Dr. Carl-Eric Wegner


Phone: +49 (0)3641 9-494 48









  (Foto: Jan-Peter Kasper/FSU)


With a strong background in microbial physiology and (applied) bioinformatics, my research is dedicated to (1) microbial life under metal exposure in anthropogenic habitats, (2) microbial carbon turnover in complex ecosystems and in general “big data” analysis in environmental microbiology.

 (1) Microbial life under metal exposure in anthropogenic habitats

The mineral leaching of aluminium-sulfur minerals from soft coal was common practice for early industrial applications. Tremendous amounts of leached slags were generated as by-product of this low yield process. Considering the low pH and high aluminium content of these slags we are interested in how microbes persist in this anthropogenic environment, which, at the same time, represents a late-stage acid mine drainage system and acid mine drainage source material.

 (2) Microbial carbon turnover in complex ecosystems

Life on earth is strongly linked to the global carbon cycle, which in turn relies on microbial top-down and bottom-up processes. The application of up-to-date, high-throughput techniques allows us to bridge the gap between the metabolic potential of microbes and carbon cycling in complex environments such as peatlands, rice fields, and the Earth’s Critical Zone.

See also: www.exploringmicrobes.de 



 Google scholar


26. Li Q., Cooper R.E., Wegner C.-E., Küsel K. (2020) Molecular mechanisms underpinning aggregation in Acidiphilium sp. C61 isolated from iron-rich pelagic aggregates. Microorganisms 8(3): 314. Doi: 10.3390/microorganisms8030314.

25. Cooper R.E., Wegner C.-E., McAllister S.M., Shevchenko O., Chan C.S., Küsel K. (2020) Draft genome sequence of Sideroxydans sp. strain CL21, an Fe(II)-Oxidizing bacterium. Microbiology Resource Announcements 9(2): e01444-19. Doi: 10.1128/MRA.01444-19.



24. Geesink P., Wegner C.-E., Probst A.J., Herrmann M., Dam H.T., Kaster A.-K. and Küsel K. (2019) Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in oligotrophic groundwater. Environmental Microbiology, accepted.

23. Wegner C.-E., Gorniak L., Riedel S., Westermann M., Küsel K. (2019) Physiological and genomic insights into lanthanide-dependent methylotrophs of the family Beijerinckiaceae. Applied and Environmental Microbiology, accepted. Doi: 10.1128/AEM.01830-19.

22. Herrmann M., Wegner C.-E., Taubert M., Geesink P., Lehmann K., Yan L., Lehmann R., Totsche K.U., Küsel K. (2019) Predominance of Cand. Patescibacteria in groundwater is caused by their preferential mobilization from soils and flourishing under oligotrophic conditions. Frontiers in Microbiology 10: article 1407.

21. Abdallah RZ, Wegner CE, Liesack W (2019) Community transcriptomics reveals drainage effects on paddy soil microbiome across all three domains of life. Soil Biol. Biochem. accepted

20. Wegner C.-E., Gaspar M., Geesink P., Herrmann M., Marz M., Küsel K. (2019) Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of elements of nitrogen, sulfur and carbon. Applied and Environmental Microbiology 85(5): e02346-18.

19. Kügler S., Cooper R.E., Wegner C-E., Mohr J.F., Wichard T., Küsel K. (2019) Iron-organic matter complexes accelerate microbial iron cycling in an iron-rich fen. Science of the Total Environment 646: 972-988.



18. Peng J, Wegner CE, Bei Q, Liu P, Liesack W (2018) Metatranscriptomics reveals a different temperature effect on the structural and functional organization of the anaerobic food web in rice field soil. Microbiome 6:169

17. Ivanova AA, Wegner CE, Kim Y, Liesack W, Dedysh SN (2018) Metatranscriptomics reveals hydrolytic potential of peat-inhabiting Planctomycetes. Antonie van Leeuwenhoek 111:801-809. 



15. Cooper, R. E., Eusterhues, K., Wegner, C.-E., Totsche, K. U., Küsel, K. 2017. Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia. Biogeosciences 14(22): 5171-5188.

15. Wegner CE, Liesack W (2017) Unexpected dominance of elusive Acidobacteria in early industrial soft coal slags. Front. Microbiol.8:1023 doi: 10.3389/fmicb.2017.01023

14. Wagner T, Wegner CE,  Kahnt J, Ermler U, Shima S (2017) Phylogenetic and structural comparisons of the three types of methyl-coenzyme M reductase from Methanococcales and Methanobacteriales. J. Bacteriol. 199(16):e00197-17

13. Peng J, Wegner CE,  Liesack W (2017) Short-term exposure of paddy soil microbial communities to salt stress triggers different transcriptional responses of key taxonomic groups. Front. Microbiol. 8:400. doi: 10.3389/fmicb.2017.00400



