Research for the Environment

Dr. Jana Seifert

Research activities and methods

The Microbial Ecology and Biodegradation group focus on the proteome analysis of microbial cultures involved in the degradation of BTEX and chlorinated compounds under aerobic and anaerobic conditions. The recently established protein-based stable isotope probing (Protein-SIP) method is applied to investigate well-defined mixed as well as enrichment cultures by the metabolic incorporation of isotopes using labelled substrates.

Projects

Cooperations

- University Leipzig, Institute Biochemistry
- Friedrich-Schiller University Jena, Applied and Ecological Microbiology
- TU Bergakademie Freiberg, Institute of Bioscience, Environmental Microbiology
- BGR Hannover, Division Geomicorbiology
- Martin-Luther University Halle, Institute of Biology, Division of General Microbiology
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology, Bremen
- Netherlands Institute of Ecology, Department of Microbial Ecology, Wageningen (NL)
- CSIC - Institute of Catalysis, Laboratory of Enzyme Discovery, Madrid (Spain)
- University of Aberdeen, Institute of Biological & Environmental Sciences, Aberdeen (UK)
- University Vienna, Department of Microbial Ecology, Vienna (At)

CV / Scientific Career

Publications

2013 (12)

• Ferrer, M., Ruiz, A., Lanza, F., Haange, S.-B., Oberbach, A., Till, H., Bargiela, R., Campoy, C., Segura, M.T., Richter, M., von Bergen, M., Seifert, J., Suarez, A., (2013):
  Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure
  Environ. Microbiol. 15 (1), 211 - 226
  full text (url)
• Guazzaroni, M.-E., Herbst, F.-A., Lores, I., Tamames, J., Peláez, A.I., López-Cortés, N., Alcaide, M., del Pozo, M.V., Vieites, J.M., von Bergen, M., Gallego, J.L.R., Bargiela, R., López-López, A., Pieper, D.H., Rosselló-Móra, R., Sánchez, J., Seifert, J., Ferrer, M., (2013):
  Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation
  ISME J. 7 , 122 - 136
  full text (url)
• Herbst, F.-A., Bahr, A., Duarte, M., Pieper, D.H., Richnow, H.-H., von Bergen, M., Seifert, J., Bombach, P., (2013):
  Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP)
  Proteomics
• 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
  Mol. Cell. Proteomics
  full text (url)
• Jahn, M., Seifert, J., von Bergen, M., Schmid, A., Bühler, B., Müller, S., (2013):
  Subpopulation-proteomics in prokaryotic populations
  Curr. Opin. Biotechnol. 24 (1), 79 - 87
  full text (url)
• Jechalke, S., Franchini, A., Bastida, F., Bombach, P., Rosell, M., Seifert, J., von Bergen, M., Vogt, C., Richnow, H.H., (2013):
  Analysis of structure, function, and activity of a benzene-degrading microbial community
  FEMS Microbiol.Ecol.
  full text (url)
• Jechalke, S., Franchini, A.G., Bastida, F., Bombach, P., Rosell, M., Seifert, J., von Bergen, M., Vogt, C., Richnow, H.H., (2013):
  Analysis of structure, function, and activity of a benzene-degrading microbial community
  FEMS Microbiol.Ecol.
  full text (url)
• Pérez-Cobas, A.E., Gosalbes, M.J., Friedrichs, A., Knecht, H., Artacho, A., Eismann, K., Otto, W., Rojo, D., Bargiela, R., von Bergen, M., Neulinger, S.C., Däumer, C., Heinsen, F.A., Latorre, A., Barbas, C., Seifert, J., Martins dos Santos, V., Ott, S.J., Ferrer, M., Moya, A., (2013):
  Gut microbiota disturbance during antibiotic therapy: a multi-omic approach
  Gut
  full text (url)
• Schipp, C.-J., Marco-Urrea, E., Kublik, A., Seifert, J., Adrian, L., (2013):
  Organic cofactors in the metabolism of Dehalococcoides mccartyi strains
  Philos. Trans. R. Soc. B-Biol. Sci. 368 (1616), 20120321
  full text (url)
• Seifert, J., Herbst, F.-A., Nielsen, P.H., Planes, F.J., Ferrer, M., von Bergen, M., (2013):
  Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities
  Proteomics
  full text (url)
• Tang, S., Chan, W.W.M., Fletcher, K.E., Seifert, J., Liang, X., Löffler, F.E., Edwards, E.A., Adrian, L., (2013):
  Functional characterization of reductive dehalogenases using blue native polyacrylamide gel electrophoresis
  Appl. Environ. Microb. 79 (3), 974 - 981
  full text (url)
• Taubert, M., von Bergen-Tomm, M., Seifert, J., (2013):
  Limitations in detection of 15N incorporation by mass spectrometry in protein-based stable isotope probing (protein-SIP)
  Anal. Bioanal. Chem. 405 (12), 3989 - 3996
  full text (url)

