Astounding Complexity of Bacterial Genomes Revealed

Agroscope researchers have cracked an especially tricky bacterial genome code and published an analysis of the complexity of genetic information of nearly 10,000 bacteria. Such knowledge makes it possible inter alia to explore the mechanism of action of microorganisms, with the aim of inhibiting pathogens that cause plant diseases.

Decoding the DNA of bacteria is an important step in understanding what varied functions these microorganisms can perform, allowing us to learn, for example, which antibiotics a particular bacterium is resistant to, or which factors can help control plant pathogens. Such information, which is of great relevance for Agroscope, was investigated as part of the Microbial Biodiversity (MikBioDiv) Research Programme.

The team led by Christian Ahrens – a bioinformatician at Agroscope and a member of the Swiss Institute of Bioinformatics – has now succeeded in revealing the unexpected complexity of bacterial genomes. This enables researchers to choose the optimal strategy for completely decoding even the genomes of bacteria with very complex DNA. In the case of the studied bacterium, Pseudomonas koreensis, very long, nearly identical sequence repetitions (so-called ‘repeats’) made a complete decoding difficult. Ultimately, the Agroscope team succeeded in determining the entire DNA sequence with the help of very long sequences which it generated on site with the new Oxford Nanopore technology. Despite the commonly-held opinion that such repeats are not functionally relevant, and contain no important genes, the researchers discovered in this case several copies of genes conferring an advantage to the bacterium in terms of survival on plant surfaces.

In addition, the experts have made analyses of the repeat complexity of almost 10,000 bacterial genomes freely available. These analyses show that approx. three per cent of all bacterial genomes are highly complex. What’s more, the sequencing technology used has led to the conclusion that some of these genomes are not fully decoded, and still contain errors.
This approach is also currently benefiting a joint project with Switzerland’s Research Institute of Organic Agriculture (FiBL), in which individual microorganisms isolated from compost microbiomes are being completely sequenced. The researchers plan to study which mechanisms of action allow the microorganisms to inhibit pathogens triggering plant diseases. Both this project and the collaboration with Agroscope’s Phytopathology Research Group make important contributions to the National Action Plan for Plant Protection.

The analysis is currently being refined, in order to further strengthen the team’s portfolio of methodologies in the promising research area of functional genomics. The intention is to contribute to an increasing translation of aspects of basic research to applied practice, such as a more targeted use of microbiomes.