Darwin's theory of evolution was formulated based on the competition he saw among animals and plants. But his insights turned out to apply with organisms he couldn't see. At the microbial level, organisms compete fiercely with each other for resources, and often devote a fair bit of energy to trying to kill off the competition (and, in some cases, eat it).

So it shouldn't come as a surprise that this sort of competition extends to the smallest biological realms possible: the viruses. A new paper takes a look at viruses that infect just a single species of bacteria, and finds that many of them carry genes that allow them to block the competition from infecting their hosts.

Many of the viruses that infect bacteria are brutal killers, exploding their hosts shortly after infection in order to spread their progeny to new victims. But others are quite a bit more devious in their infections. They'll integrate themselves into their host's genome, lying low for many generations before undergoing the normal explosive infection cycle. This lets them infect more hosts each time their current one divides, and allows their victims to grow and spread, rather than wiping them out at once.

But these moderate viruses (called "temperate phages") face a bit of a dilemma. Hiding out in a host and waiting for some indeterminate future infection doesn't do any good if some other virus comes along and blows up your host. So, some researchers suspect that viruses will have turned to biological warfare to block further invaders. This was already known to happen to some degree, as temperate phages have mechanisms for preventing any others of the same type from re-infecting the same cell.

To figure out the extent of this sort of virus-on-virus competition, a large team of researchers sequenced a lot of samples of a single bacterial species, the poetically named Mycobacterium smegmatis (named for precisely the reason you think it was). Many of these genomes turned out to have viruses integrated within them, which the authors gave equally poetic names, like "Tweety," "SkinnyPete," and "MichelleMyBell." An examination of the genes encoded by these proteins showed that they have a variety of means for targeting their fellow viruses.

Some of these were borrowed from things bacteria use to protect themselves. For example, some viruses carry an enzyme that can cut DNA, pair with an activity that protects it. The DNA of their bacterial host remains uncut, while that of invading viruses gets sliced to pieces. Others have proteins that block viruses from entering the cell. And still others make proteins that stick to the DNA of other viruses and prevent its genes from being made into proteins. Some of these systems targeted a variety of different viruses; other's suppressed just one. (Cataloging the virus' interactions led to sentences like "Tweety is targeted by Xerxes, MMB, Phrann and Panchino, but Che8 (and to a lesser extent Fruitloop), is targeted by Panchino alone.")

But the most elaborate system appears to plug into M. smegmatis' basic biochemistry. A virus called Phrann encodes a protein that manufactures a molecule that the bacteria use to signal that there's a critical shortage of amino acids. This molecule essentially shuts down the bacteria's metabolism until the crisis passes. To keep its host happy, Phrann also encodes a protein that keeps the manufacturing process shut off. But when another virus infects, the system is activated, the bacteria shut down, and the new infection fails.

Tweety was one of the viruses affected by this system. So, the researchers gave it a few generations and then selected for mutations that restored its ability to infect cells with Phrann in the genome. The Tweety virus that emerged made a protein that shut down the entire defense system, allowing it to successfully infect.

There are plenty of successful viruses with what seems to be a bare minimum of genes needed to take over a host and reproduce. But work like this shows that there's also space for complexity in the viral lifestyle. And, once you allow complexity, it's apparently just a matter of time until the viruses start fighting each other.

Nature Microbiology, 2016. DOI: 10.1038/nmicrobiol.2016.251 (About DOIs).