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!
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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!)

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Andrii fighting with the tree ring corer.

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

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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)