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

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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!

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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!
DeltoidesForce1_sm
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!)

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Andrii fighting with the tree ring corer.

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Greg, Jessie and Cassandra in the process of excavating a tree root.

Announcing PROFESSOR’S Sullivan and Steinweg.

Good news! Two of our postdoctoral associates, Tarah Sullivan and Meg Steinweg, have been offered and accepted Assistant Professor positions starting this fall! Given the tight job market these days I was a little surprised that within one week of each other a couple of months ago, two of my postdocs were in my office to let me know they had received position offers.

Tarah will be moving in October to Washington State University in Pullman to start a position in the Department of Crop and Soil Sciences.

Meg Steinweg will be moving in August to University of Wisconsin – Baraboo to start a position in the Department of Biological Sciences.

As a project manager I’m concerned it is going to leave a big hole in the lab to fill, but as a colleague and mentor I couldn’t be more excited for their success (and even if Tarah is going to my old rival WAZZU)!

Congrats to both!

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!

Modeling microbial communities and two new papers

There is a lot of emphasis these days in my field on figuring out how to best translate our results from gene-based microbial community studies, into predictive mathematical models of (eco)system functions.  While still not easy, the new methods we now have on hand for microbial community analyses do finally allow us to collect enough data, on enough replicates, that it is no longer impossible.

Thanks to the work of a talented scientist I got to work with at ORNL named Gouping Tang, I can finally say we (mostly Gouping) have been able to make the leap from our data sets to mathematical models.  These two new papers take the data and theoretical model we proposed in a paper led by Tom Gihring in late 2011, and develop full mathematical simulations of our experimental systems.  These data are from a large scale field test we worked on with numerous collaborators that demonstrated the use of emulsified vegetable oil to stimulate reducing conditions in a contaminated groundwater system. This is somewhat bittersweet though as due to funding changes, these may be some of the final opportunities our lab will have for work on metal bioreduction in groundwater microbial communities that I have toiled on ever since leaving graduate school and coming to Oak Ridge.

Here are the citations with the links to PDF files.

Tang, G., Wu, W. M., Watson, D. B., Parker, J. C., Schadt, C., Shi, X., & Brooks, S. C. (2013). U (VI) Bioreduction with Emulsified Vegetable Oil as the Electron Donor–Microcosm Tests and Model Development. Environmental Science & Technology.  (Tang_EST_MicrocosmModel)

Tang, G., Watson, D. B., Wu, W. M., Schadt, C., Parker, J. C., & Brooks, S. C. (2013). U (VI) Bioreduction with Emulsified Vegetable Oil as the Electron donor–Model Application to a Field Test. Environmental Science & Technology. (Tang_EST_FieldModel)

Cool toys = Hot data? (part 1)

As part of our work on a the SPRUCE experiment, we have been quantifying the various microbial activities in a peat bog in MN. We have also been lucky enough to explore some new approaches to improve our research methods as part of this. Two of these efforts involve some pretty cool science ‘toys’. Im going to discuss one below, and save the other for a future post.

One of the ways we are trying to accomplish the above, is to understand more thoroughly how the enzyme activities of microorganisms may vary in response to a range of temperatures. These enzyme potential analyses have been around for years and allow us to understand how microbial activity contributes to the cycling of carbon and nutrients under various specific stimuli. These work are possible now, thanks to work in the past by Bob Sinsabaugh, Don Zak, and many others. We accomplish this by adding peat (or soil) to mixtures that contain a fluorescent dye labeled substrate compound, that the enzymes the microorganisms secrete into the soil (or peat) can breakdown. When the fluorescent label is liberated from the the substrate compound, it fluoresces, and we can quantify it. If we want to quantify this response over a range of temperatures, it usually involves hunting up a host of large incubators in which to do the studies. At most usually 4 or 5 of these are available at any given time. Last month, Meg Steinweg and I visited the lab of collaborator Joel Kostka at Georgia Tech that had a cool toy that allowed us to do this much more efficiently.

HeatBlockThis is a gradient heat block (much like those used for PCR, but bigger) that allowed us to fairly precisely conduct our experiments. It is a custom designed tool that was machined from a block of solid aluminum, and has an electric heater attached on the high temperature end, as well as ports that allow circulation of a chilled glycol solution on the low temperature end. To this they added holes at an even spacing that we can add test tubes too. This creates a precise gradient of temperatures over a range of about 0 to 40 degrees Celsius (~32 to 104 degrees Fahrenheit) to do our enzyme assays. Once we set the temperature, this gradient was repeatable each day as seen below (there are three separate measurements in the graph, taken over two days, that largely overlap!)
BlockPerformance

This science ‘toy’ is translating to some really cool data sets for our SPRUCE projet. In SPRUCE we will be using a belowground heating system to warm up the peat in the bog to understand how all the carbon stored in the peat will respond (a paper on this technology is here). This could have implications for the potential of future climate change to feedback and cause additional releases of carbon dioxide and methane to the atmosphere from bogs and other ecosystems. To get an initial handle on this in laboratory experiments, we used the ‘toy’ above to look at three different microbial enzyme responses tied to carbon, nitrogen and phosphorus cycling using peat collected from Minnesota at different times of the year. Typically we would expect responses leading to a rather smooth exponential curve showing increased activity with increased temperature (up to the point where the enzymes become denatured and activity drops off). Somewhat surprisingly, Meg’s work using this tool, looks to be showing two different responses in at least some samples. In an example of one of our Beta-Galactosidase activity assays below, we see a linear response at lower temperatures (below about 15C), and what seems to be a separate linear response at higher temperatures (above about 15C), instead of the expected exponential curve. While this graph is only showing a set of data originating from one peat sample, for one enzyme activity, collected at one time of year… When we look at a range of such samples, Meg’s data is showing trends that vary by depth in the peat, and time of year the samples were taken. B-Glucosidase

Im not sure exactly how these data should be interpreted yet (we need more of them of course), but what it could suggest, is that what we are seeing is enzyme responses from multiple communities of microorganisms, that exist separated by space (depth in the peat) and time (season in which the samples are collected). That would be pretty cool to prove, as it might effect the interpretation of the seasonal responses we will see in Minnesota when we heat up the bog. This is not unprecedented, as we saw similar phenomena when I was studying alpine tundra communities in Colorado during graduate school. However, this could justify more winter trips to MN, which believe it or not, I enjoy!

We have recently began some work collaborating with a group that does sensor development at ORNL, that is related to the SPRUCE project objectives. Hopefully in the near future I will be able to blog about it as well. However, as of now, while im convinced we are producing some really cool toys, the project has yet to produce enough cool data. Hopefully the data arrives soon!

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 www.anl.gov/careers, 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): 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

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.”

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