Dr. Manuel Kleiner

Assistant Professor

Microbiomes and Complex Microbial Communities Cluster

Twitter: @Manuel_Kleiner


Research Interests
Microbial physiology and metabolism, bacteria-animal symbiosis, metagenomics and metaproteomics, environmental microbiology, marine microbiology, and renewable resources

Microbial communities are ubiquitous in all environments on Earth that support life, and they play crucial roles in global biogeochemical cycles, plant and animal health, and biotechnological processes. However, most microbial species from a given habitat cannot be cultured and thus cannot be experimentally characterized in the laboratory. Therefore, to study environmental microbes we rely on so-called cultivation-independent methods that allow us to study microorganisms directly in their environment.

We study the metabolism, physiology, and evolutionary ecology of microbial symbioses and uncultured microorganisms. To this end we develop and use cultivation-independent approaches such as metagenomics, metaproteomics, and metabolomics, as well as more targeted approaches such as enzyme assays, single-cell imaging methods, and stable isotope-based experiments. We combine the study of uncultured microorganisms with genetic, molecular, and biochemical studies on cultivable microorganisms to gain an in-depth understanding of specific metabolic pathways and physiological strategies.

The current projects focus on:

  • factors governing energy efficiency of metabolism in free-living and symbiotic bacteria, looking specifically at a novel CO2 fixation pathway
  • the role of horizontal gene transfer in the metabolic evolution of bacterial symbionts
  • development of cutting-edge methods for microbial community analyses focusing on metagenomics and high-end mass spectrometry based metaproteomics

Selected Publications (See full list  in GoogleScholar)

Ponnudurai, R. P., M. Kleiner, L. Sayavedra, J. M. Petersen, M. Moche, A. Otto et al. (2017). Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis. The ISME Journal 11: 463-477. doi:10.1038/ismej.2016.124

Wippler, J., M. Kleiner, C. Lott, A. Gruhl, P. Abraham, R. Giannone et al. (2016). Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis. BMC Genomics 17(1): 942. doi.org/10.1186/s12864-016-3293-y

Yu, Y.-T. N., M. Kleiner and G. J. Velicer (2016). Spontaneous reversions of an evolutionary trait loss reveal regulators of a sRNA that controls multicellular development in the myxobacteria. Journal of Bacteriology 198(23): 3142-3151.

Petersen, J. M., A. Kemper, H. Gruber-Vodicka, U. Cardini, M. van der Geest, M. Kleiner et al. (2016). Chemosynthetic sulphur-oxidizing symbionts of marine invertebrate animals are capable of nitrogen fixation. Nature Microbiology 2:16195. doi:10.1038/nmicrobiol.2016.195

Hamann, E., H. Gruber-Vodicka, M. Kleiner, H. Tegetmeyer, D. Riedel, S. Littmann et al. (2016). Environmental Breviatea harbor mutualistic Arcobacter epibionts. Nature 534: 254-258. doi:10.1038/nature18297

Kleiner, M., C. Wentrup, T. Holler, G. Lavik, J. Harder, C. Lott, S. Littmann, M. M. M. Kuypers and N. Dubilier (2015). Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments. Environmental Microbiology 17(12): 5023-5035doi: 10.1111/1462-2920.12912

Sayavedra, L., M. Kleiner, R. Ponnudurai, S. Wetzel, E. Pelletier, V. Barbe et al. (2015). Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. eLife 4:e07966. doi: 10.7554/eLife.07966

Kleiner, M., L. V. Hooper and B. A. Duerkop (2015). Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 16(7). doi:10.1186/s12864-014-1207-4

Kleiner, M., J. C. Young, M. Shah, N. C. VerBerkmoes and N. Dubilier (2013). Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts. mBio 4(3): e00223-13. doi: 10.1128/mBio.00223-13

Kleiner, M., C. Wentrup, C. Lott, H. Teeling, S. Wetzel, J. Young et al. (2012). Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proceedings of the National Academy of Sciences 109(19): E1173-E1182. Original publication (open access)

Kleiner, M., J. M. Petersen and N. Dubilier (2012). Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer. Current Opinion in Microbiology 15(5): 621-631. doi:10.1016/j.mib.2012.09.003