European Union’s Horizon 2020 research and innovation programme PROSPECTOMICS

Project PROSPECTOMICS (part of the Future and Emerging Technologies (FET) initiative as part of Horizon 2020), aims towards providing multi-omics solutions to lower the environmental impacts of hydrocarbon prospection in marine context. Despite the development and use of renewable energy technology, the societal dependence on hydrocarbons (oil and gas) will be maintained in coming decades. PROSPECTOMICS will analyse environmental microbial DNA, RNA and proteins as well as local geochemistry in shallow marine sediments in the Barents Sea to identify multi-omics markers of microbial responses to hydrocarbon presence. To achieve this, metagenomes, metatranscriptomes, metaproteomes as well as detailed geochemical data will be analysed individually and finally integrated via machine learning. The GAME will deliver on the metagenomics work package of this project.

For more information see:

Ongoing until 2024

BMBF MultiKulti 1.0: Cultivation of previously uncultivated microorganisms from different aquatic habitats

Although microorganisms are the most diverse and abundant life forms on Earth only a few of them can be kept alive in the laboratory for longer periods. For the directed cultivation of previously uncultivated microorganisms, the project’s vision is the development of an automated bioreactor system that simulates habitat conditions as closely as possible and – controlled by biological measured variables – makes target organisms available for systematic isolation experiments in the long term. The “MultiKulti reactor” will be used exemplarily for the cultivation of scientifically relevant groups of organisms from aquatic habitats, which do not have a cultivated representative yet. Out target organism is an archaeal phylotype, called Altiarchaeota, with biotechnological application potential from a cold-water geyser. To this end, the ecophysiology of Altiarchaeota will first be investigated using genome-resolved metagenomics, microscopy, and NanoSIMS. Based on these results the bioreactor will be used for in-situ cultivation. For innovative reactor control, a “live sequencing” coupled with live/dead staining will be established and applied. The findings of the project will contribute substantially to the understanding of Altiarchaeota and generally improve the possibilities to cultivate previously uncultured microorganisms.

For more information see:

Ongoing until 2024

Project A01 - Direct and indirect effects of multiple stressors in freshwater ecosystems on microbial parasites and scavengers CRC RESIST - Multilevel response to stressor increase and release in stream ecosystems

Freshwater ecosystems can be exposed to multiple stressors over time, some of them being imposed due to natural (e.g. seasonal) fluctuations, others due to human activity. While the effects of stressors on microbial community composition have been investigated for several freshwater ecosystems, the resulting impacts on microbial interactions including virus-host dynamics remain unexplored. Here, we propose to investigate the dynamics and interactions of microbial parasites, including viruses and microbial scavengers, and their potential hosts when exposed to multiple stressors in freshwater systems.

For more information see: Project A01 of CRC  RESIST

Ongoing until 2024.

NRW return award eSym EcoSystems Biology of a subsurface environment

The subsurface houses more than 100 million gigatons of carbon (mostly in form of carbonate) and represents the greatest resource of carbon on this planet. However, no climate change model considers this carbon reservoir, as it is believed not to be bioavailable. Our investigations of subsurface microbial communities, particularly those in high-CO2 and anaerobic environments, showed a high capacity for carbon fixation. In fact, this process sustains complex microbial communities, which span most of the known tree of life. In eSym, we are studying how carbon compounds in subsurface community are recycled between community members. We utilize state-of-the-art genome-resolved meta’omics methods by coupling genomes from metagenomes to isotopic lipid analyses and proteomics. Understanding carbon cycling in subsurface ecosystems will ultimately have profound implications on carbon climate change models.

Ongoing until Sept 2022

DFG PR1603/2-1 NOVAC - Novel viruses of terrestrial subsurface archaea impacting global carbon cycling

The (deep) continental subsurface is home to a great abundance and diversity of archaea and bacteria, yet little is known about the viruses that infect these organisms. Of particular interest are dominant primary producers as they jump-start the food chain in these oligotrophic ecosystems and could in theory be an important target for viruses. In this proposal we hypothesize that Altiarchaeota, an uncultivated group of autotrophic subsurface archaea that occur in hot spots across the globe, are frequent targets of novel viruses that consequently impact carbon cycling. Using a combination of several state-of-the-art approaches including genome-resolved metagenomics, metatranscriptomics, and genome-informed microscopy, this project will result in a comprehensive dataset of a uncultivated virus-host system in order to unravel the different infection stages of a virus in the actual ecosystem. The results of this proposal will shed new light on the diversity and function of deep subsurface viruses that infect autotropic archaea and thus alter carbon cycling in these environments.

Ongoing until 2022

Finished Projects

ESA / DLR DISPERS - Dispersal of microorganisms and viruses to the Antarctic with implications for space exploration

In this ESA and DLR funded project, we intend to decipher the dispersal routes of microbes to the Antartic continent. We use genome-resolved metagenomics as well as cultivation experiments in collaboration with Ralf Möller's group at the DLR.

Finished mid of 2021

BMBF MultiKulti (exploratory phase)

The Project MultiKulti ("Schöner Wohnen - Reality Lofts für Anspruchsvolle") deals with the cultivation of uncultured microorganisms (bacteria and archaea) from deep oceanic and continental subsurface environments. Therefore, we teamed up with engineers to design an in situ bioreactor for continuous sampling of ecosystems. This project is in its definition phase.

Finished Nov 2020

Sloan Foundation Subaward Deep Life Deep Life - novel autotrophs in aquifers rich in carbon dioxide

Prokaryotes can transform carbon dioxide to organic matter using several different pathways, which is termed autotrophy. In this project we analyze untapped high carbon dioxide aquifers to identify previously unknown carbon dioxide fixers. Thereby, we employ genome-resolved metagenomics and couple it to lipidomics using bioinformatics and biostatistics.

Finished Nov 2019