2012 (13)

• Baumgarten, T., Sperling, S., Seifert, J., von Bergen, M., Steiniger, F., Wick, L.Y., Heipieper, H.J., (2012):
  Membrane vesicle formation as multiple stress response mechanism enhances cell surface hydrophobicity and biofilm formation of Pseudomonas putida DOT-T1E
  Appl. Environ. Microb. 78 (17), 6217 - 6224
  full text (url)
• Bozinovski, D., Herrmann, S., Richnow, H.-H., von Bergen, M., Seifert, J., Vogt, C., (2012):
  Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing
  FEMS Microbiol.Ecol. 81 (1), 134 - 144
  full text (url)
• Haange, S.-B., Oberbach, A., Schlichting, N., Hugenholtz, F., Smidt, H., von Bergen, M., Till, H., Seifert, J., (2012):
  Metaproteome analysis and molecular genetics of rat intestinal microbiota reveals section and localisation resolved species distribution and enzymatic functionalities
  J. Proteome Res. 11 (11), 5406 - 5417
  full text (url)
• Jehmlich, N., Kopinke, F.-D., Lenhard, S., Vogt, C., Herbst, F.-A., Seifert, J., Lissner, U., Völker, U., Schmidt, F., von Bergen, M., (2012):
  Sulfur-³⁶S stable isotope labeling of amino acids for quantification (SULAQ)
  Proteomics 12 (1), 37 - 42
  full text (url)
• Kermer, R., Hedrich, S., Taubert, M., Baumann, S., Schlömann, M., Johnson, D.B., 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
  full text (url)
• Marco-Urea, E., Seifert, J., von Bergen, M., Adrian, L., (2012):
  Stable isotope peptide mass spectrometry to decipher amino acid metabolism in Dehalococcoides strain CBDB1
  J. Bacteriol. 194 (16), 4169 - 4177
  full text (url)
• Morris, B.E.L., Herbst, F.-A., Bastida, F., Seifert, J., von Bergen, M., Richnow, H.-H., Suflita, J.M., (2012):
  Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium
  Environ. Microbiol. Rep. 4 (3), 297 - 306
  full text (url)
• Oberender, J., Kung, J.W., Seifert, J., von Bergen, M., Boll, M., (2012):
  Identification and characterization of a succinyl-coenzyme A (CoA):benzoate CoA transferase in Geobacter metallireducens
  J. Bacteriol. 194 (10), 2501 - 2508
  full text (url)
• Reinhold, A., Westermann, M., Seifert, J., von Bergen, M., Schubert, T., Diekert, G., (2012):
  Impact of vitamin B₁₂ on the formation of the tetrachloroethene reductive dehalogenase in Desulfitobacterium hafniense strain Y51
  Appl. Environ. Microb. 78 (22), 8025 - 8032
  full text (url)
• Seifert, J., Taubert, M., Jehmlich, N., Schmidt, F., Völker, U., Vogt, C., Richnow, H.H., von Bergen, M., (2012):
  Protein-based stable isotope probing (protein-SIP) in functional metaproteomics
  Mass Spectrom. Rev. 31 (6), 683 - 697
  full text (url)
• Sultana, M., Vogler, S., Zargar, K., Schmidt, A.C., Saltikov, C., Seifert, J., Schlömann, M., (2012):
  New clusters of arsenite oxidase and unusual bacterial groups in enrichments from arsenic-contaminated soil
  Arch. Microbiol. 194 (7), 623 - 635
  full text (url)
• 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 J. 6 (12), 2291 - 2301
  full text (url)
• Wagner, A., Cooper, M., Ferdi, S., Seifert, J., Adrian, L., (2012):
  Growth of Dehalococcoides mccartyi strain CBDB1 by reductive dehalogenation of brominated benzenes to benzene
  Environ. Sci. Technol. 46 (16), 8960 - 8968
  full text (url)

