Dr. Denny Popp

Dr. Denny Popp


Denny Popp


Department of Environmental Microbiology
Working Group Systems Biology of Microbial Communities
Helmholtz Centre for
Environmental Research - UFZ
Permoserstr. 15, 04318 Leipzig, Germany

Phone +49 341 235 482247


2016 –

Helmholtz Centre for Environmental Research – UFZ, Department of Environmental Microbiology, Group Systems Biology of Microbial Communities

09 - 12/2015

Guest Scientist
Wageningen University, Laboratory of Microbiology, group Microbial Physiology (DAAD scholarship)

2012 – 2016

PhD student
Helmholtz Centre for Environmental Research – UFZ, Leipzig in cooperation with Deutsches Biomasseforschungszentrum (DBFZ), Department of Environmental Microbiology, Group Microbiology of Anaerobic Systems
PhD thesis: "Alternative substrates for biogas production: Impact of plant secondary metabolites on the anaerobic digestion process" (Leipzig University)

2010 – 2012

Applied Science (M.Sc.)
TU Bergakademie Freiberg, Germany
Master thesis: “Elastic networks: Study of large-scale conformational motions of membrane proteins” at the Fritz Haber Institute of the Max Planck Society in Berlin

2007 – 2010

Applied Science (B.Sc.)
TU Bergakademie Freiberg, Germany

Internships and thesis

You are interested in supporting our group? Just send us in email with your interests, intended date and duration of your research stay and a CV!


Contributions to teaching:

HIGRADE course: Introduction to Systems Biology: From OMICS data analysis to metabolic network modeling (in autumn every year)

Develop course: Introduction to Amplicon and Metagenome Analyses (in summer every year)

Develop course: Introduction to long read sequencing for (meta)genomics (in winter every year)

University Leipzig - Quantitative Biology for a Sustainable Environmental and Industrial Biotechnology - Lecture and exercise (summer term 2018 and 2019)

TU Dresden - Continuous Bioprocesses: Anaerobic Digestion - Lecture and exercise (winter term 2017/18 - 2019/20)

Social Media


Peer reviewed publications


Bin Liu, Denny Popp, Heike Sträuber, Hauke Harms, Sabine Kleinsteuber. Draft Genome Sequences of Three Clostridia Isolates Involved in Lactate-based Chain Elongation. Microbial Resource Announcements 2020 9:e00679-20 doi:10.1128/MRA.00679-20

Denny Popp & Florian Centler. µbialSim: constraint-based dynamic simulation of complex microbiomes. Frontiers in Bioengineering and Biotechnology 2020 8:574 doi:10.3389/fbioe.2020.00574

Daniela Becker, Denny Popp, Hauke Harms, Florian Centler. A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion. microorganisms 2020 8(5):669 doi:10.3390/microorganisms8050669

Song-Can Chen, Guo-Xin Sun, Yu Yan, Konstantinos T. Konstantinidis, Si-Yu Zhang, Ye Deng, Xiao-Min Li, Hui-Ling Cui, Florin Musat, Denny Popp, Barry P. Rosen, Yong-Guan Zhu. The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling. PNAS 2020 doi:10.1073/pnas.2001063117

Washington Logroño, Denny Popp, Sabine Kleinsteuber, Heike Sträuber, Hauke Harms, Marcell Nikolausz. Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH. microorganisms 2020 8:614 doi:10.3390/microorganisms8040614


Sören Weinrich, Sabine Koch, Fabian Bonk, Denny Popp, Dirk Benndorf, Steffen Klamt, Florian Centler. Augmenting biogas process modeling by resolving intracellular metabolic activity. Frontiers in Microbiology 2019 10:1095 doi: 10.3389/fmicb.2019.01095

Song-Can Chen, Niculina Musat, Oliver J. Lechtenfeld, Heidrun Paschke, Matthias Schmidt, Nedal Said, Denny Popp, Federica Calabrese, Hryhoriy Stryhanyuk, Ulrike Jaekel, Yong-Guan Zhu, Samantha B. Joye, Hans-Hermann Richnow, Friedrich Widdel, Florin Musat. Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature. 2019 568:108-111 doi: 10.1038/s41586-019-1063-0

