I first met Troy when he presented at the 2019 NC State vermicomposting conference. He has been involved with composting and organic farming since 2011 starting at the Rodale Institute where he was compost research specialist. Troy an expert microscopist, owner of the Living Roots Compost Tea , and who I consider to be the world's leading vermitea and extract brewer.
In 2022, Troy and I were again both slated to present at the NC State Vermicompost Conference. Unfortunately, I got scheduled for the afternoon on the last day of the conference which would have caused me to miss my flight back home. Troy stepped up and offered to switch presenting time with me. In return, I offered to do some sequencing of his vermicompost, teas, and extract. I might have also been looking to test a new sequencing protocol for liquid samples and get a look at extracts... so who better to ask than Troy.
So, let's take a look at Troy's microbial communities of vermicompost, tea, and extract. I think you'll see that the data backs up his reputation and experience.
Let's start by looking at Troy's vermicompost. He makes his vermicompost primarily with woodchips, food waste, horse manure, and spent mushroom blocks.
In the green blocks I have outlined 3 key groups of plant growth promoting bacteria - Rhizobiales (11%), Bacilli (22%), and Actinobacteria-Order (15%). There is significant evidence that nearly every organism I have found in these groups from vermicompost samples contain plant growth promoting organisms. I'll go over these groups in more detail in the next blog post. Flavobacterium and Pseudomonas are also underlined in green as they are also potent plant growth promoters. Just looking at these key groups of organisms, Troy's vermicompost bacterial community is composed of over 50% beneficial organisms. While these groups of organisms appear in other vermicomposts, I have not seen them in such abundance. This is likely the best vermicompost sample I have seen and my current "gold standard" of what vermicompost can be.
Another indicator of good vermicompost is the low level of anaerobic (oxygen intolerant) organisms such as Clostridia (1%) and Anaerolinea (0.01%). Additionally, if we look at the diversity of his vermicompost it has a Shannon index of 6.3 while most other vermicompost is between 4-5. We'll look at the diversity of all Troy's samples at the end.
Next up is Troy's vermitea brewed from this same vermicompost. He makes his tea by aerating vermicompost with humic acid, and fish hydrosolate. I recently looked at another vemitea sample in this post which you might find to be interesting to compare to this sample. In short, Troy's sample is much less diverse but this isn't necessarily a bad thing.
The community is dominated by Acinetobacter (82%) with a little Pseudomonas (7%) and Massilia (5%). The Acinetobacter genus very likely a great plant growth promoting organisms with nearly all the plant growth promoting abilities including phytohormone production (auxins/gibberellins), can solubilize phosphorus, iron, and zinc, and can suppress some diseases (reference). Pseudomonas organisms have been highly studied for plant growth promoting properties and contains similar benefits to Acinetobacter. We have seen these organisms in other teas but not nearly enriched to this level. What's also great to see in this tea sample is the lack of potential human pathogens (Enterobacteriaceae) which we saw in the previous tea sample.
Vermi-extract is simply made by bubbling vermicompost in water without any additional nutrients. I had never sequenced a sample like this before, so we were excited to see what it looked like. The idea behind extract is that you pull out the microbial community from the vermicompost and put it in liquid form. Our hypothesis was that the extract microbial community would mirror the vermicompost microbial community (although I was pretty skeptical).
As Troy predicted, the microbial community of his extract was almost the same as his vermicompost. The three key groups of organisms we saw in vermicompost were all slightly less abundant with Bacilli showing the largest decrease from 22% to 13%. What's also interesting is we can see a spike in the abundance of Acinetobacter from basically nothing (0.03%) in vermicompost to 11% in the extract. Clearly, Acinetobacter has some kind of advantage in aerated liquid.
Diversity and Quantity of Organisms
We can look at the diversity of each of these sample types using the Shannon diversity index.
Without worrying too much about what the y axis numbers mean (higher means more diversity) we can see that the vermicompost has the highest diversity at ~6.3 while the extract only drops in diversity slightly to 6.0. Meanwhile, the vermitea is close to the lowest possible Shannon diversity of 1. I wanted to show this just to demonstrate that much of the diversity of vermicompost is not lost when making extract.
Finally, the last aspect to consider is how many total organisms are in each sample type. Sequencing typically only gives you relative abundance, but Aggrego Data is currently working on a sequencing method to quantify the number of organisms in each sample. For now we can look at the amount of DNA extracted from each sample for a rough estimate. The final concentration of DNA from ~100mg vermicompost was 57.6 ug/nl. From 500 ml (or 500mg) of tea and extract the final concentration was 9.1 ug/nl and 2.2 ug/nl. I'm not sure it makes sense to compare vermicompost to tea and extract because it's solid and the other are liquid. However, we can see that the tea has about 4 times more DNA than the extract which roughly correlates to 4 times more organisms. This is expected because the nutrients added to the tea allow the organisms to grow while it's brewing.
That's all I have for now. If you are interested in piloting quantitative bacterial sequencing for vermicompost, tea, or extract at a discount please contact me at email@example.com for more information.
As always, please feel free to comment below with any questions!