2011 (9)

• Bastida, F., Jechalke, S., Bombach, P., Franchini, A.G., Seifert, J., von Bergen, M., Vogt, C., Richnow, H.H., (2011):
  Assimilation of benzene carbon through multiple trophic levels traced by different stable isotope probing methodologies
  FEMS Microbiol.Ecol. 77 (2), 357 - 369
  full text (url)
• Georgieva, D., Seifert, J., Ohler, M., von Bergen, M., Spencer, P., Arni, R.K., Genov, N., Betzel, C., (2011):
  Pseudechis australis venomics: adaptation for a defense against microbial pathogens and recruitment of body transferrin
  J. Proteome Res. 10 (5), 2440 - 2464
  full text (url)
• Hedrich, S., Lünsdorf, H., Kleeberg, G., Heide, G., Seifert, J., Schlömann, M., (2011):
  Schwertmannite formation adjacent to bacterial cells in a mine water treatment plant and in pure cultures of ‘Ferrovum myxofaciens’
  Environ. Sci. Technol. 45 (18), 7685 - 7692
  full text (url)
• Jehmlich, N., Seifert, J., Taubert, M., Schmidt, F., Vogt, C., Richnow, H.H., von Bergen, M., (2011):
  Protein stable isotope probing
  In: Murrell, J.C., Whiteley, A.S., (eds.)
  Stable isotope probing and related technologies
  ASM Press, Washington, DC, p. 71 - 93
• Kuntze, K., Kiefer, P., Baumann, S., Seifert, J., von Bergen, M., Vorholt, J.A., Boll, M., (2011):
  Enzymes involved in the anaerobic degradation of meta-substituted halobenzoates
  Mol. Microbiol. 82 (3), 758 - 769
  full text (url)
• Marco-Urrea, E., Paul, S., Khodaverdi, V., Seifert, J., von Bergen, M., Kretzschmar, U., Adrian, L., (2011):
  Identification and characterization of a Re-Citrate synthase in Dehalococcoides strain CBDB1
  J. Bacteriol. 193 (19), 5171 - 5178
  full text (url)
• Sultana, M., Härtig, C., Planer-Friedrich, B., Seifert, J., Schlömann, M., (2011):
  Bacterial communities in Bangladesh aquifers differing in aqueous arsenic concentration
  Geomicrobiol. J. 28 (3), 198 - 211
  full text (url)
• 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)
  Anal. Bioanal. Chem. 401 (6), 1975 - 1982
  full text (url)
• 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 - 2274
  full text (url)

2010 (8)

