Prof. Carl Woese – 1928-2012

Professor Carl Woese has passed from this world. While I recently discussed one of his papers in a post, I simply dont have the time to properly eulogize his loss and what he has meant to microbiology right now. It would be a long article. Also, I did not have the pleasure to know him personally and so im sure there are scientists better qualified to do so. Many others are noting his loss and what he has meant to them and the science of microbiology, and will likely continue to do so for some time. A few posts from other sites are linked below for now.

RIP Professor Woese!

Announcement from Univ. Illinois: http://www.igb.illinois.edu/news/carl-r-woese-1928-%E2%80%93-2012
Microbes Rule Blog Post: http://microbesrule.blogspot.com/2012/12/a-sad-post-rip-carl-woese.html
News Gazette: http://www.news-gazette.com/news/university-illinois/2012-12-30/visionary-ui-biologist-carl-woese-84-dies.html
Phylogenomics Blog Post: http://phylogenomics.blogspot.com/2012/12/rip-carl-woese-collecting-posts-notes.html
T. Taxus Blog Post: http://ttaxus.blogspot.com/2012/12/carl-woese-1928-2012.html
NY Times: http://www.nytimes.com/2013/01/01/science/carl-woese-dies-discovered-lifes-third-domain.html?smid=fb-share&_r=0
Pharyngula Blog Post: http://freethoughtblogs.com/pharyngula/2012/12/30/so-long-and-thanks-for-all-the-archaea/
Wired Magazine: http://www.wired.com/wiredscience/2013/01/carl-woese-revolutionary-biologist/

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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): http://biology.unm.edu/graduate/graduate-procedures.shtml

General information about the department can be found here: http://biology.unm.edu/index.shtml

Information about the Taylor Lab research program can be found on these sites:
http://mercury2.iab.uaf.edu/lee_taylor/ & http://www.borealfungi.uaf.edu/

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

Announcement for Stable Isotope Short Courses

2013 Stable Isotope Short Courses at the University of Utah
Stable Isotope Biogeochemistry and Ecology, June 3-14, 2013
Isotopes in Spatial Ecology and Biogeochemistry, June 17-28, 2013

https://itce.utah.edu/courses.html

Applications will be accepted until February 8, 2013. Application forms for both courses can be reached through the webpage https://itce.utah.edu/apply.html.  We will notify applicants about February 28, 2013 regarding acceptance into the course and how to begin planning for lodging arrangements, tuition payments, reading materials, etc.

We will be offering a limited number of scholarships to support course fees and lodging expenses for participants in each course. If you are interested in being considered for one of the scholarships, additional information beyond the initial application is required. Details are posted on the application website. We will announce scholarship recipients on or about February 28, 2013 as well.

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.

jbacter00019-0025

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.

NoProkaryotes

 

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

KanlowVsSunburstRoots

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!
HydroponicallyGrownSwitchgrass
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