trace the uptake of carbon and nitrogen derived from C1 compounds in active microorganisms, and reconstruct their metabolism using state-of-the-art ‘omics techniques. This allows the correlation of the employed biochemical pathways with the mode of C1 substrate usage, yielding information about the role of the corresponding microorganisms in the environment.

Research Details

One carbon (C1) compounds, as well as compounds with multiple carbon atoms but no carbon bonds, are typically present in aquatic ecosystems in nano- to micromolar concentrations. C1 compounds, such as methanol, methane as well as methylated amines or sulfur compounds, are produced by the breakdown of biomass. These volatile organic compounds (VOCs) can cross the air-water-interface to be released into the atmosphere, where some of them have an influence on climate processes: Methane, for example, acts as a greenhouse gas 10fold more potent than CO2 and plays a major role in global warming. Methanol is one of the most reactive and most abundant volatile organic compounds (VOCs) in the troposphere. Dimethylsulfide, on the other hand, is involved in the formation of cloud condensation nuclei leading to global cooling. The transition of C1 compounds from marine ecosystems into the atmosphere or vice versa is thus of global relevance.

Microorganisms that can metabolise C1 compounds are ubiquitous in the environment. Methylotrophs are organisms which can use reduced organic C1 compounds as their sole source of carbon and energy. Other microorganisms, termed methylovores oxidise C1 compounds to CO2 to obtain energy, but do not use them as carbon source. Nevertheless, both groups contribute to the removal of C1 compounds from the environment, thus their activity is modulating the emission behaviour of aquatic ecosystems, determining whether these act as source or sink for C1 compounds. Furthermore, the microbial breakdown also leads to a complete recycling of biomass derived C1 compounds to CO2, including release of ammonium or hydrogen sulfide from nitrogen or sulfur containing compounds, respectively. The breakdown of C1 compounds consequently plays an important role in the biogeochemical cycles.

Microorganisms involved in C1 metabolism are phylogenetically diverse: Over 200 species of bacterial methylotrophs, belonging mostly to the Alpha-, Beta-, and Gammaproteobacteria, but also to Verrucomicrobia, Bacteroidetes, Firmicutes, and Actinobacteria, have been described so far. Furthermore, several known species so far not classified as methylotrophs exhibiting genes putatively involved in C1 metabolism. Previous work has shown the presence of multiple biochemical pathways or enzymatic systems involved in the breakdown of the same C1 compound, and environmental surveys of functional genes often show a high diversity of organisms being present in aquatic ecosystems.

In this project, we aim to identify the active microorganisms involved in C1 metabolism in aquatic ecosystems, and assess their contribution to C1 cycling. Given the diversity of these organisms, a key question considers the influence of changes of environmental parameters on the active fraction of the microbial community, as well as their association with other biochemical processes. Furthermore, the utilisation of alternative pathways for breakdown of certain C1 compounds, and their distribution in the microbial communities, are of interest for this project and might be of relevance to link microbial physiology to ecosystem function.

For the identification of active microorganisms involved in metabolism of C1 compounds, different metabolic labelling approaches employing heavy, nonradioactive isotopes are used. In stable isotope probing (SIP), 13C or 15N labelled C1 compounds are used to enable the tracking of carbon and nitrogen incorporation from these sources in microbial biomass. In combination with metagenomics and metaproteomics investigations and gene marker analytics, this approach will also provide information about the physiology and C1 metabolism of the microorganisms investigated. In Raman microspectroscopy, incorporation of heavy isotopes into cellular biomass can be monitored on single cell level. Using heavy water (D2O) as the source of heavy isotopes, this allows the investigation of the specific stimulation of microbial activity after addition of C1 compounds.


21. 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



20. 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. Methods in Molecular Biology DOI: 10.1007/978-1-4939-3369-3_14



19. 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

18. 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.

17. 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.

16. Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Chen, Y., Neufeld, J.D., Murrell, J.C. 2015. Analysis of active methylotrophic communities: when DNA-SIP meets high throughput technologies. In: Martin FM, Uroz S (eds) Microbial Environmental Genomics. Springer, New York. 1-18. DOI 10.1007/8623_2015_81.

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.



University training and degree

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


Advanced academic qualifications

20082012 Ph.D. studies in Biochemistry (magna cum laude), Leipzig University; supervisor: Prof. Dr. Matthias Boll


Postgraduate professional career

Since 2015 Senior researcher, Aquatic Geomicrobiology, FSU

2012–2015 Senior research associate, School of Environmental Sciences, University of East Anglia, Norwich, UK

2012 Postdoctoral research associate, UFZ, Department of Proteomics


Other (Awards, Grants, Memberships)

Since 2016 Member of the International Society for Microbial Ecology (ISME)

Since 2013 Member of the Society for Applied Microbiology (SfAM)

Since 2008 Member of the Association for General and Applied Microbiology (VAAM)

2010 Short time scholarship of the DAAD (German Academic Exchange Service) for a research stay at the University of Aberdeen, School of Biological Sciences, Aberdeen, UK


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)