New Populus deltoides microbiome paper accepted in PLoS One!

Been waiting on a decision on a long developing story for the past few weeks. We first began watershed level sampling of the roots and rhizosphere of Populus deltoides in the Spring of 2010. Took us until about the Spring of 2011 to get all the microbial sequence data collected. About another 6 months for Migun Shakya’s data analyses to come to near fruition. Then several more months of drafting, redrafting, and refining his paper (I think we made it V7 before submission). The accepted version is linked here on PLoS ONE.

Apparently the work paid off! Just got an acceptance letter from PLoS One unlike any I have ever seen. Two reviews, nothing but praise. Literally, NO changes from either peer reviewer. The editor requested one. We apparently forgot to reference Supplemental Figure 5 in the text. After telling the news to a colleague down the hall, he told me something like “You might as well retire now. Not going to get much better than that!”

Back when we were doing the sampling, we came up with a nickname for the team. Deltoides Force! Picture Chuck Norris in a classic action pose, but then instead substitute ecologists wielding shovels, tree ring corers, and archeological trowels to excavate root systems.

Anyway, Deltoides force, congratulations! May we reunite for a sequel performance soon!
The spring 2010 sampling team shortly after finishing our last sampling/tree of the trip along the Yadkin River in North Carolina (We are not normally this clean in the field, some of us changed for the trip home!)

Andrii fighting with the tree ring corer.

Greg, Jessie and Cassandra in the process of excavating a tree root.


A Rant on Strawberries, Open Access Licenses, and the Reuse of Published Papers

The open access movement in scientific publishing had almost fully converted me.  I have been moving towards publishing more of my work in open access journals for several reasons.  1) The idealist in me likes the fact that anyone, anywhere, anytime can download and read my work free of charge.  Thus likely increasing public/layperson access as well as that of scientists and institutions in the developing world that might not be able to afford access otherwise. 2) The pragmatist in me has noticed than when I add up the open access fee vs. page charges and color figure charges, etc. in traditional journals, they are not all that different. For the most part any small difference there may be will likely be affordable by my research budgets.

Im still ready to make the move towards putting most of my papers in open access journals. I even recently signed up as an editor for the an open access journal (BMC Microbiology).  However in the last couple of weeks at least certain aspects, that primarily have to do with reuse of published papers, have come the fore that bother me.

Anyway, here’s the story.

A few years ago I had the opportunity to host a Ph.D student from Washington State University while she worked in my lab on the analysis of some soil microbial community data derived from organic and conventionally grown strawberry fields.  Long and short of it was we ended up with two pretty good papers out of the work, one describing the overall study in PLoS One (open access from Public Library of Science) and another more focused on the microbial community part in the International Society for Microbial Ecology Journal (from Nature Publishing Group, which features a moving paywall so older articles become free after a year or so).  The PLoS One paper made a bit of a splash, primarily among organic agriculture advocates, because in this case there were clear differences in the cropping systems.  These differences were pretty low hanging fruit so to speak, because the conventional cultivation used the rather extreme practice of fumigating the soil with methyl bromide in an attempt to kill off the all the microbes (good and bad) in the soil.

But thats another story.  If your interested in the details of the science, please download the linked papers (both are now available for free!)

Most open access journals also seem to have an open reuse policy vs. traditional journal where you must get the permission of both the authors and journal publisher to reuse the material (whether it’s just one figure or the whole paper).  I guess I assumed that by paying the open access fee we retained the ability to say yay or nay to reuse (or at least be notified).  Much to my surprise, that is not the case in many open access journals I recently checked out.  Both BMC Microbiology and PLoS one use a version of the same policy from the Creative Commons for example.

This is where the story converges, I promise.

While browsing through my Google Scholar profile page recently I noted this rather strangely formatted entry that features author names where the title should be.  Turns out this  links to a chapter in a recently published book titled Sustainable Soil Management “edited” by Deirdre Rooney and published by Apple Academic Press – CRC Press – Taylor Francis.  Actually I think Apple is the “original” publisher of the book and CRC/Taylor Francis are just distributors, but they are hopelessly inter-tangled so I’m not sure.  Judging by what I can see for free on the Google Books preview, this turns out to be just a lightly reformatted and retitled version of our PLoS One paper.  Not really much editing involved in the traditional sense of the word.

