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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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!

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

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.