• Bastida, F., Rosell, M., Franchini, A.G., Seifert, J., Finsterbusch, S., Jehmlich, N., Jechalke, S., von Bergen, M., Richnow, H.H., (2010):
  Elucidating MTBE degradation in a mixed consortium using a multidisciplinary approach
  FEMS Microbiol.Ecol. 73 (2), 370 - 384
  full text (url)
• Fetzer, I., Jehmlich, N., Vogt, C., Richnow, H.H., Seifert, J., Harms, H., von Bergen, M., Schmidt, F., (2010):
  Calculation of partial isotope incorporation into peptides measured by mass spectrometry
  BMC Res. Notes 3:178
  full text (url)
• Georgieva, D., Öhler, M., Seifert, J., von Bergen, M., Arni, R.K., Genov, N., Betzel, C., (2010):
  Snake venomic of Crotalus durissus terrificus-correlation with pharmacological activities
  J. Proteome Res. 9 (5), 2302 - 2316
  full text (url)
• Jehmlich, N., Fetzer, I., Seifert, J., Mattow, J., Vogt, C., Harms, H., Thiede, B., Richnow, H.H., von Bergen, M., Schmidt, F., (2010):
  Decimal place slope: a fast and precise method for quantifying ¹³C incorporation levels for detecting the metabolic activity of microbial species
  Mol. Cell. Proteomics 9 (6), 1221 - 1227
  full text (url)
• Jehmlich, N., Kleinsteuber, S., Vogt, C., Benndorf, D., Harms, H., Schmidt, F., von Bergen, M., Seifert, J., (2010):
  Phylogenetic and proteomic analysis of an anaerobic toluene-degrading community
  J. Appl. Microbiol. 109 (6), 1937 - 1945
  full text (url)
• Jehmlich, N., Schmidt, F., Taubert, M., Seifert, J., Bastida, F., von Bergen, M., Richnow, H.-H., Vogt, C., (2010):
  Protein-based stable isotope probing
  Nat. Protoc. 5 (12), 1957 - 1966
  full text (url)
• Leibeling, S., Taubert, M., Seifert, J., von Bergen, M., Harms, H., Müller, R.H., (2010):
  Adaptation of the herbicide-degrading strain delftia acidovorans mc1 through carbonylation of rdpa as key enzyme
  J. Biotechnol. 150 (Suppl. 1), S262 - S263
  full text (url)
• Öhler, M., Georgieva, D., Seifert, J., von Bergen, M., Arni, R.K., Genov, N., Betzel, C., (2010):
  The Venomics of Bothrops alternatus is a Pool of Acidic Proteins with Predominant Hemorrhagic and Coagulopathic Activities
  J. Proteome Res. 9 (5), 2422 - 2437
  full text (url)

2009 (6)

• Ehinger, S., Seifert, J., Kassahun, A., Schmalz, L., Hoth, N., Schlömann, M., (2009):
  Predominance of Methanolobus spp. and Methanoculleus spp. in the archaeal communities of saline gas field formation fluids
  Geomicrobiol. J. 26 (5), 326 - 338
  full text (url)
• Gniese, C., Kruger, M., Frerichs, J., Kassahun, A., Hoth, N., Seifert, J., (2009):
  Determination of active microorganisms in the gas reservoir Altmark and their role in CO2 turnover
  Geochim. Cosmochim. Acta 73 (13), A442 - A442
  full text (url)
• Heinzel, E., Hedrich, S., Janneck, E., Glombitza, F., Seifert, J., Schlömann, M., (2009):
  Bacterial diversity in a mine water treatment plant
  Appl. Environ. Microb. 75 (3), 858 - 861
  full text (url)
• Heinzel, E., Janneck, E., Glombitza, F., Schlömann, M., Seifert, J., (2009):
  Population dynamics of iron-oxidizing communities in pilot plants for the treatment of acid mine waters
  Environ. Sci. Technol. 43 (16), 6138 - 6144
  full text (url)
• 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 Commun. Mass Spectrom. 23 (12), 1871 - 1878
  full text (url)
• Seifert, J., Jehmlich, N., Schmidt, F., Taubert, M., von Bergen, M., Richnow, H.H., Vogt, C., (2009):
  Protein-stable isotope probing (Protein-SIP) for simultaneous identification of bacterial species and determination of metabolic activity
  Geochim. Cosmochim. Acta 73 (Suppl. 13), A1191 - A1191
  full text (url)

