When is an innovation not an innovation? If by innovation you mean the evolution of something new, a feature not present before, then it would be stretching it to call the trait described by Blount et al. in “Genomic analysis of a key innovation in an experimental Escherichia coli population” an innovation.
Dr. Richard Lenski’s lab has been conducting a long-term experiment in bacterial evolution, growing E. coli under starvation conditions for 50,000 generations and following the changes that occur. Most of the changes reported so far have involved streamlining the genome, deleting genes no longer needed under such limiting conditions, or reducing protein expression. For a review of the kinds of changes observed, go here.
A few years ago, though, they published a paper describing the evolution of a “new” function in E. coli: the ability to use citrate as a carbon source for growth. Citrate had always been present in their minimal medium, but it was inaccessible to E. coli under normal lab growth conditions. After about 30,000 generations, though, the bacteria evolved the ability to take up and use the abundant citrate in the medium, thus allowing them to grow and reproduce faster. This announcement was splashed across headlines as evidence for the power of evolution to produce new adaptive traits.
But how significant was this innovation? In his paper in Quarterly Review of Biology, Dr. Michael Behe pointed out that E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available). He postulated that a change in gene regulation could turn on citrate transport and permit growth on citrate under aerobic conditions.
After an enormous amount of work, having sequenced the genomes of many clones along the lineages that led to the ability to use citrate, as well as lineages that never did, and testing the phenotypes of identified mutations, Blount et al. have now reported that Behe was largely right. The key innovation was a shift in regulation of the citrate operon, caused by a rearrangement that brought it close to a new promoter.
Figure 2 from Blount et al.
The new trait additionally required one or two pre-adaptive steps that could not be definitively identified, perhaps because of variable or weak phenotypic effects, perhaps because of epistatic interactions. Once in place though, those mutations enabled the next step, a duplication of the citrate operon that moved it next to another promoter, enabling the aerobic transport of citrate and its metabolism.
The total number of mutations postulated for this adaptation is two or three, within the limits proposed for complex adaptations by Axe  and Behe in Edge of Evolution. Because the enabling pre-adaptive mutations could not be identified, though, we don’t know whether this was one mutation, a simple step-wise series of adaptive mutations, or a complex adaptation requiring one or two pre-adaptations before the big event.
But does this adaptation constitute a genuine innovation? That depends on the definition of innovation you use. It certainly is an example of reusing existing information in a new context, thus producing a new niche for E coli in lab cultures. But if the definition of innovation is something genuinely new, such as a new transport molecule or a new enzyme, then no, this adaptation falls short as an innovation. And no one should be surprised.