When my friend Steve Finkel and I get together, the talk is almost always about bacteria. He and I are both huge fans, from different angles. I’m a spectator. He studies them (E. coli) in his lab at the University of Southern California. I used to work down the hall from him, so I’m sure that some of my enthusiasm for the tiny creatures can be blamed on him, along with USC’s out-of-control microbe-lover Ken Nealson (Shewanella oneidensis is his bug, among others).
Single-celled though they may be, bacteria and other microbes are far from simple. They can thrive in hostile spots — from the acidic, low-oxygen environment of the stomach to boiling hot springs or frozen tundra. Some even breathe rock (see Nealson’s bug). They can adapt rapidly in rough times, switching their metabolic scheme or just going dormant. Bacteria have many admirable qualities that many of us would want for our children: grit, perseverance, flexibility and seemingly limitless creativity (albeit mostly biochemical).
Their flexibility and creativity were on full display at a recent meeting, a few blocks away from the Science News offices (and the occasion for Finkel’s visit to Washington, D.C.). Reports from the meeting all involve science that takes advantage of the latest techniques for probing the bacterial experience — be that finding out how bacteria can survive without “essential” enzymes and how offensive attacks can actually give rise to bacterial cooperation. Now that bacterial genome sequencing is cheap, Finkel and fellow scientists can watch microbes evolve in the lab, in real time. Taking genetic snapshots along the way, scientists are building up a detailed picture of the genetic shifts that allow a new strain to become dominant in a given experiment. It is watching evolution in action, Finkel says, quite literally.
But microbes are organisms, much more than little sacks of evolving biochemistry. They have immune systems, of a sort. It was through studies of one bacterium’s antiviral defense that scientists first discovered what’s become the most versatile and headline-grabbing gene editor of all time: CRISPR/Cas9. These ingenious molecular scissors work within microbes to target viral DNA that has invaded bacteria and literally cut it to shreds. Harnessed and aimed at the DNA of other organisms, CRISPR/Cas9 has proved much easier to work with, cheaper and more precise than existing editing tools. It’s been wildly successful at precisely deleting genes, helping to reveal gene functions that have long remained hidden, as Tina Hesman Saey reports in “CRISPR gets a makeover.”
But even this wonder tool has its limits. So, as a legal battle over who owns the patent to the technique rages on, scientists (including the current patent holder) are already tweaking it, adjusting it, engineering it and searching for CRISPR-like alternatives, an effort Saey describes in her cover story. Some scientists are going back to the source (bacterial immune systems) to find new enzymes that might help build a library of precision gene-editing tools — one for each job.
That brings me back to why I love microbes — resilient, creative survivors that they are. Like the best humans, they are always coming up with new solutions.