2005 (1)

• Ferraroni, M., Seifert, J., Travkin, V.M., Thiel, M., Kaschabek, S., Scozzafava, A., Golovleva, L., Schlomann, M., Briganti, F., (2005):
  Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation
  J. Biol. Chem. 280 (22), 21144 - 21154
  full text (url)

publications

Kliemt S, Lange C, Otto W, Hintze V, Möller S, von Bergen M, Hempel U, Kalkhof S. 
Sulfated hyaluronan containing collagen matrices enhance cell-matrix-interaction, endocytosis, and osteogenic differentiation of human mesenchymal stromal cells.
J Proteome Res. 2012 Nov 21. [Epub ahead of print] PMID:23170904

Haange SB, Oberbach A, Schlichting N, Hugenholtz F, Smidt H, von Bergen M, Till H, Seifert J.
Metaproteome analysis and molecular genetics of rat intestinal microbiota reveals section and localisation resolved spec ies distribution and enzymatic functionalities.
J Proteome Res. 2012 Nov 2;11(11):5406-17. PMID: 23016992

Müller SA, van der Smissen A, von Feilitzsch M, Anderegg U, Kalkhof S, von Bergen M.
Quantitative proteomics reveals altered expression of extracellular matrix related proteins of human primary dermal fibroblasts in response to sulfated hyaluronan and collagen applied as artificial extracellular matrix.
J Mater Sci Mater Med. 2012 Dec;23(12):3053-65. PMID: 22990618

Goettsch C, Kliemt S, Sinningen K, von Bergen M, Hofbauer LC, Kalkhof S.
Quantitative proteomics reveals novel functions of osteoclast-associated receptor in STAT signaling and cell adhesion in human endothelial cells.
J Mol Cell Cardiol. 2012 Dec;53(6):829-37. PMID: 22985931

Salbach J, Kliemt S, Rauner M, Rachner TD, Goettsch C, Kalkhof S, von Bergen M, Möller S, Schnabelrauch M, Hintze V, Scharnweber D, Hofbauer LC.
The effect of the degree of sulfation of glycosaminoglycans on osteoclast function and signaling pathways.
Biomaterials 2012 Nov;33(33):8418-29. PMID: 22954516

Guazzaroni ME, Herbst FA, Lores I, Tamames J, Peláez AI, López-Cortés N, Alcaide M, Del Pozo MV, Vieites JM, von Bergen M, Gallego JL, Bargiela R, López-López A, Pieper DH, Rosselló-Móra R, Sánchez J, Seifert J, Ferrer M.
Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.
ISME J. 2012 Jul 26. doi: 10.1038/ismej.2012.82.[Epub ahead of print] PMID: 22832345

Taubert M, Vogt C, Wubet T, Kleinsteuber S, Tarkka MT, Harms H, Buscot F, Richnow HH, von Bergen M, Seifert J
Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium.
ISME J. 2012 Jul 12. doi: 10.1038/ismej.2012.68. [Epub ahead of print] PMID: 22791237. 

Boll K, Reiche K, Kasack K, Mörbt N, Kretzschmar AK, Tomm JM, Verhaegh G, Schalken J, von Bergen M, Horn F, Hackermüller J.
MiR-130a, miR-203 and miR-205 jointly repress key oncogenic pathways and are downregulated in prostate carcinoma.
Oncogene. 2012 Mar 5. doi: 10.1038/onc.2012.55. [Epub ahead of print] PubMed PMID: 22391564.

Haas S, Jahnke HG, Moerbt N, von Bergen M, Aharinejad S, Andrukhova O, Robitzki AA
DIGE proteome analysis reveals suitability of ischemic cardiac in vitro model for studying cellular response to acute ischemia and regeneration.
PLoS One. 2012;7(2):e31669. Epub 2012 Feb 22. PubMed PMID: 22384053