Dr. Jochen A. Müller

Helmholtz Centre for Environmental Research - UFZ
Department Environmental Biotechnology
Permoserstraße 15
04318 Leipzig

Tel. +49 341 235 1763
Fax +49 341 235 451694

Foto Jochen Müller

Research Areas

Microbial transformations constitute a major determining factor for the chemical fate of organic compounds in complex systems. One of my aims is to develop and implement new molecular biological tools for characterizing and quantifying the role microbes play in the in situ transformation of organic pollutants. Particular emphasis is on techniques that (1) allow for quantification of the respective biocatalysts, and (2) provide information of relevant microbes on the single cell level. In the past, my contributions were in the areas of anaerobic transformation of chlorinated ethenes and aromatic compounds, as well as in genomics and functional genomics of sulphur compound-metabolizing microbes.

Curriculum Vitae


Diploma in Microbiology, Universität Konstanz, Germany


Ph.D. in Microbiology with Prof. Bernhard Schink (Schink Lab), Universität Konstanz


PostDoc in the Department of Civil and Environmental Engineering, Stanford University, CA, USA, with Prof. Alfred Spormann (Spormann Lab).


PostDoc at the Center of Biotechnology, University of Maryland, USA, with Prof. Shiladitya DasSarma (DasSarma Lab).


Assistant Professor in Microbiology at Morgan State University, Baltimore, USA (Morgan State)

seit 2010

Senior Scientist at the Helmholtz-Centre for Environmental Research- UFZ, Leipzig

Funded Projects

  • Genomics of Beggiatoa alba, a sulfide-oxidizing g-Proteobacterium (NSF, JGI/DOE)

Professional Service

Member of the Editorial Board of

  • Applied and Environmental Microbiology (seit 2009)
  • Saline Systems (seit 2009)

2019 (2)

  • Arslan, M., Devisetty, U.K., Porsch, M., Große, I., Müller, J.A., Michalski, S., (2019):
    RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification
    BMC Genomics 20 , art. 489
    full text (url)
  • Wahla, A.Q., Iqbal, S., Anwar, S., Firdous, S., Müller, J.A., (2019):
    Optimizing the metribuzin degrading potential of a novel bacterial consortium based on Taguchi design of experiment
    J. Hazard. Mater. 366 , 1 - 9
    full text (url)

2018 (2)

  • Adelowo, O.O., Helbig, T., Knecht, C., Reincke, F., Mäusezahl, I., Müller, J.A., (2018):
    High abundances of class 1 integrase and sulfonamide resistance genes, and characterisation of class 1 integron gene cassettes in four urban wetlands in Nigeria
    PLOS One 13 (11), e0208269
    full text (url)
  • Adelowo, O.O., Vollmers, J., Mäusezahl, I., Kaster, A.-K., Müller, J.A., (2018):
    Detection of the carbapenemase gene blaVIM-5 in members of the Pseudomonas putida group isolated from polluted Nigerian wetlands
    Sci. Rep. 8 , art. 15116
    full text (url)

2017 (4)

  • Arslan, M., Ullah, I., Müller, J.A., Shahid, N., Afzal, M., (2017):
    Organic micropollutants in the environment: ecotoxicity potential and methods for remediation
    In: Anjum, N.A., Gill, S.S., Tuteja, N., (eds.)
    Enhancing cleanup of environmental pollutants. Volume 1: Biological Approaches
    Springer International Publishing, Cham, p. 65 - 99
    full text (url)
  • Meyer-Cifuentes, I., Fiedler, S., Müller, J.A., Kappelmeyer, U., Mäusezahl, I., Heipieper, H.J., (2017):
    Draft genome sequence of Magnetospirillum sp. strain 15-1, a denitrifying toluene degrader isolated from a planted fixed-bed reactor
    Genome Announc. 5 (32), e00764-17
    full text (url)
  • Meyer-Cifuentes, I., Martinez-Lavanchy, P.M., Marin-Cevada, V., Böhnke, S., Harms, H., Müller, J.A., Heipieper, H.J., (2017):
    Isolation and characterization of Magnetospirillum sp. strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model
    PLOS One 12 (4), e0174750
    full text (url)
  • Wiessner, A., Kuschk, P., Nguyen, P.M., Müller, J.A., (2017):
    The sulfur depot in the rhizosphere of a common wetland plant, Juncus effusus, can support long-term dynamics of inorganic sulfur transformations
    Chemosphere 184 , 375 - 383
    full text (url)

2016 (7)

