I got pointed to this by Uri Gophna (in an email and in a comment on my blog)(all see this on Twitter) Sure - some people debate the structure of the tree of life. But I am pretty certain the authors here (Siddhesh S. Kamat, Howard J. Williams, Lawrence J. Dangott, Mrinmoy Chakrabarti & Frank M. Raushel) are not trying to make a statement about monophyly of bacteria or just what archaea are. They just made what seems to be a colossal screw up. And Nature not only let them, but added to it with things like their "Editors Summary":
Novel bacterial biosynthesis of methane
Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S-adenosyl-L-methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate.
And for this taxonomic alchemy (converting an archaeon to a bacterium) I am awarding them and Nature my coveted "Twisted Tree of Life Award #16".
UPDATE 5/28 7AM
I love the ad that came up while I was writing this post and searching for some information. I think Nature could use the services from this ad: