Fall Semester

The Fall semester of my senior year has begun!

I'm sorry I couldn't resist inserting one of my favorite Michael Scott moments...

More importantly, I will be continuing the research I began over the summer for credit this semester! I am also happy to say my partner in crime, Sarah, will be continuing research with me! She and I will be meeting with Dr. Chaudhary and other students working on lab related projects regularly in a small lab group meeting. My main goals for the semester are:  

• Collect the ibutton data in September, reset the ibuttons, replace them back outside in their experimental postions and then analyze the data
• If I have time, I will analyze the data with R, a statistical package, and compare it with daily temperature/precipitation data. This will provide us with a little more information on transpiration rate. If the temperature varies within the trays after rainfall, we will know that the cooler trays have the ability to not loose water as quickly as the other warmer trays.
•  Sample soil from experimental trays and measure water holding capacity of the different soils
•  Once collected, the soil is inundated with water using a can and filter setup. The soaked soil is weighed and then dried in an oven and then weighed once dry. The difference is the water-holding capacity in ml of water per gram of soil.
•  Complete my prospectus, which I will share with you of course! 

 I will keep you updated all along the way!

Measuring soil stablity - sieving soil!

 A few weeks ago, Sarah and I measured the soil stability of each of our experimental trays. That meant that we collected a soil aggregate (a very small clump of soil particles) very carefully from each tray. Each soil aggregate was placed in a sieve basket. I am going to take this opportunity now to finally mention what sieving is (since it is in the title of my blog and all)! Sieving through soil is essentially separating the soil by particle size. In our slake test, we want to know how fast the soil sieves apart. We do this by placing it in water once its in its sieve basket. This will tell us a little bit about the stability of the soil aggregate (or ped), or its ability to resist breakdown by water. 

The sieve with the soil aggregate is placed in water for 5 minutes and examined for signs of dissolution. If the aggregate of soil makes it past 5 minutes without completely dissolving, it is then dunked 5 times. Throughout the test, a soil stability class is assigned. 


Assigning soil stability class: 

• If the soil is not even stable enough to sample, the soil stability class is 0 (which is really, really bad - the soil will not resist erosion to wind or water). 
• If 50% of the structural integrity is lost within 5 seconds of inserting the ped into water, the soil stability class is 1 (pretty bad). 
• If 50% of the structural integrity is lost within 5-30 seconds of insertion in water, the soil stability class is 2 (ok). 
• If 50% of the structural integrity is lost within 30 - 300 seconds after insertion or <10% of the soil remains on the sieve after 5 dipping cycles, the soil stability class is 3 (good). 
• If there is 10 - 25% of the soil remaining on the sieve after 5 dipping cycles, the class is 4 (pretty good).
• If there is 25 - 75% of the soil remaining on the sieve after 5 dipping cycles, the soil stability class is 5 (really good).
• If there is 75 - 100% of the soil remaining on the sieve after 5 dipping cycles, the soil stability class is 6 (REALLY GOOD i.e. make sure you don't have a rock instead of a soil aggregate!)

But we love doing it!

Finding peds is hard

The results were great! The average soil stability class was 4.43 with a standard deviation of 1.34! These results will be analyzed further to draw conclusions about the soil stability class of our different treatments. The results will also be analyzed in comparison with other data we gather on the trays to start making informed conclusions about whether green roofs with native plants and/or added native arbuscular mycorrhizal fungi perform as health natural habitats and improve heat insulation and storm water retention. More to come later!

Staining & mounting roots

The next step in the analysis of the roots harvested from the MIP is staining and mounting. The 0.15 grams of roots from each corn plant grown in our different treatments of soil was placed in a small cassette and then placed in boiling 10 % KOH for 3-5 minutes. The potassium hydroxide clears the roots of the cellular contents of their cortical cells so that the fungi, which lives inside the roots, can be seen better. The fungus isn't killed because the fungus is made of chitin which is very recalcitrant and resists breakdown. 

 KOH and ink in vinegar solution

Roots in boiling KOH

The next step after the roots have been boiled in KOH is to place them in boiling 5 % ink in vinegar solution for 3 minutes. After this step has been completed, the fungi inside of the roots will have been stained and will be completely visible under a microscope. The roots are then mounted in PVLG on a microscope slide to be viewed. 

