Each year the KBS LTER program awards two graduate students with summer research fellowships. Here Michelle Quigley describes the research her 2015 summer fellowship supported. Michelle is a Ph.D. student in Sasha Kravchenko’s lab at Michigan State University.
Michelle Quigley setting up an aggregate to be scanned at Argonne National Lab Advanced Photon Source.
When most people think of studying soils in agricultural systems, they picture someone out in a field taking soil samples or surveying crops or in a lab running samples. That is fairly typical for most soil scientists. However, while I do get out in the field, most of my time is spent staring at a computer screen.
Carbon is very important to agricultural systems. Most people know if they pick up a handful of dirt and it is black, then it is likely pretty good soil for growing things. The black color comes from the carbon. In addition to helping plants grow, carbon in soils can also aid in climate change mitigation, as most terrestrial carbon is stored in soils. However, soils in the US and around the world have been losing carbon for many years. This loss of carbon results in poorer performing soils and more carbon dioxide (CO2) in the atmosphere. But what does that have to do with me staring at a computer screen?
The soil aggregate is the infrastructure of the soil. Their pores are the highways through which bacteria travel as well as water, air and nutrients. Changes in pore structure restrict or provide access to carbon present in the soil aggregates to bacteria for consumption. Soil aggregates and, more importantly, stable soil aggregates are where soil carbon is stored in soils. Soil aggregates come in various sizes, but the aggregates of greater than 250 μm, referred to as macro-aggregates, are thought to be most important for storing carbon. Trying to study the pore structure of soil aggregates is very difficult due to their small size and the destructive nature of most analyses. To get around this, my advisor, Dr. Alexandra Kravchenko, and I use a technique known as computed microtomography (μCT). This technology is identical to a medical CT scan done at a doctor’s office. The only real difference is instead of scanning a human body, we are scanning soil aggregates, so X-rays of much higher energy are required. The facility we use to do scanning is Argonne National Lab Advanced Photon Source, in Argonne, IL.
This past summer I received support from the KBS LTER Summer Fellowship Program for a scanning trip to Argonne. Scanning time is very limited at Argonne, and I only had 24 hours to get everything I needed scanned. Planning for these trips takes weeks and careful sample selection to maximize the amount of data that can be obtained from each sample. Careful sleep planning is also essential, as samples are run through the entire 24-hour period and someone needs to be able to drive back to Lansing the next day. Jordan Beehler and Jessica Fry, fellow graduate students, graciously helped me on this scanning trip. The results of the scanning trip are hundreds of gigabytes worth of gray scale images of soil aggregates. Unlike a medical CT scan that takes a few days or hours to analyze, it can take months to analyze the data from one scanning trip. This is mostly because the majority of the analysis is done by hand for the soil aggregates, while computer algorithms handle most of the medical CT analysis. That’s why I spend most of my time looking at soil aggregate images on the computer.
The inset and the main image are the same aggregate scanned at 13 um (inset) and 2 um (main picture). The blue bar on both pictures indicates 200 um.
Last summer’s scanning trip was specifically used to scan aggregates at very high resolution to look at the micro-porosity of KBS LTER soil aggregates. Routinely we scan aggregates at approximately 7 to 13 μm to capture the entire 5 mm aggregate in one image. This lets us see the macro-porosity of the aggregates. However, this means that porosity less than 7 to13 μm cannot be seen on the images. The objective of last summer’s scanning trip was to scan a section of several 5 mm aggregates to see if the micro-porosity varied between LTER treatments, specifically between conventional and biologically-based (organic) management of corn, soybean, and wheat rotations, and the early successional “old field” community. We know from 25 years of research on these plots that carbon is being accumulated in the biologically-based and early successional fields, but not in the plots under conventional management. My research is trying to help us understand exactly how that carbon is being protected in these soils.
Aggregates were scanned at 2 μm resolution, which is about the size of a bacteria. The results were actually surprising. While the macro-porosity varied between treatments, the micro-porosity did not. This means that any difference in carbon protection between treatments because of porosity is due to the macro-porosity. How these differences physically protect or expose carbon in soil aggregates from/to bacteria is a question of my continuing research. Currently, I am using stable carbon isotopes to identify which carbon bacteria are consuming (newly added or already present carbon) and how macro-porosity relates to this use.
3D image of a soil aggregate scanned at 13 μm with the pores identified (purple). Just one of many things that can be identified from μCT images.