DNA Sequencing for Vermicompost: 23 and Me for Worm Poop

A growing body of field tests demonstrates vermicompost’s effect on plant growth, yield, and pest and pathogen suppression.

What those field tests can’t do quite as well is say exactly why vermicompost can produce such positive results in comparison to other composts.

The work started by Dr. Zack Jones of The Vermi-Microbiome Project can go a long way towards giving vermicompost producers *and* users answers to these questions.

I met Zack in 2019 at the NC State Vermiculture Conference in Raleigh, NC where he gave a talk on a small upcoming project to sequence the DNA present in vermicompost.

Zack is a different dude: young, incredibly smart, and oddly curious about the DNA of soil, specifically worm castings. (Check out Zack’s Google Scholar CV here.)

As you read this article, there may be thinking the same thing I did when I heard Zack present on this topic:

  • What on earth would motivate someone to do a study like this?
  • What could even be learned?
  • What application could this have on the end use of vermicompost?

The topic can be a little difficult to wrap your head around. But it becomes easier to understand when you consider that…..

  • soil is an ecosystem
  • ecosystems have life
  • protein is the building block of life
  • all naturally-occurring proteins are made from unique instructions stored in DNA

What Zack is trying to answer is “what can we learn about our vermicomposts from its DNA?”

Well I can tell you that if he is only sequencing the DNA from one sample, the answer is: Not much.

But 100 samples? OK.

1000 samples? Better.

10,000 samples? Now we’re cooking with gas.

As of now, Zack doesn’t have 10,000 samples. But if his grant to extend this intriguing research gets approved, he’ll need them.

And that’s where you come in! More on that in the end, but for now, enjoy this Q&A with Dr. Zack Jones!

UWC: Can you give us a Reader’s Digest version of your study and what you hoped to learn from it?

The Vermi-Microbiome Project set out to bring DNA sequencing and microbial ecology to vermicomposters. It is a research and education project that started at the 2019 NC State Vermiculture Conference, and funded by WSARE which stands for Western Sustainable Agriculture, Research, & Education.

Unlike most soil amendments, the value in vermicompost is thought to be mostly in the living microbial communities within the compost. Because compost is so biologically diverse and always changing, most thought that trying to apply DNA sequencing would be too complicated or provide no benefit. Basically there would be too much noise in the data. With this project, we mainly just wanted to see if we could work with vermicompost producers to see if we could make it useful and valuable through a community science-based approach.

We didn’t just collect DNA samples.

We also had every sample sent for a traditional compost analysis. Each participant also filled out a questionnaire so we could try to understand how different feedstocks or vermicomposting method might affect the microbial communities. We need all this extra information to use as filters to help interpret the DNA sequencing data because the microbial communities are so complicated.

Ultimately we wanted to see if we could use the information and data we collected to allow vermicompost producers to make better management decisions or market their product in new ways.

UWC: How many samples did you collect? And do you feel like it was enough to learn what you needed to?

We ended up collecting about 225 samples from 25 different vermicompost producers in the US and Canada. About half of those samples were vermicompost samples with the rest being vermi-teas, compost, manures, and a few soils. I think we collected enough samples to learn a few things, highlight future research needs and most importantly demonstrate that this technology can be useful. We did lose data for some samples along the way so we might fall short of some goals. We could always use more samples, but I was overwhelmed with the number of participants and support for the project.

UWC: What were some of the difficulties in pulling it off?

It felt like this project was filled with hurdles from the moment it started. I found out the project was funded the same week my first child was born which also coincided with the first wave of COVID in March 2020. While the kid was expected, COVID took away planned laboratory access for the whole duration of the study. I wasn’t able to do some preliminary tests before collecting samples so we had to just go for it. This led to some downstream issues with shipping and DNA extraction.

Overall, we had to get creative to get the samples ready for sequencing since the universities were closed. On top of it all, the sequencing instrument we were going to use broke so we had to find an alternative for that as well.

We ultimately pulled it off, but it cost me a few gray hairs!

UWC: Once you got the results back, what about them surprised you? Did you learn something that you just hadn’t anticipated?

We are still in the middle of exploring the all of the data, but we’ve already had some nice surprises. The initial analysis demonstrated how different vermicompost can be. For example, the pH range of our vermicompost samples was 4.7- to 8.1. The feedstocks of the vermicompost were more diverse than I imagined too. About half of the producers used at least 20% manure while half used little or no manure at all so we had a really broad range of different food for the worms.

By far, our most exciting finding has been from a core microbiome analysis to see which bacteria were the most common among all the vermicompost samples. We found that a small group of organisms were found in almost every vermicompost sample. The most common organisms found at the highest abundance is from the genus Chryseolinea. Species from this genus have been isolated and demonstrated to be plant growth promoters. A species has even been patented in Korea for promoting cabbage growth. A recent study with tomatoes showed them to be the defining organism of the root microbiome of plants treated with vermicompost. In this study, vermicompost-amended tomatoes performed just as well as synthetically fertilized tomatoes, hinting that this genus of organism could in part be responsible.

