Viral biogeochemistry

PI: Prof. Dr. Michael Pester, Co-PI: Dr. David K. Ngugi

Environmental viruses heavily influence the genetic diversity and ecology of microbial communities and thus exert control on biogeochemical cycling. This has been exemplified for the carbon cycle in concepts like the viral shunt and the viral shuttle. However, very little is known how viruses modulate N-cycling microbial communities and in turn the nitrogen cycle. In this project, we study the effect viruses have on the virocell metabolism of nitrifying microorganisms, in particular ammonia oxidizing archaea (AOA) and bacteria (AOB).

Funding: DFG priority programme SPP 2330 - New Concepts in Prokaryotic Virus-host Interactions – From Single Cells to Microbial Communities

Freshwater microbiology and N cycling

PI: Prof. Dr. Michael Pester

Freshwater lakes are important for drinking water, fisheries and have high societal significance as recreational areas. Ammonium accumulation would endanger these ecosystem services. At the same time, ammonium is an important constituent of agricultural fertilizers and its concentrations in the environment have increased dramatically with the consequence that the global nitrogen cycle has long exceeded safe operational boundaries. Using state-of-the-art methods in environmental systems microbiology (amplicon sequencing, metagenomics, metatranscriptomics) and biogeochemistry (stable isotope-based rate measurements), we study bacterioplankton dynamics, toxic cyaonobacterial blooms, sediment microbiomes and ammonia-oxidizing microorganisms in the background of climate change and steadily increasing water temperatures in lakes.

Selected references:

  1. Ngugi, D.K., Salcher, M.M., Andrei, A.-S., Ghai, R., Klotz, F., Chiriac, M.-C., Ionescu, D., Büsing, P., Grossart, H.-P., Xing, P., Priscu, J.C., Alymkulov, S., Pester, M. (2023). Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. Science Advances 9:eadc9392
  2. Klotz, F., Kitzinger, K., Ngugi, D.K., Büsing, P., Littmann, S., Kuypers, M.M.M., Schink, B., Pester, M. (2022). Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels. Nature ISME J. 16:1647–1656
  3. Herber, J., Klotz, F., Frommeyer, B., Weis, S., Straile, D., Kolar, A. Sikorski, J., Egert, M., Dannenmann, M., Pester, M. (2020) A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environ. Microbiol. 22: 212–228


PI: Prof. Dr. Michael Pester

Pyrite, better known as fool’s gold, is the most abundant iron-sulfur mineral in sediments. Over geological times, its burial in sediments controlled oxygen levels in the atmosphere and sulfate concentrations in seawater. The conversion of iron sulfide and hydrogen sulfide to pyrite was also postulated as the energy-delivering process to drive auto-catalytic synthesis of organic matter in micro-compartments of marine hydrothermal vents. The latter are currently regarded as the most likely place for life to have emerged on Earth. To date, pyrite formation was considered to be a pure (geo)chemical reaction. Currently, we study the first enrichment culture capable of converting of iron sulfide and hydrogen sulfide to pyrite when coupled to a methanogenic partner. Our research has impact on the understanding of global biogeochemical cycles on geological time scales and provides an experimental window in a postulated primordial iron-sulfur world predating the origin of life.

Selected references

  1. Thiel, J., Byrne, J.M., Kappler, A., Schink, B., and Pester, M. (2019) Pyrite formation from FeS and H2S is mediated through microbial redox activity. Proc Natl Acad Sci USA.116: 6897-6902

Synthetic soil microbiomes

PIs: Prof. Dr. Michael Pester, Dr. Katharina Fischer-Huber,
PD Dr. Meina Neumann-Schaal

Soils are essential to sustain life in terrestrial ecosystems. However, a conceptual framework that describes how the structural and functional diversity of the soil microbiome and its interaction to higher trophic levels influences energy and matter fluxes in soil is still largely missing. We use a synthetic soil community reflecting the major microbial taxa and microbial grazers in soil to study causal relationships between the energy and matter input to soils, the structure and function of the soil microbiome, and the resulting energy and matter fluxes.

Funding: DFG priority programme SPP 2322 - SoilSystems

Wetlands and sulfur cycling

PI: Prof. Dr. Michael Pester

Freshwater wetlands are not only important for sustainability of biodiversity, water quality, flood protection, and recreational value but play an integral part in Earth’s biogeochemical cycles. In particular, they are considered key habitats in the upcoming climate change, influencing both positive and negative climate feedback cycles to the atmosphere in a warmer world. We study the cryptic sulfur cycle in freshwater wetlands, which plays an important role in controlling the emission of the greenhouse gas methane from these environments. Our aim is to identify microorganisms that drive the hidden sulfur cycle in wetlands using amplicon sequencing and genome-centric metagenomics and to study their ecophysiology using metatranscriptomics and metaproteomics.

Selected references

  1. Diao, M., Dyksma, S., Koeksoy, E., Ngugi, D.K., Anantharaman, K., Loy, A., Pester, M. (2023) Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. bioRxiv, 2023.06. 27.546762

  2. Zecchin, S., Mueller, R.C., Seifert, J., Stingl, U., Anantharaman, K., von Bergen, M., Cavalca, L., Pester, M. (2018) Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium. Appl Environ Microbiol. 84: e02224-17.

  3. Hausmann, B., Pelikan, C., Herbold, C.W., Koestlbacher, S., Albertsen, M., Eichorst, S.A., Glavina del Rio, T., Huemer, M., Nielsen, P.H., Rattei, T., Stingl, U., Tringe, S.G., Trojan, D., Wentrup, C., Woebken, D., Pester, M. (corresponding author), Loy, A. (2018). Peatland Acidobacteria with a dissimilatory sulfur metabolism. The ISME J. 12: 1729–1742.

  4. Pester, M., Knorr, K.-H., Friedrich, M.W., Wagner, M., and Loy, M. (2012) Sulfate reducing microorganisms in wetlands – fameless actors in carbon cycling and climate change. Front. Microbiol. 3: doi: 10.3389/fmicb.2012.00072.