Fabian Bonk, Denny Popp, Sören Weinrich, Heike Sträuber, Daniela Becker, Sabine Kleinsteuber, Hauke Harms, Florian Centler. Determination of Microbial Maintenance in Acetogenesis and Methanogenesis by Experimental and Modeling Techniques. Frontiers in Microbiology. 2019 10:166 doi: 10.3389/fmicb.2019.00166


Fabian Bonk, Denny Popp, Sören Weinrich, Heike Sträuber, Sabine Kleinsteuber, Hauke Harms, Florian Centler. Ammonia inhibition of anaerobic volatile fatty acid degrading microbial communities. Frontiers in Microbiology. 2018 9:2921 doi: 10.3389/fmicb.2018.02921

Fabian Bonk, Denny Popp, Sören Weinrich, Heike Sträuber, Sabine Kleinsteuber, Hauke Harms, Florian Centler. Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion. Biotechnology for Biofuels 2018 11:274 doi: 10.1186/s13068-018-1279-5

Fabian Bonk*, Denny Popp*, Hauke Harms, Florian Centler. PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. Journal of Microbiological Methods. 2018 153:139-147 doi: 10.1016/j.mimet.2018.09.015 (*contributed equally)

Babett Wintsche, Nico Jehmlich, Denny Popp, Hauke Harms, Sabine Kleinsteuber. Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation. Frontiers in Microbiology. 2018 9:405
doi: 10.3389/fmicb.2018.00405


Denny Popp, Caroline M. Plugge, Sabine Kleinsteuber, Hauke Harms, Heike Sträuber. Inhibitory effect of coumarin on syntrophic fatty acid oxidizing and methanogenic cultures and biogas reactor microbiomes. Applied and Environmental Microbiology. 2017;83(13):e00438-17 doi: 10.1128/AEM.00438-17

Denny Popp, Philipp von Gillhaussen, Emanuela W.A. Weilich, Heike Sträuber, Hauke Harms, Vicky M. Temperton. Methane yield of biomass from extensive grassland is affected by compositional changes induced by order of arrival. GCB Bioenergy. 2017; doi: 10.1111/gcbb.12441


Denny Popp, Hauke Harms, Heike Sträuber. The alkaloid gramine in the anaerobic digestion process—inhibition and adaptation of the methanogenic community. Applied Microbiology and Biotechnology. 2016.
doi: 10.1007/s00253-016-7571-z


Denny Popp, Steffi Schrader, Sabine Kleinsteuber, Hauke Harms, Heike Sträuber. Biogas production from coumarin-rich plants—inhibition by coumarin and recovery by adaptation of the bacterial community. FEMS Microbiology Ecology. 2015;91(9).
doi: 10.1093/femsec/fiv103


Holger Flechsig, Denny Popp, Alexander S. Mikhailov. In Silico Investigation of Conformational Motions in Superfamily 2 Helicase Proteins. PLoS ONE. 2011:6(7): e21809
doi: 10.1371/journal.pone.0021809

(My publon profile)

Book chapter

P. Walter Stinner, Arno Deuker, Tina Schmalfuß, Christopher Brock, Nadja Rensberg, Velina Denysenko, Paul Trainer, Kurt Möller, Joachim Zang, Leandro Janke, Wilson Mozena Leandro, Katja Oehmichen, Denny Popp, Jaqueline Daniel-Gromke. Perennial and Intercrop Legumes as Energy Crops for Biogas Production. In: Legumes for Soil Health and Sustainable Management. Ram Swaroop Meena, Anup Das, Gulab Singh Yadav, Rattan Lal (Eds.) 2018, Springer Singapore
doi: 10.1007/978-981-13-0253-4


  • Young Investigator Group Award - e:Bio Status Seminar 2017 BMBF, September 2017, Dresden, Germany
  • Best Poster Prize - 3rd International Conference on Biogas Microbiology (ICBM3), May 2017, Wageningen, The Netherlands
  • Best Poster Slam - 3rd International Conference on Monitoring and Process Control of Anaerobic Digestion Plants, March 2017, Leipzig, Germany