A Nature chain retraction for Arabidopsis paper, and some unanswered questions
If a paper is retracted, should papers that cite it get retracted, too? We’ve been on the lookout for this kind of move, which we figure is consistent with cleaning up the scientific record. Today, one appears in Nature.
The original paper, “Mediation of pathogen resistance by exudation of antimicrobials from roots,” purported to show how a particular bug evades the immune system of Arabidopsis, a plant commonly used in the lab. It has been cited 51 times, according to Thomson Scientific’s Web of Knowledge.
The retraction notice says that the paper’s conclusions could no longer be supported because one of the key references — a paper in the Journal of Agricultural and Food Chemistry by many of the same authors — had been retracted:
The authors wish to retract this Letter after a key reference by Walker et al. (ref. 9 in this Letter) was retracted from the scientific literature. The withdrawn paper reported ten compounds exuded by Arabidopsis thaliana roots, which were used in this Letter to monitor the defence response in Arabidopsis seedlings. In this Letter, these ten compounds were shown to have antimicrobial activity against specific pathovars of the bacterial phytopathogen Pseudomonas syringae but not against the pathovar Pseudomonas syringae pv. tomato strain DC3000 that is a highly virulent pathogen of Arabidopsis.
Moreover, wild-type P. syringae DC3000 suppressed the exudation of the ten compounds whereas a DC3000 hrcC mutant did not, leading to the conclusion that DC3000 type III effectors block the exudation or synthesis of the ten compounds. As a consequence of the retraction of the Walker et al. paper, the validity of the use of the ten compounds as markers of the Arabidopsis defence response is now in doubt. Thus, the data in Fig. 3, Table 1, Supplementary Figs 5–8 and Supplementary Table 1 cannot be used to support the conclusions that P. syringae DC3000 is generally resistant to antimicrobial compounds exuded by Arabidopsis or that P. syringae DC3000 type III effectors block the exudation or synthesis of antimicrobial compounds.
Here’s the Journal of Agricultural and Food Chemistry retraction notice:
We have been unable to find experimental data that document the actual isolation of butanoic acid, trans-cinnamic acid, ocoumaric acid, p-coumaric acid, ferulic acid, p-hydroxybenzamide, methyl p-hydroxybenzoate, 3-indolepropanoic acid, syringic acid, and vanillic acid from root exudates of Arabidopsis thaliana Col ecotype. Therefore, the original publication is being retracted, and the authors deeply regret any inconvenience to the scientific readership.
The Nature retraction seems like the right thing to do, and we applaud that step. But we had some questions, key among them what exactly the inability “to find experimental data that document the actual isolation” meant. Was this simply a result that couldn’t be replicated? Were lab notebooks lost? Or was there something more sinister?
We checked with the lead author of both papers, Jorge Vivanco of Colorado State University:
The co-authors and I reached the decision to retract the Nature paper because we were no longer certain about the validity of ten marker compounds used in an assay to prove the point that plants defend themselves more aggressively by means of secreting phytochemicals from the roots against non-pathogens (as compared to the opposite when infected by pathogens). However, I should mention that the general assertion that plants defend themselves more aggressively against non-pathogens as compared to pathogens has been corroborated widely in the literature. Therefore, it was very hard for all of us to retract this paper because the general assertion was valid but the validity of the particular assay used to reach this conclusion was not too clear.
Those ten marker compounds were originally reported in the J Ag. Food Chemistry paper that you mentioned in your email. We had a very hard time repeating those studies and it seems that there was an issue with the original identification of those ten compounds. This paper was retracted from the journal.
Vivanco also asked his co-authors to respond. One of them, the University of Delaware’s Harsh Bais, did so:
Drs. Vivanco’s, Ausubel and my lab are independently working on elucidation of root secretions from Arabidopsis and other plant systems. As indicated in Dr. Vivanco’s email that his lab was not able to replicate the secretion profile in Arabidopsis as retracted in JAFC. My lab also faced similar difficulty in replicating Arabidopsis secretion results. Dr. Ausubel’s lab also tried to replicate the Arabidopsis secretion work and found that the compounds reported as free metabolites in retracted JAFC paper to be conjugates and glucosides.Some of these replication efforts confirm that majority of these compounds (retracted in JAFC paper) are indeed synthesized by Arabidopsis, even though they may not be exuded as free compounds under the conditions of our experiments. In contrast, a different lab has shown the secretion of same compounds in Arabidopsis secretions (Narasimhan et al. 2003.Plant Physiol. 132:146-53). The bottom line is that this is a very complicated issue and even though we have been working on this project for a couple of years, we still do not have a definitive understanding of it.
It certainly does appear to be complicated scientifically, but we still aren’t sure why there were issues with the original data.
We have other questions, after coming across two other retractions by many of the same authors, in Phytochemistry in 2009 and 2010. Many of them were also on a Journal of Agricultural and Food Chemistry paper that was the subject of a correction.
When we asked, Bais told us that the 2009 Phytochemistry retraction and the Journal of Agricultural and Food Chemistry correction had nothing to do with the Nature retraction or the work it was based on.
We didn’t see the 2010 Phytochemistry retraction until after we had asked the group about the others. Like the Journal of Agricultural and Food Chemistry retraction that led to the one in Nature, it too refers to missing data:
The authors have been unable to find written experimental data of the isolation of the purported beta-carbolines (harmine and harmaline) from root exudates. The source of the compound in question as originally reported is unclear. While Oxalis tuberosa roots do release fluorescent exudates, the identity of the fluorescient compound(s) awaits actual purification and structural determination.
The authors therefore wish to retract the original publication and deeply regret any inconvenience to the scientific readership.
If we hear back about the circumstances, we’ll update.