Dr. Barbara Bayer

Group Leader
University of Vienna
Djerassiplatz 1
A-1030 Vienna
Phone: +43 1 4277 91236


Microorganisms influence the environment around them and are the “engines” that drive large biogeochemical cycles on our planet. Oceans and lakes are home to a plethora of different microorganisms which comprise most of the living biomass in these ecosystems. We want to understand the interactions between aquatic microorganisms and their environment, with a focus on carbon and nitrogen cycling. We combine diverse isotope approaches, cultivation, and multi-omics techniques to quantify biogeochemical processes and identify novel microorganisms and metabolic pathways.



The influence of nitrifiers on the oceanic carbon cycle

Understanding how carbon is cycled on the way to the ocean floor has important implications for the way we model the carbon cycle, and predict the ocean's role in mitigating climate change. In addition to microorganisms that consume organic carbon, the deep ocean is also home to an abundant community of microorganisms that can use chemical energy to convert inorganic carbon into biomass (chemoautotrophy). These organisms are able to oxidize, for example, reduced nitrogen compounds such as ammonia and nitrite to generate the energy they need for the fixation of inorganic carbon. This newly fixed carbon represents an important nutritional foundation for heterotrophic food webs in the deep ocean.

Nitrifying microorganisms, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB), are the most abundant chemoautotrophs in the ocean. The results of this study elucidate the diverse roles of nitrifying microorganisms in the oceanic carbon cycle, including the release of dissolved organic carbon into the environment (Bayer et al. 2019Bayer et al. 2023) and the use of alternative energy sources (Bayer et al. 2021). Furthermore, our findings provide values for biogeochemical models of the global carbon cycle, and help to further constrain the relationship between carbon and nitrogen fluxes in the nitrification process (Zakem et al. 2022).



Selected publications on this topic:

  • Bayer B, McBeain K, Carlson CA, Santoro AE. Carbon content, carbon fixation yield and dissolved organic carbon release from diverse marine nitrifiers (2023). Limnology and Oceanography 68: 84-96. https://doi.org/10.1002/lno.12252
  • Zakem EJ, Bayer B, Qin W, Santoro AE, Zhang Y, Levine NM. Global-scale abundances, nitrification rates, and carbon fixation rates of marine nitrifying microorganisms (2022). Biogeosciences 19:5401-5418. https://doi.org/10.5194/bg-19-5401-2022
  • Bayer B, Saito MA, McIlvin M, Lücker S, Moran DM, Lankiewicz TS, Dupont CL, Santoro AE. Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions (2021). The ISME Journal. 15:1025-1039. https://doi.org/10.1038/s41396-020-00828-3
  • Bayer B, Hansman R, Bittner MJ, Ortega-Noriega BE, Niggemann J, Dittmar T, Herndl GJ. Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean (2019). Environmental Microbiology 21:4062-4075. https://doi.org/10.1111/1462-2920.14755


  • Austrian Science Fund (FWF) Erwin Schrödinger project J4426-B (2020-2023), PI: Barbara Bayer
  • DOE Joint Genome Institute CSP New investigator grant 506203 (2020-2022), PI: Alyson Santoro, co-PI: Barbara Bayer



Microbial methane cycling in aquatic ecosystems

Aquatic ecosystems are a major source of the potent greenhouse gas methane, accounting for half of the global methane emissions. Biogenic methane is microbially produced in anoxic sediments and typically rapidly consumed by methanotrophic microorganisms, largely limiting emissions to the atmosphere (“microbial methane filter”). However, methane concentrations are often elevated in oxic surface waters of oceans and lakes (“methane paradox”). Due its proximity to the atmosphere, aerobic methane production in surface waters might constitute a particularly important source of methane, which might escape the aquatic “microbial methane filter”. Yet, we currently lack a comprehensive understanding of the involved processes and microorganisms. Moreover, enhanced eutrophication of coastal ocean and lake ecosystems due to human activities has been linked to increased methane emissions. However, we know remarkably little about how changes in environmental conditions affect the in situ activities of diverse methane-cycling microorganisms, which is of central importance to better predict future climate developments.

We will address these knowledge gaps by i) resolving and quantifying aerobic methane production in surface waters of aquatic ecosystems with different trophic states, and ii) unravelling how eutrophication affects methane-consuming microorganisms in water columns of coastal ocean and lake ecosystems.

Newly funded by the Austrian Science Fund (FWF) START Award (“METHANIAQ”).

Start date: January 2024

PhD and Postdoc positions are available. Get in touch to learn more and/or to apply. Details here

Lab members: