Some photos and info on our recent field work sampling Populus trees here in East Tennessee.

We completed field work during the week of August 11th, for a new study  to create a “microbiome atlas” of symbiotic associations in Populus as part of our Plant-Microbe Interfaces project at ORNL.  We partnered locally this time to sample trees in Blount County, Tennessee that are part of a field trial run by the UTIA Center for Renewable Carbon and Dr. Tim Rials. Due to the large sample sizes required for our new metagenomics approaches, and the fact that we needed to dissect out many different tissues, this was a large effort and required bringing in some help and power equipment from experts at Wolf Tree Company.

While there have been numerous studies of the microbial associations of individual plant environments (e.g. the rhizosphere, phylosphere or endosphere) very few have simultaneously examined variation across habitats of the plant as a whole. Simultaneous examination should allow us to better understand microbial the niche specialization and niche overlap of symbiotic partners across the overall tree environment. This will allow us to build an “atlas” of the microbial interactors with Populus trees and better links to their potential functions across Populus. The sampling strategy employed will enable us to comprehensively survey rRNA based microbial diversity across approximately 30 different tissue level habitats in Populus. These were sampled accross different locations within individual trees, between five replicate clonal trees, and across two contrasting genotypes (P. deltoides and P. deltoides X trichocarpa hybrids). Selected plant habitats are also to be examined using metagenome DNA sequencing that will include soils, rhizospheres, root endospheres, heartwood, and leaves that are replicated from samples pooled across the individual trees. Samples are also being used for culture isolations and single cell genomics of targeted microbial species (ectomycorrhizae, Atractiella, Acenitobacter, etc.). 

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Three new in press papers on microbial and geochemical characterization of the peatland ecosystem at the future SPRUCE site

Here are links to three new accepted papers that are just out online.  These papers represent some of the first of our hopefully continued fruitful efforts to characterize the peatland SPRUCE site characteristics prior to the onset of warming treatments next year.  These come from core support of the SPRUCE project itself as well as an additional DOE funded effort led by my long-time collaborator Joel Kostka at Georgia Tech and of course the hard work of several fabulous students and postdocs!

Lin et al. Microbial metabolic potential for carbon degradation and nutrient acquisition (N, P) in an ombrotrophic peatland. Applied and Environmental Microbiology, In Press.

Lin et al. Microbial community stratification linked to the utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest. Applied and Environmental Microbiology, In Press.

Tfaily et al. Organic Matter Transformation in the Peat Column at Marcell Experimental Forest: Humification and Vertical Stratification. Journal of Geophysical Research: Biogeosciences, In Press.


It has been some time since I posted on the blog and I hope this will be one of several upcoming updates on projects, papers and personnel!

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.

Off to ESA in Minneapolis!

Several of us are off to MN Sunday for the Annual Meeting of the Ecological Society of America.  Unfortunately all three presentations by Myself, Meg and Tarah are scheduled for Thursday and Friday (2 posters and 1 talk).  Please stick around and prove Alan Townsend wrong by filling up those late meeting sessions!

Then Friday after the meeting I’m off to do some fieldwork on the SPRUCE project.  

Fair the well and see you in MN!

New Experimental Field Site? Maybe….

New Experimental Field Site?

Just finished a lengthy grant proposal effort. For those of you who don’t know it can be an arduous process; coming up with new ideas, thoroughly researching them, writing the 15 pages of the proposal, getting all the collaborators to agree on it, and making sure you have the other 15 pages of junk that is required all formated correctly. Always difficult at best, painful at worst. At the end you are never quite sure whether to declare victory or accept defeat. Then it disappears for 9 months, and just when you have forgot about it, it either reemerges as a project that you have to figure out how to really accomplish, or it collects dust until the next RFP deadline. I’m happy to say, I am now in the waiting phase.

Anyway, this is one of the sites we chose to propose to do work in, when I hiked up last week to check out this place on a ridgetop about 2 miles from my office. Definitely would be great to get the opportunity to visit this place more often! Here is a link to the Project Summary for those that are curious. Thanks to Aimee Classen, Greg Hurst, and Emily Austin for all there help in putting this together!

Job Post: Graduate Student/Postdoctoral openings In Anna Rosling’s new lab in Uppsala

Multiple Positions in the Department of Evolutionary Biology, EBC, Uppsala University exploring life strategies in the Archaeorhizomycetes

-PhD position in Soil fungal ecology
-Post doc fellowship

Deadline for application is March 15, 2013.

