We like to explore the environmental phage diversity, understand their role in the overall ecological context, and explore this field’s potential for diverse applications. To keep this task manageable, we use Bacillus subtilis as a model host organism. In nature, it inhabits soil, one of the most diverse habitats on our planet. For decades it serves as a model system for molecular biology and industrial applications. Thus, it offers an excellent starting point for our investigations on (1) the Bacillus-based viral diversity, (2) virus interaction network and the (3) application-oriented implementation of our findings.
1. Bacillus subtilis-based viral diversity
Phages have no conserved analogue to the bacterial 16S rRNA gene enabling classical marker gene-based metagenomics. Thus, phage isolation and genome sequencing are essential to access the Bacillus-associated phage diversity and their environmental role and impact. In my opinion, the standard phage isolation methodology is strongly biased and does not allow accessing the present diversity. For example, phage G, a giant phage of Bacillus megaterium, was accidentally isolated only ones in the last century (1968) and almost got lost as it proved itself incompatible with the standard methods. Consequently, a whole „world“ of viral diversity with all its potentials has remained hidden to us due to limited capabilities to tap into it. To overcome this limitation, we explore new isolation procedures to obtain rare phages of B. subtilis.
2. Phage interaction networks
Knowledge about prokaryotic virus diversity associated with a host is the first step to understanding their environmental impact and interaction networks. However, the phage-host relationship is not limited to one host and its diverse predators. Each individual phage-type has a specific host range and defines an interaction range to act as a genetic vehicle. Furthermore, it is assumable that phages of diverse types infect the same host cell. In such a case, a hybrid virocell would be established where both phages interact with each other. Besides, a phage does not ultimately have to kill its host. Some phage-types are capable of the temperate life-cycle and establish stable relationships by forming prophages and creating lysogenic bacteria. The prophage can significantly impact its lysogens properties to serve itself or for the good of both. Some of these questions we like to address within the following projects.
When two phages quarrel, does the bacterium rejoice?
3. Application-oriented implementation
To use phages as a tool for industrial or medical applications, one should be aware of their complexity. To determine the essential genes of various Bacillus phages, we have established a CRISPR-Cas9 based mutagenesis system and optimised it for high throughput. We will use it to determine the replication essential gene-set of a phage. Knowledge about the core genome is essential for developing phage-based tools and can also provide a new anchor point for phage taxonomic classification.
The Bacillus phage SPβ: Identification and characterisation of lifestyle-dependent gene sets