Here is what really irks me about this.  1) Neither I nor the corresponding author had any idea this had been (re)published until after the fact.  Had to run across it on Google like everyone else.  A simple email from the “editor” or “publisher” would have been nice to let us know that they loved our paper so much they wanted to disseminate it in this book.  2) The publishers are charging over $100 for this book.  This, when we already paid when we published this paper to make it freely available!  Not only are we not getting any kickback on this, I was not even sent a complimentary copy as is traditional when you publish in a book! 3) Maybe all the above would be OK if the book just did one thing.  Prominently state (maybe on the 1st page of the chapter and the table of contents) that this is a reprint from the PLoS One paper and cite/link the paper.  This would seem to actually be a requirement of the Creative Commons license linked above (however this is vague and open to various interpretations). Credit in the form of a citation is really the only thing I hope for in anything I publish. As a scientist this is a measure of the importance of the work and that the work is important to others. If the readers of the book don’t know how to cite the original article, it does me little good.  4) Unfortunately I cannot see the whole article on Google Books so I would have to buy the book in order to verify that the PLoS One paper is not credited/cited somewhere.  This is not going to happen. No way. No how. 5) Countless papers are retracted in journals each year where the authors reuse data without citing the original source.  People get fired for this.  I certainly would not want to be accused of this by my institution because an editor or publisher absconded with our paper for some book and didn’t properly acknowledge that it was in fact a reprint.

Anyway, Im not sure who to be more upset with.  The editor and publisher that (re)published the article, or myself for not noticing the reuse clause in the open access license.  From now on I vow that I will pay closer attention to this, and it may influence where I end up submitting future papers.

By the way, if anyone has paid for a copy of this book.  I would appreciate a scanned copy of the chapter…

–Note added 7/3/13–

Please see the comments section below for replies from the publishers and other interesting points of view. It seems there were oversights and errors on a variety of fronts.

Also I received an apology from Dr. Rooney.  Apparently she was misled by the publishers as well, and the publishers have failed to follow through their promise to contact us and give proper attribution. She merely agreed to write a forward to the volume and was not really the editor/selector of the papers included.  I would like to apologize to Dr. Rooney.  I SHOULD HAVE CONTACTED HER FIRST, rather than whipping off this rant/blog entry that partially blamed her.  My apologies.


Modeling microbial communities and two new papers

There is a lot of emphasis these days in my field on figuring out how to best translate our results from gene-based microbial community studies, into predictive mathematical models of (eco)system functions.  While still not easy, the new methods we now have on hand for microbial community analyses do finally allow us to collect enough data, on enough replicates, that it is no longer impossible.

Thanks to the work of a talented scientist I got to work with at ORNL named Gouping Tang, I can finally say we (mostly Gouping) have been able to make the leap from our data sets to mathematical models.  These two new papers take the data and theoretical model we proposed in a paper led by Tom Gihring in late 2011, and develop full mathematical simulations of our experimental systems.  These data are from a large scale field test we worked on with numerous collaborators that demonstrated the use of emulsified vegetable oil to stimulate reducing conditions in a contaminated groundwater system. This is somewhat bittersweet though as due to funding changes, these may be some of the final opportunities our lab will have for work on metal bioreduction in groundwater microbial communities that I have toiled on ever since leaving graduate school and coming to Oak Ridge.

Here are the citations with the links to PDF files.

Tang, G., Wu, W. M., Watson, D. B., Parker, J. C., Schadt, C., Shi, X., & Brooks, S. C. (2013). U (VI) Bioreduction with Emulsified Vegetable Oil as the Electron Donor–Microcosm Tests and Model Development. Environmental Science & Technology.  (Tang_EST_MicrocosmModel)

Tang, G., Watson, D. B., Wu, W. M., Schadt, C., Parker, J. C., & Brooks, S. C. (2013). U (VI) Bioreduction with Emulsified Vegetable Oil as the Electron donor–Model Application to a Field Test. Environmental Science & Technology. (Tang_EST_FieldModel)