Measuring Water-Holding Capacity and the Fall Semester is Complete!

Good news! I have measured the water-holding capacity of all 80 soil samples from both the Loyola and Chicago Botanic garden sites! Here are the results (more to come later on what this all actually means!):

Graph of Primary Results of Measuring Water-holding Capacity

I've also completed the Fall semester of my senior year! I have one more to go, and I will be continuing research next semester! Next semester, I will focus on learning the statistical package R and analyzing all the temperature and water-holding capacity data. I will present my results in a poster format and possibly a presentation in the Spring at the Undergraduate Research Symposium during Loyola's annual Weekend of Excellence. More to come on this later! 

Tomorrow and the next day, Kelly and I are going to take out and reset the i-buttons at both of our experimental sites before the harsh part of winter freezes them in the soil. I will take pictures to show you all what the other site looks like. Until then! 

Happy Holidays! 

Signing off...

More on Measuring Water-Holding Capacity

I am working hard to measure all of the water-holding capacities of the different experimental trays. I've gotten through over a 1/4 of all the 80 trays! Here is a graph of the first 25 trays from the Loyola experimental site. 

For both Prairie A and Prairie B, adding native inoculum increased water-holding capacity. However, it did not increase it significantly. Once all the trays have been completed, I am going to do significance tests in R with the data so more to come later of the results and analysis of the results. 

Have a great thanksgiving!

Measuring Water-holding Capacity

I've begun taking water-holding capacity tests for all of our experimental trays! The process took some thinking to develop, but once we nailed it down, it was pretty easy going.

Measuring water-holding capacity

The procedure is: 
 

I. Drying Soil

1.     Heat up soil drying oven to 105ºC for an hour

2.     Take bag of soil out of freezer and let thaw

3.     Sample 45 ml of soil and place in aluminum weight boat

4.     Place remaining soil in bag back in freezer

5.     Place the aluminum weigh boat with soil in drying oven

6.     Dry for at least 48 hours

7.     Remove weigh boat and place in desiccator if not used immediately

II. Measuring Water-holding Capacity

1.     Measure and record 40 ml of dried soil alone in a tared weigh boat

2.     Wet a folded filter paper by submerging entirely in a water bath

3.     Let the wet filter paper drain for one minute until it is no longer dripping

4.     Weigh and record the wet filter paper alone in a tared weigh boat

5.     Add the soil to the wet filter paper

6.     Add 50 ml of water slowly and all over to the soil

7.     Repeat step 6 two times

8.     Wait three minutes for the water to drain until it is no longer dripping

9.     Weigh and record wet soil in the wet filter paper in a tared weigh boat

10.  Measure and record volume of water that filtered through

I've already gotten through the first 10 trays which are all Prairie A native plants. The first five are with added native inoculum, the next five are added with sterilized inoculum. The average water holding capacity of the added native inoculated soils was higher than the average of the sterilized inoculated soils for Prairie A! This is great news because for the Prairie A, the addition of native inoculum improved storm water retention!

More results to come later!

I-button data collection and soil sampling

Green roof in September

Putting the ibuttons back and collecting soil

The last week of September was big week for us! Dr. Chaudhary and I collected all of the ibuttons from their experimental trays and downloaded the data off of them. Then, Kelly and I restarted their missions and placed them back in their locations. Sarah and I also took soil samples from each tray to begin doing tests on the soil. I will do water-holding capacity tests and Sarah will analyze for carbon! I am currently researching water-holding capacity methods and will hopefully have news on that in the next two weeks. Until then, I am going to start compiling the temperature data from the ibuttons! 

 



Here are some pictures from the big day! Yay data!

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!

Making Progress

With week two coming to a close, I figured a blog post was appropriate to wrap up the week. Sarah and I have made quite a bit of progress and have checked several things off our list. We set up a computer in the lab and installed software for a balance (seen on the left below) in order to weigh something and have it directly record the weight in excel. This function will help us cut out the human error that is often a part of recording and rewriting data. In addition, this week we installed a ductless fume hood on the 2nd floor of IES in a teaching lab (see below). We didn't do it all ourselves this week, in fact, I've had to make several phone calls for help; I called the company that produces the fume hoods in order to track down the manual (the fume hood was donated to us), ITS at Loyola to obtain access to download software on the computer, and the company that produces the balance because we ran into a "connection lost" error! Here are a couple pictures:

Our computer station and balance all set up!

Fume hood in the second floor teaching lab

Additionally, we've continued to research soil nutrient analysis methods and have contacted William Kent, Chemistry reference specialist, at Loyola University Chicago to help us track down essentially a how-to-guide for the IC pro. Amazing, right, a machine as complicated at the IC pro, doesn't even come with directions on how to perform analysis! We have also set up a meeting with Katrina and we look forward to talking to her next week about methods for using the machine.

Lastly, the MIP is doing great! We replaced one of the corn seeds in placement # 8 that did not survive the transplant. In a few weeks, we will begin to analyze the mycorrhizal colonization of each of the corn plants' roots in order to learn a little more about the presence of fungi in each of our different soils. With this crucial information, we will be able to make a more educated analysis of how the different treatments of soils have progressed throughout our experiment in terms of mycorrhizal fungal growth.

