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 Summer Student Joins the ORNL Crew

I was fortunate to find a great summer ‘intern’ that joined the lab this week.  Stacey Travis just finished the first year of her Masters program at University of Florida in Soil and Water Sciences. For her thesis she is working soil chemistry and phytoaccumulation of PAHs in the floodplains of the Tennessee River near Chattanooga.  This summer she will be working closely with Tarah Sullivan as we make a final push to wrap up work on our DoD/SERDP project investigating the effects of soil fungi on Pb speciation that ends this year.  Here they are seiving soils for our next incubation experiment (Tarah on the left and Stacey on the right)!


Job Post: Ph.D.-positions in Biodiversity Research (Netherlands Institute of Ecology)

The Deutsche Forschungsgemeinschaft (DFG) funds a large-scale grassland project “The Jena Experiment” ( on the relationship between Biodiversity and Ecosystem Functioning (Grant FOR 1451). On a 10ha field site in Jena, more than 470 grassland plots have been established where plant diversity is manipulated to measure the effect of diversity on multi-trophic interactions and nutrient cycling. Applications are sought for the following position:

Ph.D. position (PhD-TE-013060) – A short description of the position is given below.

The project is an international collaborative research effort of 11 universities and research institutes in Germany, three universities in Switzerland, two in The Netherlands as well as universities and research institutes in Austria, France and Canada. All Ph.D.-students will benefit from an already existing experimental set up and the interaction with other PhDs and researchers in an international research team. The ability to speak and write German will be appreciated but is not indispensable for candidates fluent in English. A full description of the project and more details about the positions can be found under:

Selection of applicants starts 10. April 2013 and continues until positions are filled. Starting dates depend on the position on offer. Applications – in a single pdf-file only – should be sent to the addresses given below.

Ph.D.-positions in Soil/Plant Ecology

We offer a PhD position in Wageningen at the department of Terrestrial Ecology at The Netherlands Institute of Ecology (NIOO-KNAW, Prof. Wim van der Putten), in close collaboration with the Soil Quality department at Wageningen University (Dr. Gerlinde De Deyn) and the department of Ecology and Biodiversity at Utrecht University (Prof. George Kowalchuk).

The research focuses on the role of plant-soil feedbacks in the relation between plant (trait) diversity and ecosystem functioning. Plant species influence the composition of soil biota and these influences have feedback effects to the role of plant species in plant communities and the ecosystem processes that emerge from these communities. Previous research has shown that plant species differ in the strength and direction of plant-soil feedback. However, the roles of different soil microorganisms (bacteria, fungi) have yet to be elucidated.  In the present project, you will relate the composition of soil microorganisms to plant traits in plant communities and consequent ecosystem functioning. We intend to investigate to what extent plant species create specific rhizosphere communities and how these communities differentially impact on plant growth. Candidates should have a MSc degree in soil biology/ecology, microbiology or plant ecology. We are looking for candidates with:

  • good ability to think conceptually and quantitatively
  • good knowledge of plant-soil (biotic) interactions
  • experience with working with soil organisms
  • affinity with state-of-the art soil molecular biological techniques
  • excellent ability to communicate in English, both orally and in writing
  • experience with writing scientific papers is highly appreciated
  • good organisational skills and ability to work independently
  • ability to work in multidisciplinary research teams

Contact: Dr. Gerlinde De Deyn, Dept. of Soil Quality, Wageningen University, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands. Email:

Applications: Please send your application with vacancy number (PhD-TE-013060), including a cover letter detailing your motivation for and expectations from this position, your CV including a summary of your past research, and contact information for three references to The closing date is 10th of April 2013.

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.

A universe of soil, rhizosphere and endosphere bacteria

I got this cool figure from my postdoc Mike Robeson to contemplate over the weekend. It shows the Bacterial species network (or OTUs as small white squares) we recovered from bulk soil (orange connections), rhizosphere (blue connections) and root endophyte (green connections) samples from 6 sites taken last fall where we sampled Populus deltoides and surrounding tree species on the Caney Fork River in Tennessee (squares of different colors indicate different riparian sites) as part of our Plant Microbial Interfaces project.  Still not sure exactly what it means, except that it is fun to look at and ponder.  Seems to indicate that the effect of habitat (soil, rhizosphere, endosphere) > site location > tree species.  Anyway, kind of mesmerizing.