As mammals, I think we sometimes take sex for granted. I'm not talking about the frequently messy act of having sex, or the extensive effort most of us go through in order to have sex. I'm talking about the fact that sexual reproduction gives rise to some pretty impressive genetic diversity in a population. But from an evolutionary perspective, sex doesn't make a lot of sense. For one thing, it means that each of your offspring only gets half of your genes. When the driving force of natural selection favors passing as many of your genes as possible to the next generation, arbitrarily choosing to divide them in half to mix with some other individual's genes is madness.
This fact can be a bit hard to wrap our heads around since we perceive the many benefits of diversity at a population level, but natural selection works at the level of individuals, not groups. What this means is that the benefit to an individual of diversity in their offspring must be quite high, otherwise no organism, once discovering sex, would stick with it.
But not all organisms have sex, in fact, most don't. The vast majority of microbes reproduce asexually - each round of replication results in more or less identical offspring. So do they simply forsake the benefits of diversity? Hardly.
It turns out, the tree of life for the smallest creatures is more of a tangled bush - extensive sharing of genetic information occurs between different members of the same species, or even distantly related species. This sharing is called "horizontal gene transfer" or HGT (as opposed to vertical gene transfer, which is parent to offspring), but it's unclear exactly how or how often it happens. We can rarely catch HGT in the act, but we can scour through genomes and infer.
In organisms that don't reproduce sexually, identifying HGT is relatively straightforward so long as you have a lot of genetic information from a lot of different species. Basically, it involves comparing genomes of one species to that of both closely related and distantly related species. All genes change over time through accumulation of mutations, but in general, the genes in closely related species should be more alike than genes of a distant relative. In the same way that your genes should look more similar to your cousin's than to that of a chimp, E. coli genes should look more similar to the genes of other E. coli than to those of Salmonella. By the same token, if you happen to find a gene in E. coli #1 that looks more like Salmonella than to E. coli #2, there's a decent chance you've found evidence of horizontal gene transfer.
To be sure, this sort of inference is going to miss a lot of transfer events. There are a lot of microbes out there, and we only have genomic information for a tiny fraction of them. In addition, transfers that happened a long time ago may have spread far and wide, making it look as if they're a normal part of a species' genome. But a lot of HGT in asexual organisms has been discovered, with more discovered all the time.
But finding HGT in microbes that routinely have sex is a bit more complicated. Imagine comparing the genes of a random European to that of another European and an African. In general, you might expect most of the Europeans genes to look more similar to each other than to that of the African, but if you found a few genes where the reverse was true, it wouldn't be that surprising. Plenty of people with African ancestry have had children with people of European ancestry, such that the genes are all mixed up. We're pretty sure that horizontal gene transfer doesn't happen in people, but how could we tell?
In a paper published last year in Nature Communications, Kevin Cheeseman (an apt name as you'll see) and colleagues identified an incredibly large region of horizontal gene transfer between species of Penicillium associated with cheese, but not in Penicillium from other environments. The key piece of evidence suggesting horizontal rather than vertical transmission was not in the transferred genes themselves, but in the regions of DNA surrounding them. Penicillium is a fungus, so even though it's a microbe, its DNA is organized into chromosomes just like ours. When organisms have sex, the mixed genes typically stay in the same place on the chromosome, but Cheeseman showed that this region (which they called wallaby for reasons I don't understand) was on different chromosomes in each species. Further evidence came from the fact that all of the species with wallaby came from microbes found on cheese, while those that didn't have it were found in other environments.
All of this suggests that these fungi, though distantly related, all found themselves hanging out on cheese together and started passing around genes, just not through sex (though the mechanism is unknown). This also raises the possibility that looking for other HGT in fermented food products might be fruitful - the environment of fermented food products is quite unique, but has been around for a long time, providing ample opportunity for evolutionary relationships to form between the microbes involved.