Dr. Chaudhary's perfect example slide

All of our roots stained and mounted

And finally our roots are ready to be examined for mycorrhizal fungi!

MIP Harvest

In other great news, the MIP* was harvested just after the corn plants matured enough to develop significant relationships with potential mycorrhizal fungi in the soil. The corn plants were grown in order to look at how our different soil treatments varied in terms of the presence of mycorrhizal fungi. Did the native inoculum truly have mycorrhizal fungi? Was the sterilized soil truly sterile? In addition to confirming our treatments, analyzing the MIP also provides a baseline, or a starting point, of how much mycorrhizal fungi was present before we started our experiment. 

The MIP just before harvest

As a reminder, our green roof experiment has several different treatments of soil and we want to analyze if and how mycorrhizal fungi benefits a green roof.

In order to analyze the mycorrhizal fungi in the soil, the roots have to be harvested since the fungi live inside the roots. But first, the above ground biomass is harvested, dried and weighed. Obviously, the plants with the most above ground biomass were the strongest and healthiest. We want to quantify the above ground biomass as a confirmation our results of the below ground biomass. 

After harvesting the above ground biomass, the below ground biomass, or the roots, are left in their respective "conetainers" and then are placed in the freezer until we are ready to begin washing the roots. The freezer halts any decomposition that may be happening in the soil which could artificially lower our results. Once the roots are ready to be washed, they are taken out of the freezer and placed in a series of water baths to ensure that the roots are clean and not "being weighed down" by any extra soil, which would also skew our results. 

Once the roots are washed, 0.15 grams is weighed out to be stained and placed on a slide. The roots are first cut into 4-5 1" sections where roots are taken from each section in an effort to sample in a stratified manner. These roots will be examined under a slide for mycorrhizal fungi relationships. The rest of the roots are weighed and dried to determine the below ground biomass weight. 

Sarah cutting corn roots into sections

This very time consuming process will tell us everything we need to know about the health and virility of our different soils; it will quantify the amount of mycorrhizal fungi in our different soils. 

*For more information on what the MIP is, please refer to my first blog post :)

I-buttons/Thermotrons!

Great news on the green roof research front! I have been diligently working to figure out how ibuttons, small computer chips that record temperature readings, work in order to begin collecting temperature data on our green roof. We want to record the temperatures inside the different trays of different soils in order to make conclusions about whether green roofs with native plants and/or added arbuscular mycorrhizal fungi improve heat insulation. In order to know this, we need to track the soil temperature at different times in the different soils. We will also compare it to the temperature on the green roof surface as a control. Luckily, we have little ibuttons, or thermotrons as Sarah and I have named them, to help us out. 

I have been performing small experiments on all of our ibuttons in order to verify that they take the exact same temperature reading while in the same environment. In order to set the experiment up, the ibuttons must be set on a mission (Sarah and I didn't make up that term, I know shocking). However, you cannot set a start time for all the ibuttons (we really wish we could). We want to start all the ibuttons at the exact same time so time is not a variable when analyzing the results. In order to do this, you have to set a mission time delay...This means that if you have 26 ibuttons it will take 26 minutes to set them up. The first ibutton mission time delay should be set at 26 minutes, the second at 25, the third at 24, etc. so all the ibuttons will start their mission at the same time. 

The next step in the small experiment I did was to place all the ibuttons in different environments, such as at room temperature, in the fridge, in the freezer, and on top of the green roof. Then, I analyzed the data. If all of the ibuttons took temperature readings at exactly the same time, then they should all have the exact same temperature readings in the different environments. 

The results were great. I calculated the averages and standard deviations for each of the ibutton's temperature readings at the different times. The standard deviations were for the most part below 1, with only a few above 1. 

This gave us enough confidence that our trusty ibuttons were able to do their job correctly. So, this morning Sarah and I set all the ibuttons to start their mission at 5:00 PM today. This gave us enough time to bury all the ibuttons about halfway down in the soil in the middle of the selected trays (the trays were selected randomly).

