Mutations DO NOT add traits. They alter the trait that would have occured if the mutation did not happen. Birth defects ae not traits, but th ey dod occur when there is a mutation. But the species DOES NOT CHANGE.
First of all, the majority of variance in most animals is not caused by mutations. I don't think this is even a common misconception but it seems to be what you are implying here. The vast majority of the genetic mixing in vertebrate species is the result of sexual reproduction. That does not apply to this species of
e coli, which reproduces asexually and does not mate. The analogy is silly on the face of it.
Anyway: the species clearly
did change. The trait went from one individual to nearly the entire isolated subpopulation rather quickly. And remember--absent asexual reproduction, this means that the new organism took over not by mating with the other members of the species, but by outcompeting the rest of the species for resources.
It is nonsensical for other reasons to argue that developing the ability to uptake citrate is like a dog being selected for size. With few exceptions, changes in dog traits do not naturally persist in populations and must be maintained by breeders. There is always a wide variety of thickness of fur, size, shape of tail, etc, throughout the population. That is obviously not the case for citrate uptake in this species of
e coli. The species did not have it. After many years of being submerged in citrate, plus some fortuitous luck,
multiple, linked mutations, no one of which directly brought about the adaptation, occurred in the subpopulations. Because they were situated in a citrus environment, it was a huge evolutionary advantage and soon attained fixation in the population. Roughly speaking: it was made possible by mutations, and natural selection made it stick around.
If you have to stretch the definition of what constitutes a "new trait" to exclude the formation of brand new metabolic pathways, viewing them instead as facets of some internal possibility space, the discussion is moot anyway because at that point you would have to basically view all living beings as being of the same kind. At the very least, in comparison with the development a brand new metabolic pathway in a species that never had it before, I would think you'd have to acknowledge that the differences between humans and chimps are rather trivial. That is: even if for some other reason (of which there isn't one) you doubted their common ancestry, you'd have to admit it was possible. But I have no reason to expect that you will ever acknowledge that because you have demonstrated the ability to
totally reject evidence that you don't like, and in fact continue to cite in support of your arguments that what was proven was impossible.
My definiion of kind does not make all animals the same thing. My definition says kinds can mate and produce offspring. A dog cannot mamte with a cat.
As I said, that species of
e coli does not reproduce sexually, so your definition is (rather trivially) met. If you were actually curious about the
real reason scientists have different definitions of species in different domains, this is why--the common definition of "species" loses its meaning in other domains. That is why I stressed that it doesn't actually
matter which of the variants you use to try to say speciation doesn't happen, because it has happened by every scientific conception thereof.
What is your definition of kind?
It's never been a pressing issue for me but I would probably say clades are the closest conceptual match. The
e coli strain in this experiment resulted in three clades. If you don't like that definition, that's fine, because whatever definition you choose is not going to get around the fact of common ancestry.
I did not say all microbes are the same. I said all microbes are micorbes. Just like a poodle and a bull dog are different but they are the same species.
There are aerobic microbes, and also microbes for whom oxygen is toxic. There are microbes thousands of times bigger than other microbes. There are microbes that can photosynthesize and microbes that cannot. There are even microbes that use slightly different amino acids than the standard ones in their genetic code (one of the most strongly conserved traits there is). Microbes are found in any environment where we have ever found any life at all. They exhibit
incredible diversity in both form and function in comparison to the staid (by comparison) macrobiological world and I didn't even scratch the surface of cataloging that documented fact. Reducing all of this to "like a poodle and a bulldog are different" is the worst kind of anthropomorphizing imaginable and has no basis in any reality-based argument about speciation. So yes, all microbes are microbes, but that says absolutely nothing about common ancestry.