12. Ivanova A, Wegner CE, Kim Y, Liesack W, Dedysh SN (2016) Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Mol. Ecol. 19:4818-4835

11. Tollot M, Assmann D, Becker C, Altmüller J, Dutheil JY, Wegner CE, Kahmann R (2016) The WOPR protein Ros1 is a master regulator of sporogenesis and effector gene expression in the maize pathogen Ustilago maydis. PloS Pathog. 12:e1005697

10. Wegner CE, Liesack W (2016) Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil. Environ. Microbiol. 18:2825-2842



9. Wu XH, Ge TD, Wang W, Yuan HZ, Wegner CE, Zhu ZK, Whiteley AS, Wu JS (2015) Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil. Front. Microbiol. doi: 10.3389/fmicb.2015.00379



8. Oshkin IY, Wegner CE, Lüke C, Glagolev MV, Filippov IV, Pimenov NV, Liesack W, Dedysh SN (2014) Gammaproteobacterial methanotrophs dominate cold methane seeps in floodplains of Western Siberian Rivers. Appl. Environ. Microbiol. 80:5944-5954

7. Kim Y, Wegner CE, Liesack W. (2014) Soil metatranscriptomics In Nannipieri P, Pietramellara G, Renell G (ed.) Omics in Soil Science, Caister Academic Press

6. Wegner CE, Richter M, Richter-Heitmann T, Klindworth A, Frank CS, Harder J, Glöckner FO (2014) Permanent draft genome of Rhodopirellula sallentina SM41. Mar. Genomics. 13:17-18

5. Richter M, Richter-Heitmann T, Klindworth A, Wegner CE, Frank CS, Harder J, Glöckner FO (2014) Permanent draft genomes of the three Rhodoprellula baltica strains SH28, SWK14 and WH47. Mar. Genomics. 13:13-14

4. Richter M, Richter-Heitmann T, Klindworth A, Wegner CE, Frank CS, Harder J, Glöckner FO (2014) Permanent draft genomes of the Rhodopirellula maiorica strain SM1. Mar. Genomics. 13:19-20

3. Richter-Heitmann T, Richter M, Klindworth A, Wegner CE, Frank CS, Harder J, Glöckner FO (2014) Permanent draft genomes of the two Rhodopirellula europae strains 6C and SH398. Mar. Genomics. 13:15-16

2. Klindworth A, Richter M, Richter-Heitmann T, Wegner CE, Frank CS, Harder J, Glöckner FO (2014) Permanent draft genome of Rhodopirellula rubra SWK7. Mar. Genomics. 13:11-12



1. Wegner CE, Richter-Heitmann T, Klindworth A, Klockow C, Richter M, Achstetter T, Glöckner FO, Harder J (2013) Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula. Mar. Genomics. 9:51-61


University training and degree

2006-2009 B.Sc. Applied Biology – B.Sc. (honours) Molecular Microbiology, University of Applied Sciences Bonn-Rhein-Sieg, Bonn, Germany – University of Aberdeen, Aberdeen, UK, Supervisors: Prof. Dr. Annette Menke (UoA Bonn-Rhein-Sieg), Dr. Anne Donaldson (University of Aberdeen)

2009-2011 M.Sc. Microbiology, University of Oldenburg, Oldenburg, Germany – Max Planck Institute for Marine Microbiology, Bremen, Germany, Supervisors: PD Dr. Thorsten Brinkhoff (University of Oldenburg), Prof. Dr. Frank Oliver Glöckner (Max Planck Institute Bremen)


Advanced academic qualifications

2011-2014 Ph.D. Microbiology (magna cum laude), Max Planck Institute for Terrestrial Microbiology, Marburg, Germany, Supervisor: PD Dr. Werner Liesack, Department of Biogeochemistry


Postgraduate professional career

Since 2016 Postdoctoral researcher, Friedrich Schiller University Jena, Aquatic Geomicrobiology

2014-2016 Postdoctoral researcher,  Max Planck Institute for Terrestrial Microbiology, Department of Biogeochemistry

Other (Awards, Grants, Memberships)

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

Since 2012 Member of the German Society for General and Applied Microbiology (VAAM)

Since 2012 Member of the American Society of Microbiology (ASM)

2006 Award of the Federal State of Northrhine Westphalia for Exceptional Public Service

2008 Research scholarship of the German Academic Exchange Service (DAAD) for undergraduate studies abroad at the University of Aberdeen, UK (2008-2009)

2011 Award of the University of Oldenburg for Excellent Student Accomplishments

2011-2014 Scholarship of the International Max Planck Research School for Environmental, Cellular and Molecular Microbiology

2013-2014 Spokesperson of the PhD students of Max Planck Institute for Terrestrial Microbiology


Werner Liesack, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany

Svetlana N. Dedysh, Winogradsky Institute for Microbiology, Russian Academy of Sciences, Moscow, Russia

Michael Köhler, Technical University Ilmenau, Ilmenau, Germany