First look at Midwest Labs results. Bonus: DNA extraction update
Updated: Dec 7, 2020
First, I hope everyone had a great Thanksgiving. Personally, things have been a bit nuts around here, but I am happy to have time around the holidays to give you a first look at some of the data.
We have concluded all of the testing of the samples sent to Midwest Labs for their compost plus package. We had a total of 19 vermicompost samples that were tested in triplicate.
All of the samples submitted for sequencing analysis have had their DNA extracted! We had some equipment failure issues, but I think it all turned out OK. I was hoping to have a separate post with pictures of the process; unfortunately there was no photography allowed, and I can't even properly thank the people who deserve it.
DNA Extraction: Sample loading
I did allow pictures in my own basement though, where we weighed and loaded all 220 samples. This was my first time using a high thought-put kit where the extraction process takes place in a series of 96 well plates (top right). It was tricky to avoid cross contamination between wells so we used a transparent sheet with a small hole cut out. This is probably the single most time consuming step of the process. Everything else is done 8 wells at a time with a multichannel pipette.
Physical Vermicompost Properties
Moisture, pH, and conductivity mad sense to talk about together and of the results showed some of the biggest differences between vermicomposts. I am no compost expert so please chime in if anything jumps out of you.
Overall, I am really pleased with the small error bars (1 standard deviation). It generally means everything went well in terms of sampling and testing. As a producer, I would feel confident only having single test done and getting accurate results. Moisture values look pretty consistent while conductivity and pH have a higher range of values. Some of the higher conductivity might be worrisome, but from what I've seen all the values look pretty normal. I still need to input data from the questionnaires to start making sense why some of these values are higher or lower.
Nutrients and Metals
I selected the most interesting nutrient and metal profiles. I imagine most of these values are pretty standard for vermicompost. I did not include the nitrogen species because there was not much nitrogen of any type in any of the samples. I also neglected showing a bunch of the heavy metals for the same reason although there were a few outliers.
Organic carbon ranges seem low to me, but remember to double the value to get % organic matter. On average, samples have about 10% organic carbon or 20% organic matter. I would have guessed higher.
Phosphorous and potash track well together, which makes sense since potash is likely to be the main source of phosphorous.
I'll let you look through the rest of the metals but I'm glad to see some variation between producers. The variation is good because if everyone's vermicompost was about the same the it wouldn't be very helpful in determining what affects the microbial communities. Based on this initial data I would hypothesize that that the microbial communities will be quite different based on taxonomic identification (who is there).
Ultimately, we will mesh this data, the questionnaire data, and sequencing data to try and understand which factors seems to play the largest role in shaping the microbial community. Everything will be reprocessed and polished, but I wanted to give you all a first look. I am hopeful to still generate the sequencing data by the end of the year, but there are still a few variable at play.
Again, if you spot something unusual please let me know! I am no expert in with this type of data. I would like to find any potential issues before we get too far into it! Also, if you are a vermicompost producer who would like their Midwest Lab results now; I am happy to send it to you. Please just shoot me an email! Everyone will eventually get individual results of all data once the analysis is complete.