Young Investigator Programme


10 mill. DKK

[1.3 mill. EUR]

Deciphering the role of microbial dark matter by novel DNA sequencing approaches

Microbial communities underpin all processes in the environment and have direct impact on human health. Despite their importance, only a tiny fraction of the millions of different microbes is known. This is mainly due to the immense difficulties of cultivating microbes from natural systems in the laboratory. This discrepancy is also known as the “microbial dark matter”.

For any microbe, the genome is the blueprint of its physiological properties. Having this in hand, it is possible to reconstruct its potential metabolism and establish hypotheses for evolution, function and ecology. Furthermore, it provides a foundation for further validating its function through a variety of in situ methods. However, genomes are extremely difficult to obtain from the microbial dark matter.

Currently, multiple metagenomes combined with bioinformatic approaches, is used to retrieve individual genomes from complex samples. This has let to numerous fundamental discoveries, including the discovery of bacteria cable of complete ammonia oxidation (Comammox), which radically change our view of the global nitrogen cycle and granted us the “Danish research result of the year, 2015”. However, we are still far from realizing the full potential of metagenomics to retrieve genomes. Mainly due to the complexity of nature, where multiple closely related strains co-exists, which renders the current approaches useless.

In this project, we want to use cutting-edge DNA sequencing related techniques to enable access to all genomes despite strain-complexity, link genomes, plasmids and phages, and enable direct measurements of in situ bacterial activity. The ability to readily obtain activity measurements of any bacteria, in any microbial ecosystem, will radically change microbial ecology and environmental biotechnology.


AAU Talent Programme


3 mill. DKK

[0.4 mill EUR]


High-throughput and unbiased characterization of microbial communities

Microbial communities play a vital role in most processes in the biosphere and are essential for solving present and future environmental challenges, such as treatment of water and wastewater, recovery of resources (e.g. phosphorus), production of “green” chemicals (e.g. bioplastics), and production of bioenergy (methane, electricity). However, a prerequisite to realize the full potential of microbial communities is to be able to identify the key organisms. The gold standard for Bacterial identification in microbial communities is 16S rRNA gene sequencing, but it has several substantial drawbacks that needs attention. One major issue is the lack of universal primers that cover all Bacteria. Hence, potentially key species can be underrepresented or completely missed by the current primer based 16S rRNA analyses.

This project aims to enable high-throughput and unbiased characterization of microbial communities, through development of a novel primer-free full-length rRNA gene sequencing method.



Headed by

prof. Per H. Nielsen

Total 17.3 mill DKK

[2.2 mill. EUR]

Leader of WP1

OnlineDNA: Enhanced performance of environmental biotechnology systems through online DNA surveillance of microbial communities

The aim is to apply novel DNA technologies in a new way to enable fast and reliable on site identification and quantification of the important members of a given microbial community, and to integrate this information into online surveillance and control systems for wastewater treatment. This will allow diagnosis of system failure and provide diagnostics for informed guidance on early stage interventions, operational decisions and process optimizations. Furthermore, it will provide novel knowledge and tools for transforming simple wastewater treatment plants into resource producing facilities, and it will open numerous avenues for the application of microbial communities to help solve the “grand challenges” of various biotechnologies.

Responsible for WP1 development of an on-site DNA-sensor.