More information as well as links to the position advertisements on her homepage:

Job Post: Staff Microbiology Position(s) at Argonne National Lab

Argonne National Laboratory is building a dynamic microbiology team to pursue cutting-edge research in microbial systems biology. We are seeking several microbiologists interested in becoming part of this team as well as the larger established team of computational and structural biologists at Argonne. To be successful in this role the successful candidate should possess:

• The expertise to develop a robust extramurally-funded research program preferably focused on current and future topics of interest to the Department of Energy such as carbon and nutrient cycling, bioenergy, and bioremediation,
• The ability to apply systems approaches to microbial problems,
• The ability to combine both experimental and computational approaches to answering
biological questions,
• A demonstrated ability to publish in recognized journals, and
• A record of conducting research in a collaborative framework.

Argonne offers a competitive salary and an excellent benefits package. US citizenship is not required. A joint appointment at a regional university may be possible depending on the particular applicant.

A PhD in Microbiology or related fields is required. To apply please go to our website at, requisition # 320165. Argonne is an Equal Opportunity Employer; we value diversity in our workforce.

Grad Student Positions Available: Lee Taylor’s lab in New Mexico

The Taylor lab has relocated from the University of Alaska to the University of New Mexico and would welcome applications to graduate school from talented students. UNM guarantees 5 years of support to accepted PhD students.

The Department will support one or more positions. Application procedures can be found here (the fast approaching deadline is flexible):

General information about the department can be found here:

Information about the Taylor Lab research program can be found on these sites: &

Research areas include:
– assembly and function of soil fungal communities across arctic, boreal and desert ecosystems
– metagenomics of fungal extracellular enzymes
– ecological genomics of mycoheterotrophic orchids (Corallorhiza and Hexalectris)
– molecular ecology of mycorrhizal interactions of tropical epiphytic orchids

Switchgrass – Beyond the Ethanol


My former postdoc turned Assistant Professor, Marie Anne de Graaff, just had a new paper come out in Soil Biology and Biogeochemistry (DeGraaff_SBB_InPress).  In it we were able to further explore the favorite topic of our research, namely how plant root processes and properties influence soil biogeochemistry and microbial communities/processes.  While many scientists and laypeople alike have been interested in harnessing the amazing productivity of switchgrass for cellulosic biofuels for some time, not as many may appreciate that this incredible productivity takes place not only in the harvestable aboveground tissue, but also extends belowground to the root systems!  Switchgrass can send roots meters deep into the soil year after year due to its perennial nature, and in doing so may increase soil carbon storage (or sequestration) over more conventional annual crops.  Switchgrass exists in many varieties which have primarily been explored and exploited for their productivity under various potential cropping regimes for biofuel feedstock production.  In this paper we explored the potential for varietal differences in root production and properties to effect their own decomposition rates and also how this in turn may influence soil organic carbon turnover (e.g. priming).

The results were fairly impressive.  As you can see above, even with the naked eye, differences in root properties can be fairly striking.  Varieties show differences in the amount of material invested in fine (smaller) roots vs. coarser (larger) roots.  These differences in turn have effects on how fast the roots decompose, and how much they ‘prime’ the decomposition of resident soil organic carbon.  While the experiments were done in laboratory incubations so its hard to directly translate to in farma results, it certainly argues for further consideration of belowground properties of these crops in future applied ag research.  Consideration not only of their aboveground potential for ethanol, but perhaps the value of switchgrass crops on the carbon offset market could result, with a greater understanding of the role of switchgrass in increasing soil carbon storage.

Marie Anne had a very productive postodoc while here at ORNL for which I can take very little credit.  She came into our lab already motivated and well prepared, got right to work with multiple experiments and was able to move results from the lab to papers amazingly efficiently.  This recent paper represents some of the last work she initiated here at ORNL and then was able to finish up in her new position at BSU.  We are continuing this kind of research in my lab in various projects and collaborations (including this one with Professor de Graaff)

A few fun photos from past work!
Hydroponically Grown Switchgrass (photo from Chuck Garten)

Ernest cutting alleysCutting Alleys for us to get to some switchgrass plots in Milan, TN in 2007 (photo from Robin Graham)

Schadt_Milan_SwitchgrassPlotsYours truly, Out Standing In My Field in 2008

AEM Cover link and article

There it is! Great Job Tarah!  Here is the link to the cover, the AEM article website and the PDF full article on our isolate fungal-Pb interaction studies and communities.

Also another article in this issue from Melissa Cregger (recent student in the Classen Lab at UTK) on Pinon-Juniper microbial community responses to precipitation change.