The Proceedings of the National Academy of Sciences, known as PNAS, was ahead of the curve when it came to the new wave of evolution research allowed by the completion of genome sequences. They've had a dedicated evolution section for at least 10 years, although it has gotten a lot busier lately. But some of the more interesting evolutionary stories often get tucked in to a different section, and two that have come under the heading of "Microbiology" recently caught my attention. Microbes are an interesting case for evolutionary studies because, in contrast to the relatively slow pace of change in larger organisms, they can go through well over 100 generations a day, pushing selective changes into time periods we can study. They're also exquisitely sensitive to anything which can slow down their generation time or waste energy, so they'll rapidly shrink their genome size and stop protein production if given the opportunity.
The first paper is the completed genome sequence of Lactobacillus bulgaricus, commonly known as the bug that brings us yogurt. The bacterial species used for this purpose have gone from being a general plant pathogen to a milk specialist over 5,000 years ago, and comparison of this strain with related bacteria show some clear changes. For one, the genome appears to have shrunk on the order of 30-50 percent, with many of the losses happening in those pathways required for metabolizing any sugar other than lactose. As part of the streamlining, many of the genes that allow complex regulation of gene expression have also gotten the boot, including the one that allows lactose metabolism to be shut down—bulgaricus, is always ready to digest lactose. In general, it looks like this bug has traded off the ability to live outside of milk for the more rapid generation time allowed by producing fewer proteins and having a smaller genome to copy.
The second article deals with a human pathogen, Pseudomonas aeruginosa, which in most people causes lung infections before being cleared out by the immune system. In patients with Cystic Fibrosis, however, the bugs never get cleared, and they often settle down for multi-year infections. Researchers sequenced the genome of one strain that had been isolated from a single patient at two time points eight years apart, and looked at what had happened to the bacterial genome in the mean time. Armed with the information about which genes were mutated in one patient, they isolated samples from 29 other CF patients to get a better population survey. Mutations had piled up in many of the genes involved in virulent infections, as well as a lot that help with drug resistance. Another common target was the pathway that injects toxins into cells, which causes some of the worst symptoms of infection. Loss of all of these pathways mean that the CF strain of Pseudomonas probably couldn't infect a healthy person, but is much less likely to kill its unhealthy host.
Combined, these two studies show just how rapidly wholesale adaptations to a new environment can take place in a bacterial genome, even when the environment happens to be generated by us.