  • Chen, Z., Paredes Cuervo, D., Müller, J.A., Wiessner, A., Köser, H., Vymazal, J., Kästner, M., Kuschk, P., (2016):
    Hydroponic root mats for wastewater treatment—a review
    Environ. Sci. Pollut. Res. 23 (16), 15911 - 15928
    full text (url)
  • Lünsmann, V., Kappelmeyer, U., Benndorf, R., Martínez-Lavanchy, P.M., Taubert, A., Adrian, L., Duarte, M., Pieper, D.H., von Bergen, M., Müller, J.A., Heipieper, H.J., Jehmlich, N., (2016):
    In situ protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model
    Environ. Microbiol. 18 (4), 1176 - 1186
    full text (url)
  • Lünsmann, V., Kappelmeyer, U., Taubert, A., Nijenhuis, I., von Bergen, M., Heipieper, H.J., Müller, J.A., Jehmlich, N., (2016):
    Aerobic toluene degraders in the rhizosphere of a constructed wetland model show diurnal polyhydroxyalkanoate metabolism
    Appl. Environ. Microb. 82 (14), 4126 - 4132
    full text (url)
  • Richter, J., Wiessner, A., Zehnsdorf, A., Müller, J.A., Kuschk, P., (2016):
    Injection of hydrogen gas stimulates acid mine drainage treatment in laboratory-scale hydroponic root mats
    Eng. Life Sci. 16 (8), 769 - 776
    full text (url)
  • Saad, R.A.B., Kuschk, P., Wiessner, A., Kappelmeyer, U., Müller, J.A., Köser, H., (2016):
    Role of plants in nitrogen and sulfur transformations in floating hydroponic root mats: A comparison of two helophytes
    J. Environ. Manage. 181 , 333 - 342
    full text (url)
  • Seeger, E.M., Braeckevelt, M., Reiche, N., Müller, J.A., Kästner, M., (2016):
    Removal of pathogen indicators from secondary effluent using slow sand filtration: Optimization approaches
    Ecol. Eng. 95 , 635 - 644
    full text (url)
  • Wu, S., Carvalho, P.N., Müller, J.A., Manoj, V.R., Dong, R., (2016):
    Sanitation in constructed wetlands: A review on the removal of human pathogens and fecal indicators
    Sci. Total Environ. 541 , 8 - 22
    full text (url)

2015 (3)

  • Martínez-Lavanchy, P.M., Chen, Z., Lünsmann, V., Marin-Cevada, V., Vilchez-Vargas, R., Pieper, D.H., Reiche, N., Kappelmeyer, U., Imparato, V., Junca, H., Nijenhuis, I., Müller, J.A., Kuschk, P., Heipieper, H.J., (2015):
    Microbial toluene removal in hypoxic model constructed wetlands occurs predominantly via the ring monooxygenation pathway
    Appl. Environ. Microb. 81 (18), 6241 - 6252
    full text (url)
  • Pfannes, K.R., Langenbach, K.M.W., Pilloni, G., Stührmann, T., Euringer, K., Lueders, T., Neu, T.R., Müller, J.A., Kästner, M., Meckenstock, R.U., (2015):
    Selective elimination of bacterial faecal indicators in the Schmutzdecke of slow sand filtration columns
    Appl. Microbiol. Biotechnol. 99 (23), 10323 - 10332
    full text (url)
  • Zanaroli, G., Beck, H., Beimfohr, C., Cichocka, D., Corvini, P., Frascari, D., Hofmann, U., Kästner, M., Macek, T., Müller, J.A., Uhlik, O., Schlosser, D., (2015):
    Analytical and monitoring methods
    In: Hochstrat, R., Wintgens, T., Corvini, P., (eds.)
    Immobilized biocatalysts for bioremediation of groundwater and wastewater
    IWA Publishing, London, p. 15 - 48

2014 (3)

  • Chen, Z., Kuschk, P., Paschke, H., Kästner, M., Müller, J.A., Köser, H., (2014):
    Treatment of a sulfate-rich groundwater contaminated with perchloroethene in a hydroponic plant root mat filter and a horizontal subsurface flow constructed wetland at pilot-scale
    Chemosphere 117 , 178 - 184
    full text (url)
  • Scheublin, T.R., Deusch, S., Moreno-Forero, S.K., Müller, J.A., van der Meer, J.R., Leveau, J.H.J., (2014):
    Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds
    Environ. Microbiol. 16 (7), 2212 - 2225
    full text (url)
  • Wiessner, A., Müller, J.A., Kuschk, P., Kappelmeyer, U., Kästner, M., Liu, Y.L., Stottmeister, U., (2014):
    Environmental pollution by wastewater from brown coal processing – a remediation case study in Germany
    J. Environ. Eng. Landsc. Manag. 22 (1), 71 - 83
    full text (url)

2013 (4)

  • Löffler, F.E., Yan, J., Ritalahti, K.M., Adrian, L., Edwards, E.A., Konstantinidis, K.T., Müller, J.A., Fullerton, H., Zinder, S.H., Spormann, A.M., (2013):
    Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi
    Int. J. Syst. Evol. Microbiol. 63 (2), 625 - 635
    full text (url)
  • Ricken, B., Corvini, P.F.X., Cichocka, D., Parisi, M., Lenz, M., Wyss, D., Martínez-Lavanchy, P.M., Müller, J.A., Shahgaldian, P., Tulli, L.G., Kohler, H.-P.E., Kolvenbach, B.A., (2013):
    ipso-hydroxylation and subsequent fragmentation: a novel microbial strategy to eliminate sulfonamide antibiotics
    Appl. Environ. Microb. 79 (18), 5550 - 5558
    full text (url)
  • Wu, S., Kuschk, P., Wiessner, A., Müller, J.A., Saad, R.A.B., Dong, R., (2013):
    Sulphur transformations in constructed wetlands for wastewater treatment: a review
    Ecol. Eng. 52 , 278 - 289
    full text (url)
  • Wu, S., Wiessner, A., Braeckevelt, M., Kappelmeyer, U., Dong, R., Müller, J.A., Kuschk, P., (2013):
    Influence of nitrate load on sulfur transformations in the rhizosphere of Juncus effusus in laboratory-scale constructed wetlands treating artificial domestic wastewater
    Environ. Eng. Manag. J. 12 (3), 565 - 573
    full text (url)

2012 (1)

  • DasSarma, P., Zamora, R.C., Müller, J.A., DasSarma, S., (2012):
    Genome-wide responses of the model archaeon Halobacterium sp. strain NRC-1 to oxygen limitation
    J. Bacteriol. 194 (20), 5530 - 5537
    full text (url)