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. http://aem.asm.org/content/early/2014/03/24/AEM.00206-14.abstract

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. http://aem.asm.org/content/early/2014/03/24/AEM.00205-14.abstract

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. http://onlinelibrary.wiley.com/doi/10.1002/2013JG002492/abstract

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.

A good science/opinion piece… (A.K.A. the art of the logical rant)

About two years ago, a postdoc (Tom Gihring) working with me on our IFRC project brought a few graphs into my office that dumbfounded me. Which, in truth, is not hard to do.  In these graphs it was very clear that microbial community ecologists doing pyrosequence analysis were failing to take notice of some well established literature that had demonstrated a large potential for biases when pyrosequence sampling depth was unequal between the samples under comparison.  We were just starting to publish these types of studies in our ORNL group and we were all still learning a lot about how to do them properly, so he double checked his results and I quickly became convinced that what he was telling me was important and correct.

This bias was actually relatively straightforward to explain.  Basically it would be equivalent to bias observed if a plant ecologist estimating species diversity in a sample plot with the tried and true frame & count methods, was to use different sized frames for each estimate!  This inevitably led to the process of trying to get the observations written up (which did not take long thanks to Tom!) and published (which seemed to take forever!).  In the process, we read some other good science/opinion papers which influenced the way we tried to present our paper.  In particular, the paper by James Prosser entitled succinctly enough – “Replicate or Lie” – was a great model!

Our reviewers in the end did not let us publish a STRONG opinion paper.  They were uncomfortable with the language being to negative toward current methods, so we caved in and appeased them in order to get the article published (here is a pdf Gihring_EM_2012). Such reticence on the part of reviewers is commonplace and probably stemmed from the fact that at the time we did not have many pubs under our collective belts on using the latest and greatest pyrosequencing techniques.  And the related fact that, modern molecular microbial ecology has become a very technology dominated enterprise in the last few years.  I would like to think however that we each had a pretty strong record in ecology and microbiology in general (even though we were all fairly young) and this should not have been an issue given that collective record.  That could be the story for another entire post however.

Anyway, I recently pulled out a VERY STRONG science/opinion paper that I first read in graduate school, as I was preparing a lecture for some current graduate students this semester.  It is a classic and it is harsh!  Written by three very well respected scientists as the 3 domains of life was coming to the fore; Gary Olsen, Carl Woese and Ross Overbeek take the ENTIRE field of microbiology to task in various parts of this Journal of Bacteriology paper.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC205007/

In it is the crux of the argument, expounded on by Woese, Norm Pace and others in subsequent years, that the term ‘Prokaryote’ is outdated, phylogenetically invalid, and harming a correct evolutionary understanding of the nature of life!  Do not use it.  If this term is in there, and I review your paper, or your exam answer, you will not like the result.  It was reading this and other papers from Woese and associates, as well as the subsequent arrival of Prof. Pace in Colorado, that greatly influenced the direction of my dissertation research on soil fungi.  I started my studies before Prof. Pace arrived at the University of Colorado, but I probably would not have finished it without the influence and consultation of Prof. Pace and his lab members.

 

The whole paper deserves a read by any microbiologist worth his or her salt.  The quotable material in here is just too volumous to do it justice.  Below I have pasted a few of the more salient highlights from only the fourth paragraph (it would simply take to long to do it all justice here). Seriously, read the whole thing, and if you have read it before, read it again.

• “The most profound symptom of microbiology’s unfortunate condition was its reliance on the prokaryote-eukaryote dichotomy as a phylogenetic crutch, something that replaced any useful understanding of microbial relationships”
• “…it represented microbiology’s only hope of formulating a ‘concept of a bacterium’
• “With repetition (as catechism) the prokaryote-eukaryote dichotomy served only to make microbiologists easily accept their near total ignorance of the relationships among the prokaryotes”
• “This was no invitation to creative thought, no unifying biological principle.”

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)

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

Yours 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.

Upcoming Cover for Applied and Environmental Microbiology

Found out last week that some photos we submitted with our recent article in Applied and Environmental Microbiology will be used on the cover for an upcoming issue! The article described work led by Tarah Sullivan (A.K.A. Microbial Modus) on some soil fungi we isolated from a small arms firing range that can actually dissolve lead! They do this via the secretion of milieu of low molecular weight organic acids into their surroundings as they grow which changes the mineral form and solubility of the lead. We are studying these as part of DoD funded project that is trying to understand the factors contributing to lead bioavailability in contaminated soils. Makes for some pretty cool photos as well. In the age of online digital journals when I’m sure well over 95% of readers will link to our article via the web, I’m not sure if it means as much as it used too. Still it was fun to do, and hopefully it brings some further attention to the scientific work in the paper!

The photos below, clockwise from left, show:
– a sign with the abandoned firing range site where we did the work in the background
– my finger pointing to lead bullets embedded in the soil
– some of the 800 grams of bullets we sieved out and cleaned from our samples
– Several fungi growing on Petri plates with lead carbonate in suspension that are showing a “zone of clearing” around the outer edge of the colony where they have dissolved the lead.

Publications Page Now Uploaded!

Google Scholar Link

Just put up the mandatory ‘pub list’.  As of now, it is just that, a list.  Perhaps in the future I can add links to pdf files for each, but this will take some time.  

In the meantime, there is a link at the top of the page to my Google Scholar page that should allow you to link to most of these that are available on the web somewhere.  The Google Scholar page will also probably be the most up to date place to find newer pubs. If you have trouble finding something, feel free to drop me a note.