Another study showed they could be responsible for plant disease suppression.

To find this much information on the number #1 most common organism in vermicompost was really surprising. In contrast, the second most common organisms found were from the Pir_4 lineage of which we know almost nothing about. This problem is pretty common as most bacteria and fungus haven’t been well studied, but it doesn’t mean these organisms aren’t important.

The genus Devoisa was also the 5th most common found and has members known to be plant growth promoters.

Overall, I think we are already starting to help explain why vermicompost, no matter how it’s made, tends to be really beneficial to plants. I also have to give a lot of credit to Dr. Gary Vanzin, who is doing this analysis. He can do some really next-level stuff to find the signal in the noise.

UWC: Do you know if Chryseolinea is as common in other composts or soil amendments?

I’m not really sure.

This is still a pretty new finding, so I am still trying to dig into the literature. But they have been found in other compost. A recent study in 2021 that looked at composting distilled grain identified them as an indicator for compost maturity. In our study, we also found them in manure samples so they aren’t unique to vermicompost.

But vermicomposting does select for them.

UWC: Obviously, vermicompost doesn’t follow a set lineage like you might have with 23 and Me or Ancestry.com’s data. But there had to be some similarities along the way that might tell you, for instance, “Oh yeah, this looks like food waste vermicompost.”

Right, it’s a little different than the human genetic tests but the basic methodology is similar.

Instead of using the human genome, we are sequencing a gene in every type of organism to identify who makes up the microbial community. We might not know what they are doing, but this community can be a type of “fingerprint” that can potentially be used to identify other things about the sample, like whether it was made with food waste. I could also reverse this analysis and try to select for certain organisms with different compost inputs or composting methods. This is kind of the “holy grail” of microbiome analysis and to be honest I don’t think we will quite be there with this study alone.

We are still working on seeing if we can understand what the most important factors affecting vermicompost microbial communities are, but there are just so many variables.

We really need a lot of samples to work towards this approach but I think it’s possible.

UWC: You’ve analyzed more than vermicompost. What did you learn about vermicompost in comparison to regular compost, animal manures, and bokashi?

I first got into vermicomposting in about 2014 when I met an urban vermicomposter & bokashi producer in Denver. I slipped a few of his bokashi, vermicompost, and manure samples for sequencing with my other samples for grad school. I was really blown away by the lack of biological diversity in bokashi.

At the time, it was thought to be some amazing mixture of synergistic microorganisms, but it’s really just lactobacillus, your standard yogurt making organism.

On the other hand, the vermicompost sample was the most diverse sample I had ever seen. I felt like there was so much more work to do that was frankly more exciting than my grad work and what led to the start of this project.

For this study I was hoping to provide some context to vermicompost and compare it to other samples like soil, compost, try and track how diversity changes over the whole manure-to-vermicomposting process. If I tell you vermicompost has a diversity index of 5 that’s pretty meaningless. But if sand has a diversity index of 1, poor soil 2, soil 3, healthy soil 4, and vermicompost 5 it starts making more sense.

We actually found a pretty broad range of biological diversity between all the vermicomposts. I would say most were relatively high with a few that were surprising low. Overall I would say biological diversity increased from manure to precomposted manure to vermicompost but not as much as I expected.

We are still looking into what factors might affect overall diversity.

I should have some more information on that soon.

UWC: You’re really interested in the regenerative agriculture space. How would your research apply to that?

Yes, I think regenerative agriculture is right now the only space I can see myself working in.  There is such a great community with people sharing information and encouraging one another. I also see a lot of people with a lot of good ideas trying to solve problems in this area. I saw this when I attended the NC State Vermicompost conference in 2019, as well as the 2021 NCAT Soil Health and Innovations Conference

I was blown away at the high level of questions people were asking about diversity, fungal to bacterial ratios, and plant growth hormones. I felt like I could help answer so many of the questions people were asking because so much of it was related to microbiology. Really the whole concept of regenerative agriculture and soil health is based on the fact that the soil is alive and feeding the plants.

As I’ve realized with this grant, the only way to continue to try and continue to answer these questions is to start my own company and lab space.

UWC: Can you tell me more about the business?

There are a lot of people with great ideas and questions regarding microbial communities that could be answered with DNA-based microbiome analysis. I could already think of a ton of different experiments we could do with just charged biochar.

The problem is there is no easy accessible or affordable way for people to use this technology to explore their ideas, or demonstrate the value of a product such as vermicompost. This business would be a solution to those problems with the goal of providing access to DNA sequencing and a microbiome report to summarize the results.

Eventually, I’d like to take it a step further to an interactive microbiome tracking and exploration tool. I’ve recently submitted a small business grant to try and get started, but I won’t know if it’s funded for about another 6 months.

