By now you should know that PVC bacteria are very interesting for their particular features. Some of those are usually NOT observed in bacteria and usually more associated with eukaryotes or archaea. This is the base of the controversy around the PVCs, of which the McInerney paper is a good example. This point will also be addressed at the EMBO PVC workshop 2013 (please come, listen and contribute!).
Addressing the origin of those features is a difficult issue. Mostly because for the majority of those, we don't even know the proteins that are behind them. In addition, evaluating the origin of genes or proteins requires the elaboration of a multiple sequence alignment with satisfying quality assessment. This is only possible for a couple of such PVC features.
In a recent article, just published in the Frontiers PVC research topic, Budd and Devos review the few cases in which such phylogenetic reconstruction have been achieved for the PVC features. They found out that contrarily to what has been published (eg the reply to the Devos and Reynaud 2010 Science paper), no agreement has been reached on the origins of those features (which once again are only a small portion of the peculiar PVC features). In fact, about half of those analysis actually conclude against lateral gene transfer. They conclude that the HGT origin of those PVC features is still not established. In addition, they highlight the importance of taking into account alternative models and scenarios, including alternatives to the 'classical' 16S rRNA based (ie Woese-type) tree of life and HGT/no-HGT models.
Whatever it is, there is certainly more interesting surprises to expect from this intriguing bacterial superphylum.
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