MIP Day 9

Have a great weekend!

Week Two

I have some exciting and unfortunate news to share. I'll give you the bad news first because that's always what I prefer: at the end of last week, we received the word that the experiment will no longer be able to be on top of the roof of the Institute of Environmental Sustainability because of safety concerns. However, Dr. Chaudhary is hard at work looking for another roof on campus where our experiment can find a home. Until then, we've been busy setting up the MIP, which has been successful (the good news):

Germinated corn with radical

Planting germinated corn kernels

After two days of sitting in water, the corn germinated (photo on left) and we were able to plant it in our "conetainers" (photo on right). We very carefully placed our five different treatments of soil in different "conetainers" (five replicates of each treatment). Throughout this process, we continually cleaned the beakers we used to distribute the soil, the small tools we used to make holes for the corn, and our hands, to ensure that there was no cross-contamination of the different soils. Additionally, we gave each "conetainer" a number between 1 and 30. Each position was also assigned a number so that we could randomly designate where our "conetainers" would be placed (using a random generator in excel), in order to eliminate variables such as sunlight, water, etc. Here's what the finished product looked like:

MIP all ready to go

 A few days later the shoots started emerging from the soil: 

MIP: Day 6

So, the MIP is off to a great start. We water the corn daily and make sure that each plant gets the same amount of water. We will continue to track the seedlings' progress until they are more mature plants, when we will start to analyze the amount of mycorrhizal fungi that has formed a symbiotic relationship with each of the plant's roots. 

In other good news, the sedum is looking great! One variety has even bloomed!

Flowering sedum

On another note, Sarah and I are working to better understand how we can use this fancy machine (photo below), the Ion Chromatograph, to perform soil nutrient analyses. This machine analyzes the anions and cations in a sample in parts per million. We are trying to write a protocol, in addition, on how to extract the ions we are most interested in (ammonium, nitrate, and phosphate) from soil into a solution that can be analyzed, since the ion chromatograph will not be able to handle the concentrations that are directly in the soil. This is quite a task for us both, so we will keep you up to date. We are hoping to meet with Katrina Binaku, a Loyola University PhD candidate, who knows the ins and outs of this machine in hopes of receiving some guidance.

881 Compact IC Pro

Until then, wish us luck!

First Day

Today was the official start date of my and Sarah Ashcraft-Johnson's soil research internship with Dr. Bala Chaudhary! Our experiment will consist of setting up a green roof (we hope on top of the Institute of Environmental Sustainability) at Loyola University Chicago in order to examine whether native plants or the traditional green roof sedum mix provides more green roof services like water retention, carbon sequestration, reduction of the urban heat island effect, and beneficial relationships between mycorrhizal fungi and plants. 

Native plants

We have already begun growing the plants in the greenhouse of IES and will be setting up the green roof next week (we hope).

Sedum mix

 Until then, we organized the lab and set up a MIP (Mycorrhizal Inoculum Potential). 

Here's a before and after of the lab:

Before

After

The MIP will provide a baseline of data on how much mycorrhizal fungi is already present in the soil before we begin the experiment. In order to view the live fungi, a bioassay is required. Corn will be used for the bioassay because it maximizes its relationship with the fung in order to receive lots of phosphate; each plant will grow in its own "conetainer" for a month in each of our different treatments of soils. The different treatments are: 
        1) soil with a live native inoculum that Dr. Chaudhary cultivated herself!
        2) soil with a sterilized inoculum 
        3) soil that was bare that will go to the Chicago Botanic Garden 
        4) soil that was bare that will go on Loyola's campus 
        5) soil planted with sedum that will go to CBG 
        6) soil planted with sedum that will go on Loyola's campus. 

Note: Kelly Ksiazek, a PhD candidate at Northwestern University, will be focusing on the  above-ground biomass of the experiment at two different locations. Check out here blog here: http://phippsbotanyinaction.org/

Once the plants are established, we will look at the mycorrhizal colonization of each of the treatments. While this seems to be a tedious task, it will be very important in providing a starting point when trying to measure the growth of the mycorrhizal colonies throughout our experiment, which will tell us a little more about about the effect mycorrhizal fungi has on the performance of plants in green roofs.

Organic corn germinating!

"Conetainers" labeled and ready to go

The corn germinates in a dish with just a little bit of deionized water (covering it about half-way). Certified organic corn seeds are used in order to ensure that no anti-fungal treatment has been applied to the seeds which would inhibit our results. Deionized water is also used in germinating the corn in order to prevent other contaminants that may be present in the water from interfering with the seeds. Once the corn has germinated, we will fill the "conetainers" with our treated soils. We will do five replicates of our six different treatments, thus, we will have 30 little corn plants. We hope to fill the "conetainers" with soil tomorrow and place the germinated corn seed in the soil (a small radical will have developed in two days). That's all for now!