PhycoDesign

Why This Project?

Microalgae can do far more than most people realize. Some of them produce the fatty acid EPA (eicosapentaenoic acid), which today is mostly extracted from fish oil, a market worth more than 1.5 billion dollars. Fish oil comes from processing more than 20 million tonnes of forage fish every year, putting pressure on marine food webs. Microalgae are the original, natural producers of this valuable fatty acid and could replace fish oil as a sustainable alternative free of contamination.

The problem lies in the industrial cultivation of microalgae in photobioreactors. It remains unreliable to this day because bacterial contamination regularly causes cultures to collapse. That is one reason why many approaches treat bacteria as nothing but a threat and try to keep them out as much as possible. In reality, every algal cell is surrounded by what is known as the phycosphere, a nutrient rich microenvironment in which certain bacteria supply the alga with vitamin B12, siderophores (iron carriers) and phytohormones in exchange for fixed carbon. Some of these bacterial partners even measurably promote algal growth. Cultures of P. tricornutum that contain bacteria reach around 20 % higher cell densities under certain conditions than sterile pure cultures. The key question is therefore not how to avoid bacteria altogether, but how to tell the beneficial ones apart from the harmful ones.

The Idea: Designing Consortia Instead of Leaving Them to Chance

This is exactly where PhycoDesign comes in. The project combines computational analysis and laboratory experiments to identify growth promoting keystone bacteria within the phycosphere and to assemble them into rationally designed, stable consortia of algae and bacteria, instead of relying on trial and error as has been common practice so far.

To find out which bacteria really make good partners, the analysis answers three questions about every candidate. Who lives with whom? This is revealed by networks showing which organisms occur together (CON). Who actually drives whom, rather than simply appearing together by chance? This is tested using a method called convergent cross mapping (CCM). And how stable is this partnership over time? This is shown by energy landscape analysis (ELA). A bacterium that meets all three criteria, structurally central, causally growth promoting and part of a stable community state, counts as a promising partner for a synthetic consortium. These predictions are then tested experimentally in the lab. The best candidates are combined into deliberately assembled synthetic bacterial communities and benchmarked against natural and sterile control cultures.

Two well studied model organisms are being investigated, the marine diatom P. tricornutum, which produces EPA in relevant amounts, and the freshwater green alga C. reinhardtii, which is particularly accessible for genetic studies. For the latter, a large mutant library called CLiP with more than 60,000 mutants is available, allowing the discovered interaction mechanisms to be confirmed mechanistically.

What the Project Will Deliver

The goal is a designed consortium that produces at least 20 % more EPA than sterile standard cultures. It will be validated over several cultivation cycles and finally scaled up to continuous cultivation in a bioreactor. So that other groups can benefit as well, the entire methodology will be released as a freely accessible, open platform. Other research groups will be able to upload their own time series data and receive automated recommendations for stable, productive consortia. All sequence data will be openly archived, and the code will be made freely available for reuse.

In this way, PhycoDesign makes a concrete contribution to Germany's National Bioeconomy Strategy. It puts biological knowledge to use for sustainable, bio based value chains, reduces the need for chemicals and energy in algal cultivation, and creates a transferable innovation infrastructure with relevance far beyond microalgal biotechnology, for instance for research on the microbiome of crop plants.

Project Framework

PhycoDesign is funded for five years under the funding measure Creative Young Researchers for the Bioeconomy (BioKreativ). The project is based at the Institute for Quantitative and Theoretical Biology / Institute for Synthetic Microbiology at Heinrich Heine University Düsseldorf, led by Dr. Ellen Oldenburg. The group is scientifically supported by Prof. Dr. Anna Matuszyńska (RWTH Aachen) and Prof. Dr. Bodo Philipp (University of Münster).

We Are Looking for New Team Members

Over the course of the project, several positions will open up for people who want to work at the interface of microbiology, data analysis and biotechnology. Planned are three PhD positions, among others on work with P. tricornutum and C. reinhardtii and on developing the computational analysis pipeline, a postdoctoral position focused on lab management, cultivation and bioreactor scale up, and student assistant positions to support work in the lab. Anyone who is excited about microbiome research, synthetic biology or computational ecology, and who could see themselves becoming part of this team, is warmly invited to get in touch, even if no specific position is advertised yet.

Contact: Dr. Ellen Oldenburg, ellen.oldenburg@hhu.de