I have a bunch of questions born of my ignorance of microbiology:
Is it possible this organism evolved in the last few decades, with the advent of clean rooms? Or is it more likely that a few of these are around all the time, and only multiply extensively in clean rooms? Also, what do they eat or use for energy to reproduce in such environments? And if they don't really eat, how do they not die on a long space journey?
It is possible for it to have evolved in the last few decades, but really unlikely. The stated figure of less than 5% DNA commonality implies a really extensive divergence. Given the low energy environment it grows it, the bacteria likely reproduces at a very slow rate, making the divergence over the last few decades very unlikely.
That said, its probable that the strains discovered are probably some slight "modification" from the "wildtype" bacteria.
As for what they eat in a clean room, there are a couple options. A) They might be driven mostly by alcohol metabolism and feeding off residual alcohol from the containimation. Or might likely B) they're feeding off the skin flakes coming off the "unshielded" areas of the workers, and that they are just very very slow.
The stated figure of less than 5% DNA commonality implies a really extensive divergence.
Your reasoning is correct, but in case you'd like to edit, I'll point out that the article wrote, "The scientists determined that T. phoenicis shares less than 95 percent of its genetic sequence with its closest bacterial relative." The figures "less than 95 percent" and "less than 5%" imply very different degrees of similarity.
Very niche lifeforms by definition are hard to cultivate in a lab and therefore go undocumented and there are loads of them, more than we even suspect probably.
It's likely a new kind of bacteria, because of the genetic difference. But that doesn't mean it hasn't made any additional adaptions for living in clean rooms specifically. Maybe it started out as a bacteria that could survive in an environment like that but has become even better at it since.
Though the hostile environment of a clean room would keep population size relatively low and keep them from reproducing too often, compared to bacteria in normal conditions. So their evolution would be slower.
Is it possible this organism evolved in the last few decades, with the advent of clean rooms? Or is it more likely that a few of these are around all the time, and only multiply extensively in clean rooms? Also, what do they eat or use for energy to reproduce in such environments? And if they don't really eat, how do they not die on a long space journey?