Cultivating aquatic microorganisms in the laboratory

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Multicultural microbes

A new collaborative research project involving FAU is working to cultivate communities of microorganisms under laboratory conditions. The aim is to develop a bioreactor which can simulate the microbes’ natural habitats. The Federal Ministry of Education and Research (BMBF) has provided 2.5 million euros in funding for the project over the next three years.

The research project coordinated by the University of Oldenburg is named ‘Cultivation of previously uncultivated microorganisms from different aquatic habitats’ (MultiKulti) and aims to cultivate microorganisms and their natural communities in the laboratory. The project involves researchers from across the whole of Germany working together to develop a bioreactor capable of simulating the natural habitat of microbes as accurately as possible, thereby allowing them to be cultivated in the laboratory. In the long term, the researchers hope to develop a fully automated, AI-controlled system which can be used for a number of different research approaches, for example investigating the ecology of microbes or looking into other biotechnological applications.

Microorganisms can be found throughout the world and play an important role in all ecosystems. ‘Nevertheless, we know very little at all about the majority of microorganisms living in the wild,’ explains project coordinator Prof. Dr. Martin Könneke from Oldenburg. Experts use the term ‘microbial dark matter’. The problem is that only very few microbes can be kept alive in the laboratory for longer periods of time. This is a challenge for researchers, which prevents them from conducting experiments on organisms living in inaccessible regions such as the depths of the ocean, groundwater or stretches of water in areas with extreme environmental conditions.

The team of researchers now hopes to develop a bioreactor which can be used to cultivate microbes which have adapted to live in very specific environments. They are taking the novel approach of using a fully automated, modular bioreactor to create conditions for these organisms in the laboratory which mirror their natural habitat as closely as possible. Researchers will use modern methods from the field of molecular biology to analyse the communities and adjust living conditions accordingly.

Prof. Dr. Katharina Herkendell, assistant professor for decentralised energy process engineering at FAU, is involved in the project. The researcher and her team have received funding amounting to approximately 570,000 euros, and are responsible for realising the component around which the whole project revolves. The bioreactor, which was already designed during the exploratory phase under the direction of research associate Thomas Trabold and transformed into a prototype in close collaboration with Humboldt Universität Berlin now has to be adapted to meet the specific microbiological and security requirements, before being scaled and produced as a transportable system. It is particularly important for the researchers that the system is extremely flexible and suitable for implementing the chosen biological monitoring methods. FAU is also responsible for controlling and automating the bioreactor. The modular design of the system is intended to ensure that the reactor remains mobile, and can be used even when taking samples. When building the system, it is important to avoid high pressure gradients in order to ensure that the microorganisms can be transferred without any difficulties.

The MultiKulti team is focusing on three groups of microbes. One group is found in our groundwater and drinking water, and is of importance, for example, to technical water treatment plants. A second group lives in cold water geysers and may be of significance for biotechnological applications. The third group of microbes plays an important ecological role in the ocean. The researchers are also investigating the effect extraterrestrial conditions may have on certain microorganisms, for example on Mars.

The research consortium was established in 2019 during a workshop run by BMBF. As well as the University of Oldenburg and FAU, the project also involves researchers from Humboldt Universität Berlin, the University of Duisburg-Essen, the DVGW-Technologiezentrum Wasser in Karlsruhe (the German Water Centre) and the German Aerospace Center (DLR) in Cologne.

Further information:

Prof. Dr. Katharina Herkendell

Assistant professor for decentralised energy process engineering

Phone: +49 911 5302 9032