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.



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.”

Job Post: Microbial Ecology Position at Johns Hopkins

The Department of Geography and Environmental Engineering at Johns Hopkins University will begin reviewing applications on January 15, 2013 for a tenure-track position in environmental microbiology/biotechnology beginning in Fall 2013. Application materials include: 1) a letter of interest, 2) curriculum vitae, 3) a one or two-page summary of research and teaching interests, 4) relevant papers and publications, and 5) names of five referees in a single pdf file to dogee@jhu.edu. Click here for more information.

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

The ORNL ‘Vision’ Video

ORNL released a pretty cool P.R. video the other day. While it sometimes feels like you are given little attention if you are not doing research on Neutrons, Computing, or ‘Alt Energy’ at ORNL, this video gives a shout out to many areas including environmental and climate research in a few places at least. All in all, makes for a nice video to point to, when friends, family, or other non-scientists ask that famous holiday dinner question… “What is it you folks do out there at ‘The Lab'”?

How do you survive bad times? Easy, steal the genes you need from other organisms.

This is a link to a recent post of my new postdoc Mike Robeson and his first entry into the wordpress blog world…

How do you survive bad times? Easy, steal the genes you need from other organisms..

Scary graph of the day… Potential science funding cuts…

Scary graph of the day... Potential science funding cuts...

Here is the scary graph of the day for those of us generally interested in scientific progress, and more specifically for those of us that do fundamental research for a living. Almost as sad, is that most of the ‘Stimulus’ blip on the basic research side went to new state of the art facilities and equipment, that if these cuts take place, may become vacant and unused. Very sad indeed.

CERCLA, HAZWOPER and the ‘Valley of the Drums’

Valley of the Drums, KY

I took my annual refresher training for HAZWOPER site work today. For those of you lucky enough to NOT know what the heck im talking about, HAZWOPER stands for HAZardous Waste OPerations and Emergency Response. This is the worker training law that was put into place after the creation of the Superfund Act (CERCLA) in the early 1980s. It mandates the standards to protect workers during cleanup operations at some of the most polluted and toxic sites in the country. Protections for these workers is one the things our government does right, they deserve it, and I’m glad that it was made a priority and a law.

Because some of my scientific work deals with and requires access to these types of sites to understand how microorganisms might contribute to their cleanup, I have to sit though a full day of refresher training each year to continue the work. While this can be kind of dry, I usually learn something new each year.

Not least of all, I as a scientist get to sit in a room with folks that are the real ‘boots on the ground’ in these cleanup situations. I take this training at the local union hall in Oak Ridge of the Atomic Trades and Labor Council. I hear their stories of what the bad old days were like, what happened to them and their loved ones who were exposed to this nastiness, and what is and is not working in terms of cleaning up these messes. I have tremendous respect for what these folks do and what it has meant to our generation to get these messes dealt with once and for all, and am thankful that we have regulations in place that this kind of stuff should not (and better not) happen again.

Some of you may know of Love Canal up in the NY area and how it contributed to the new environmental regulations that eventually led to CERCLA and HAZWOPER. This year in my class I learned a little about the ‘Valley of the Drums’ near Louisville, KY, and came home and did a little more reading about it. Unlike Love Canal where the source of the toxins was pretty much invisible and buried underground (so much so that houses were built right up to it without the developers, owners or families living there knowing), in Bullitt County this was right out in the open, in all its ugliness, for anyone to see. When it caught fire, it not only brought it to the full and immediate attention of the sites many neighbors, but it also became a powerful visual image nationwide that helped push through the cleanup laws and safety regulations that we are now lucky to have.

This link and the video linked below is from the Courier Journal in Louisville, KY and is about the site history and ongoing issues.
Valley of the Drums Video

The 4rd Annual Summer Soil Institute at Colorado State

The 4rd Annual Summer Soil Institute at Colorado State

Fort Collins, CO
July 7-20, 2013

Gain an integrated perspective with world-renowned faculty to address critical questions using current analytical techniques, experimental approaches, and instructional models.

What are the physical, chemical and biological components of soil? What do molecular techniques tell us about soil biodiversity? How does soil chemistry affect carbon and nutrient cycling? How are soil processes affected by global change?

The Summer Soil Institute is designed for graduate students, post-docs, professionals, faculty, and K-12 teachers. Located at the confluence of the Rocky Mountains and the Great Plains.

The course is limited to a maximum of 24 students. Tuition is $2000 for current graduate students and $2500 for others. A limited number of scholarships will be awarded to support tuition costs. Applications are now being reviewed.

Apply now!
Sign up for Updates on the Summer Soil Institute.

Job Posting for Hobbie Lab at UNH on our collaborative SPRUCE project.

Ph.D. opportunities in terrestrial ecosystem ecology and mycorrhizal fungi at the University of New Hampshire (this posting is for a collaborator on our SPRUCE project)

The Hobbie lab invites applications to the UNH Natural Resources and Earth Systems Science (NRESS) Ph.D. Program. We welcome inquiries from motivated students interested in how the interactions of organisms with their environment influence carbon and nutrient cycling. Our lab is an interactive group with interests in ecosystem modeling, remote sensing, the application of stable isotopes in ecology, and belowground processes, particularly mycorrhizal fungi. We are currently looking for students on two projects, one to work on a new global change experiment in northern Minnesota, another to work on biogeochemical consequences of shrub expansion in the Arctic. Incoming Ph.D. students are encouraged to develop their own research projects in these areas. For more information on research projects in the lab, please visit our website http://www.isotope.unh.edu/research.shtml>.

Interested applicants should email Dr. Hobbie <erik.hobbie@unh.edu>. The deadline for domestic and international applications is Jan. 15, 2012. In your email, include “Ph.D. opportunity” in the subject line, and a brief statement of your current or future research interests (please be as specific as you can), and a curriculum vitae. For information on applying to the NRESS Program, visit < http://www.unh.edu/nressphd/>.

New site for research and lab news

Just starting to put together this site as a spot for research news from my lab, and posts about related scientific work on the web. This will replace the web page I used to have hosted at ORNL, that unfortunately had become difficult to manage and out of date due to onerous IT requirements.