Twisted Tree of Life Award #16: Nature & Authors doing taxonomic alchemy converting an archaeon to a bacterium

Well, this is one of the bigger screw ups in terms of evolution I have seen at a major journal in a while.  See the following paper in Nature: The catalytic mechanism for aerobic formation of methane by bacteria : Nature. The paper discusses some functions of “the ocean-dwelling bacterium Nitrosopumilus maritimus.” Some of what is reported in the paper is perhaps interesting (alas I do not have access).  But painfully, there is one big big big big mistake – you see Nitrosopumilus maritimus is not a bacterium.  It is an archaeon (see for example this paper on its genome).

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″.


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:

About Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

3 thoughts on “Twisted Tree of Life Award #16: Nature & Authors doing taxonomic alchemy converting an archaeon to a bacterium

  1. I found this post while searching for the Nature article discussed here. I read the article and it is actually about a pathway in E. coli, not N. maritimus. The only mention of N. maritimus I could find was in the abstract. Do you think that a typo in an abstract is a “colossal screw-up”? I understand it would be if Nature published an article about a pathway in N. maritimus suggesting it was a bacterium. It appears that this is not the case.



  2. Obviously the tongue in cheek part of this post did not come through. I thought the “Taxonomic Alchemy” pic would make it clear I was being a bit silly … but I guess not. I agree with you. It is not that big of a screw up in the grand scheme of things.


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