Here are the trusty ibuttons ready to start their mission! 

26 ibuttons in plastic bags

An ibutton ready to be buried alive!

The ibuttons were placed in a plastic bag because unfortunately they are not water proof. While the plastic bag may affect the temperature reading slightly, all of the ibuttons are in a plastic bag, so all the temperature readings will be affected in the exact same way. The small piece of paper labeled each ibutton's location and ID. The ibuttons are able to store 2,048 temperature readings. We set the ibuttons to take a temperature reading every hour. That means we will be able to leave the ibuttons out on the roof until late September when we will have to take them back inside to retrieve data and restart their missions . 

Me planting the ibuttons

An ibutton being buried in a control tray

A control ibutton taped to the green roof

Green roof extravaganza

In addition to the green roof experiment we set up last week on the Quinlan terrace garden, we set up Kelly Ksiazek's gene (pollen) flow experiment on 9 different green roofs around campus this week (we walked a total of 5 miles that day in order to do it!). The experiment will aim to track the movement of pollinators on all of the green roofs. In order to identify if pollinators travel to different roofs and pollinate a variety of locations, a DNA analysis will take place on three different varieties of native plants (Asclepias tuberosa, Penstemon hirsutus, Oenothera macrocarp) once they have been pollinated. There will be 15 of each of these species arrayed in a square with three plants (one of each species) at the corner points and in the center of the square. The square will be identical on all of the green roofs.

In this experiment, Kelly hopes to identify that pollinators do in fact move from green roof to green roof, or micro-climate to micro-climate, in order to relay the importance of neighboring green roofs acting as a diverse, pollinator-attracting, habitat islands that rely on and influence one another.

Here's a picture of the three plant species amongst the existing green roof: 

Top: Penstemon hirsutus, Left: Oenothera macrocarpa, and Bottom: Asclepias tuberosa

Each native species is pollinated by a different pollinator! The asclepias is pollinated by bumblebees and butterflies, the penstemon by small sweat bees and the oenothera by hawk moths. Kelly hopes to do many hours of pollinator observations (>100 hours) in order to verify the patterns she hopes to find in the DNA analysis. 

A corner of the "native" square

The natives surrounded by sedum!

Flourishing green roof

The green roof on de Nobili 

The de Nobili green roof overlooking IES

The hatch to the green roof on Quinlan LSB

It was quite a task to install this experiment on 9 different green roofs, but it sure was fun seeing all of the green roofs on campus. We even had to open a hatch to get to one of the green roofs. I felt pretty official.

Green roof lover

MIP

In other news, the MIP is doing very well and will be ready for analysis in a couple of weeks. I'm still working on writing the outline for my prospectus and researching soil nutrient analysis methods. There is certainly lots to do! See ya later! 

Here we go!

Last Thursday, May 29th, we set up our green roof experiment on the terrace garden of the Quinlan Life Sciences building! It's not quite a green roof, the roof is tiled, but it gets a lot of sun and is elevated (its on the 5th floor) so it mimics a green roof quite nicely.

Here are some pictures of the green roof once we set it up (it took about 2.5 hours to move all the trays from IES to the balcony!).

Green roof experiment

Today, Sarah, Kelly and I began to take data on the plants (height, width, density, notes on how it appeared). If I didn't have a farmer's tan already, I definitely do now! Soon, we will start to take data on the soil conditions (soil stability, soil organic matter, soil nutrient availability, moisture, temperature, etc.)

Our green roof in its urban setting!

Additionally, Sarah and I have decided on our own projects for the rest of our internship. I will be focusing on whether green roofs planted with native prairie plants or a non-native sedum mix are better at retaining storm water and insulating heat. I will be working with Dr. Chaudhary, Sarah, and Kelly to set up devices that will record the temperature hourly in hopes of identifying a difference in temperatures throughout the plants and tiles. I am still researching methods on how to measure storm water retention. More to come later! 

Also, we met with Katrina and are feeling a little bit better about soil nutrient analysis methods on the IC pro. We are hoping to set up some sort of training with someone who works for the company to get us off in the right direction. We are continuing to research methods for cation and anion extraction from a soil solution. Also more to come! 

Have a good week!