Feeds:
Posts
Comments

Posts Tagged ‘biological soil crust’

Lab at Zzyzx

Lab Building at the Desert Research Station at Zzyzx Road, CA.

On this third day of our research project in the Mojave Desert, we did a series of tests on the biological soil crusts and soil samples we collected yesterday at three sites along Kelbaker Road near Baker, CA.

Parag and Rakesh

Parag and Rakesh demonstrate extraction protocols

The laboratory building at the Desert Research Station is set up with standard equipment for chemical and biological tests, including flasks, test tubes, Bunsen burners, sinks, a fume hood, etc. Most of the detailed equipment and supplies was brought by Rakesh Mogul and the other scientists working on this project, including a centrifuge, a spectrometer, pipettes and pumps, and test kits and reagents for the extractions and analyses we’d be doing.

Interior of lab

Inside the lab building at Zzyzx Road

The students and scientists had set up a series of protocols for the tests and a plan of attack for how to identify each sample. First, a group were taking samples of the crusts at each location and extracting the DNA from them. Each time, the scoop was sterilized with a Bunsen burner. The solution was then centrifuged to settle out the non-dissolved portions. Another group was at work using polymerase chain reaction techniques to increase the DNA yield so that the final sequencing could be done in a specialized lab. We’ll have the lab look at the specific species in the crusts, including the cyanobacteria, fungi, lichens, mosses, and archaea present in these symbiotic communities.

Extracting DNA

Extracting DNA from the biological soil crusts

Parag Vaishampayan worked with a group to extract ATP (adenosine triphosphate), which will give us a measure of metabolic rate in the crusts at each site. We sampled not only the crust itself but the soil directly underneath each sampled crust, and will look at ATP of the crust compared as a ratio to the ATP in the soil. The hypothesis is that the healthier crust will have a higher ratio.

Extracting ATP

Testing for ATP

Meanwhile, the soil itself was analyzed. Mary Beth Wilhelm and Liza Coe used a soil test kit to look for trace elements in the soil, such as aluminum, iron, chlorine, and magnesium. I helped do some of this analysis, since my background is in chemistry and geology. Rosalba Bonaccorsi, Ruben Hovanesian, and Leonard Bacon separated the soils using sieves to find the relative sizes of particles and materials at each site.

Soil tests

Testing the soils chemically

A final group of pre-math teachers developed a series of statistical tests to look at results of all these tests, including some ANOVA (analysis of variance) tests, which I vaguely remember from my masters degree program.

Pipette instruction

Instruction on pipette techniques

We got quite far with the tests today – it helps to have a group of people who are experienced and work well together. Although they come from all over the California State University system, the students are all in their second year in the program and know what to do and what each other’s strengths and weaknesses are. We all helped out where we had experitise. It was fun to see what college students can accomplish. We have one major remaining test for tomorrow: chlorophyll extraction and spectral analysis.

Statistical tests

Allison and Kristen working on statistical models

I also talked with Geoff Chu, Paul Mans, and Ryan Piaget from NASA Ames who are developing a prototype rover built from a commercial off-the-shelf RC car, with video camera provided by an Android phone controlled from a laptop over a local network. Motor servos are controlled by an Arduino brick. The point of this rover is to analyze the soil crusts remotely without having 20-odd people stomping around on them. The rover will be equipped with a stereoscopic IR camera that can read 3D depth, along with an RGB camera. My goal is to take the height data from the IR camera and convert it into a grayscale heightmap of the various crust locations, then turn the heightmap into a 3D model in Daz3D Bryce. The RGB photo will be mapped over the top of the model as a texture. Ultimately, the model can be uploaded to an online app where people can rotate and explore the crusts themselves.

Geoff and Paul

Geoff Chu and Paul Mans working on the RC rover

We had a preliminary results meeting after supper to look at what we have so far. The ATP analysis was not consistent across sites, possibly because the results changed as the day warmed up, but we’ll send the samples to labs for more accurate results.

Review session

Review session for today's results

Advertisements

Read Full Post »

Test site 1

Site 1 for testing biological soil crusts in the Mojave Desert

I’m in the Mojave Desert with a group of astrobiologists from NASA Ames, JPL, and the California State University system, along with student teachers in the Spaceward Bound program.

Planning samples-site 1

Rakesh Mogul, Chris McKay, and Parag Vaishampayan

Today, March 19, 2012 we officially began the main activity of this field research: collecting samples of biological soil crusts. We hope our research is on the cusp of crusty research . . . or something like that. We have two questions: First, what are the components and abundances of crusts in various locations; and second, what causes these crusts to change density from site to site? We discussed how to approach these questions on Sunday night and decided on an experimental procedure. Dr. Rakesh Mogul first led us in an activity on assigning planetary protection protocols to various types of space missions as a way of looking at the variables and possibilities of contamination. Then we got down to business on the study itself. We decided to sample three locations along Kelbaker Road, which heads east from Baker across the Mojave National Preserve to Kelso Depot. We brought with us sampling tools and equipment, including a field handheld ATP analyzer and collection tubes.

Photographing site 1

Photographing Site 1 location A

We collected after breakfast on a cool morning. The wind had calmed down from the night before and it looked to be a beautiful day as we loaded the vans and headed out. We stopped first at a site about five miles east of Baker which had been scouted out earlier. This site had an intermediate or average amount of biological soil crusts (BSC). Chris McKay described the general goals at each site, and Rakesh worked through the procedures as we divided up tasks.

We had several things we needed to do: First, locate an origin point with an average amount of soil crust and lay down a frame and grid aligned to the compass and its GPS coordinates recorded. Then we set up a vertical tripod and took photos of the location. All of this was to allow for determining the density of the crust – how many of the grid squares were covered.

Second, Rakesh and some of the teachers collected samples to test for ATP using a handheld analyzer. This wound up being a slow procedure and took some

Sampling ATP at site 1

Sampling ATP at Site 1

Third, Dr. Parag Vaishampayan of JPL collected samples near the grid, both of crust and non-crust areas, that we would use to extract the DNA and perform polymerase chain reaction (PCR) procedures to increase the DNA for testing (this would be done back at the Desert Station lab). We also collected soil samples to analyze chemically. At each location, we also sampled four other locations, each randomly selected using GPS coordinates in an array around the original location.

Collecting soil samples

Collecting soil samples at Site 1

With all this done and samples labeled and stored, we moved on down the road to the second site, this one with a dense growth of BSC. We ate lunch, then followed the same procedure to collect samples at five locations at the site. Since the crust was so dense, we had to be very careful not to step on any areas unless there was a wash or stream without crust.

Site 2 sample square

Sample grid at Site 2

Site 2 dense crust

Dense, mature soil crust at Site 2

We then loaded up again and travelled back through Baker to our third site about two miles west of town across the road from Silver Lake. Here, the soil was very poor in soil crusts – we found a few small spots about the size of a quarter coin, all surrounding small puddles where organic matter and water had ponded. The BSC was much lighter in color and much sparser. We followed the same procedures, setting up grids, collecting samples, testing ATP, etc.

Site 3

Site 3 near Baker, CA.

Collection site 2

Collection Site 2

By then the afternoon had worn on and it was time to head back to the Zzyzx station. As soon as we got there our math wizards started setting up statistical searches and crunching the numbers. Tomorrow we’ll do the laboratory tests and prepare the samples by extracting DNA, sorting the soil, and testing the soil chemistry. We hope our results will be worthy of publication in their own right, as well as point to future ideas and techniques for studying life on other planets.

Chris McKay at Site 3

Chris McKay at Site 3

ATP at site 3

ATP sampling at Site 3

Read Full Post »