Master’s student reviews ecology and evolution of bacteria and phages

Even bacteria can catch a virus, and rather than causing the odd sniffle, these can make the bacteria pop, spreading new virus particles. This is why bacterial viruses are called ‘bacteriophages’ (bacteria eaters) or phages for short. But sometimes, phages and bacteria come to a mutually beneficial arrangement, as Master’s student in Evolutionary Biology Nancy Obeng has explained in an Opinion paper in Trends in Microbiology.

Nancy Obeng is in her second year of the Master’s degree programme in Evolutionary Biology at the University of Groningen. She became intrigued by phages in her first year. ‘Phages are very small, so they can’t store much genetic information, but sometimes they carry bacterial genes. I wondered why’, she explains. As phages normally dispense with any excess genes, Obeng wanted to know whether there was some benefit to this extra baggage.

She started reading up on phages, and decided to devote her first-year essay to them. Her supervisor, Professor of Microbial Ecology Jan Dirk van Elsas, read it and was impressed. He asked Obeng to expand the essay into a review article, which was accepted by the journal Trends in Microbiology and published as an Opinion paper on 1 February.

When phages infect bacteria, they often immediately force them to make new virus particles, which eventually lyse the cell to spread the new phages. But sometimes, the phages integrate their genetic material into the bacterial DNA, where it lies dormant. When the bacteria divide, the daughter cells carry a copy of the phage genome in their DNA. This is harmless, until something triggers it to produce new virus particles and lyse the cell. Bacteria have defences against all of this: they can recognize and break down phage DNA or disable integrated phage genes.

When integrated phages excise their genes from the bacterial genome, an adjacent bacterial gene may be included by accident, and they sometimes appear to tolerate this. ‘There is no direct benefit to the phage, so I would expect the extra gene to confer some sort of benefit to the bacterial host, which then feeds back to the phage’, Obeng explains.

In her review, she discusses different possibilities. ‘Phages can provide their hosts with genes that help them survive. For example, E. coli bacteria can acquire a toxin gene from phages that helps them invade the gut.’ Other genes introduced by phages have a positive effect on the metabolism of bacteria.

This helps the bacteria, but how do the phages benefit? Well, as already mentioned, when they remain integrated within the bacterial cells, they are copied into each daughter cell. So what’s good for the host is good for the phage. And the bacteria? ‘Recent literature suggests that the bacteria may actually allow phages to stay in the cell by lowering their defences. That of course is a very risky strategy, as a phage might become active and lyse the cell.’

But in fact, Obeng found evidence that in some cases the bacterial population actually benefits when a few phage-infected cells pop. ‘The nutrients and building blocks that become available can be used by the remaining bacteria.’ One use is to strengthen biofilms, the matrix in which many bacteria live. So apparently, phages and bacteria can benefit from each other.

‘What we’ve tried to do in this paper is to communicate ideas from evolutionary biology to inspire microbiology’, explains Obeng. The link between evolution, ecology and biological mechanisms is the focus of the Groningen Institute for Evolutionary Life Sciences (GELIFES), the research institute which hosts Obeng’s supervisor Van Elsas and a PhD student who also worked on the paper, Akbar A. Pratama. ‘By considering eco-evolutionary dynamics, we can gain a better understanding of the mechanisms that shape the relationship between phages and bacteria.’