The past two weeks have been laboratory heavy. Which I love! My goal is to quantify the amount of cyanobacterial genes in the biocrust samples I have in order to develop a smart plan for sample analysis. If I know the number of cyanobacteria present at each step of a restoration process, then I can more easily say which step causes a significant decline. We can then zero-in on that step and focus our money and time on that part of the process. In order to quantify cyanobacterial genes, I am using qPCR with cyanobacteria-specific primers. In order to do that, I need to extract DNA from the soil, quantify the total DNA in each sample, and then do the qPCR. In the photos above, I show how the samples are homogenized (with mortar and pestle) and then extracted for DNA through many steps. I'm always shocked at how many tubes are required for these extractions (photo on the right). Here, I am extracting only 4 samples (in replicates of three) and it requires 6 tubes per sample and just as many pipette tips. Because of this large plastic waste, I am extremely careful to not mess up the extraction and I double check that every sample is worth the effort. I'm looking forward to a month from now when I can share this data with collaborators.
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This week, I am measuring the texture of the various soils I have sampled from many different projects. Soil texture is important for dryland studies because finer grained soils can hold more water longer. We also find that biocrust recovery occurs more quickly on fine grained soils. We take ~13 g of each soil and remove carbonates and organics. We then use a 53 um sieve to separate sand from the finer grains. The sand can be seen above in aluminum tins. We then separate the silt from the clay by letting the silts fall out of solution (~5 hours). We can then pour off the water and clay, keeping the silts in the bottom of the beaker. We can then calculate the percent sand-silt-clay and classify the soil textures based on the standard system. By doing this analysis at the plot level, we have a more detailed understanding of what is happening in our plots rather than relying on large scale soil texture maps. These 16 samples took me 6 days of lab work, so I hope it is worth it!
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AuthorSierra is a graduate student in the Barger Lab at CU Boulder studying microbial ecology for dryland restoration. Archives
August 2023
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