I mainly just want to continue doing education and outreach within different agricultural communities and this company would provide the resources to do that. I’m currently looking for more vermicompost producers to participate in a similar Vermi-Microbiome Project 2.0 study. I hope the Urban Worm Company and your readers can help with that!

Why DNA Sequencing of Vermicompost Matters

You still may be wondering…..why?

But I think I know why this matters.

Field tests can tell us, for example, that vermicompost from food waste will behave differently than manure-based vermicomposts. We may even know that specific food waste vermicomposts – ie berries vs grains – can give us certain different results.

But we’re still learning why.

If proteins are the building blocks of life, then Zack’s research can give us the building blocks of understanding exactly why certain acids or proteins are more prevalent in certain vermicomposts.

If you read the answers above, then one nugget may have jumped out at you; Zack’s identification of the plant growth-promoting bacteria Chryseolinea, which is present in most vermicomposts.

A finding like this suggests the following is possible:

If we can drill down on exactly which microbes are responsible for certain benefits in the soil, and we can associate those microbes with certain inputs or conditions in the vermicomposting process, then we can design vermicomposting operations to optimize for those microbes.

For example (and I’m totally making this up), if we learn that horse manure-based vermicomposts in colder climates produce a higher concentration of bacteria that helps plants fight off root-killing parasites like Pythium, we can intentionally create designer vermicomposts with Pythium-suppressing characteristics.

This could have huge implications for harnessing nature, reducing dependence on chemicals, and adding even more environmental benefit to vermicomposting.

Would You Like 23 and Me for Your Worm Poop?

Zack and I are collecting a list of folks who would like to have their worm castings sampled for the Vermi-Microbiome Project 2.0 study . We need both home vermicomposters *and* businesses.

So as long as you’re producing castings, then we want to hear from you.

Zack’s grant for the Vermi-Microbiome Project 2.0 is far more likely to be awarded if we can show the good folks at WSARE that we have a stable of enthusiastic participants ready and willing to send him vermicompost.

2022 Update: Sadly, Zack did not win the award for the WSARE grant, but we’re going to keep trying to push the science forward!

15 thoughts on “DNA Sequencing for Vermicompost: 23 and Me for Worm Poop

  1. Super excited to have a real way to quantify quality vermicompost and hopefully get the junky stuff off the market. As a producer I am always thinking about what is going in and coming out of the bins and looking at things with a microscope only takes you so far. This is amazing work that can help us heal our planet. Thank you.

    1. Thank you for the kind words Ryan. I’m excited people are interested in the work. As Steve said, this kind of science works best with as many vermicomposters as possible. Hopefully we can get this grant funded and get the chance to work with you.

  2. This study is fascinating both from the practical side of being a vermicomposter but as a molecular geneticist as well. One of my interests professionally includes bioinformatics and microbiome therapeutics. One of the big questions involves the analysis of the sequence data. With the large number of analysis tools out there, the task of species identification is difficult. I am very excited to contribute my samples for this and would welcome any opportunity to be part of this in any other way that’s possible. Please let me know me !!!!!

    1. Hi Michael,

      Thank you for your interest in the study, I continue to find it all very fascinating as well. I recently attended a conference and heard Maria Gloria Dominguez-Bello speak about the human microbiome and highly recommend looking at her work.
      For the sequencing and species identification question: It mostly depends on the sequencing technology used. Short read sequencing, Illumina, is very accurate (99.9%), but it can’t sequencing the whole gene. Because of this limitation can only confidently predict identification down to the genus level. Long read sequencing, such as the MinION, can sequence the whole gene, but has only 90% accuracy. Happy to discuss it more, and hopefully we can get this study going.

  3. Hi Steve,
    Interesting study! We too have been working with one of only 5 labs in the world specialising in soil microbes DNA analysis.
    Amazing what can be gleaned from these studies.
    I think Zac is on the right path in wanting to start his own DNA lab. I can see a huge demand in the future.
    Are you taking samples from overseas, or is cost and time too limiting?
    George

    1. Thanks George! I’ll ask Zack about samples from Australia. I’m sure it would be more costly, but I think it’s worth giving it a shot. I’ll ask Zack about transit time required.
      Even if the time required disqualifies from your sample being used in the study, I think it would be cool to have it analyzed anyways for us to send it to you.

    2. Hi George,

      Thank you for the encouragement. In this past study we actually managed to get samples from Canada. I did a brief post doc in Sydney so I understand getting things into an out of Australia is a different beast. Please feel free to sign up; if you can get us the samples then we will process them. I plan on using a DNA preservative so shipping shouldn’t be time sensitive.
      Cheers,
      Zack

  4. I’ve been personal scale vermicomposting with a variety of feedstocks, both indoor and outdoors for close to two decades. I hope that I can help the science behind the product I’ve been promoting to anyone who will listen. My hope is that my anecdotal results can be bolstered with science that I can not replicate at home.

    1. Hi Ian,
      Great to have you on board! It sounds like there is a lot we can learn from your experience and variety of vermicomposts. You guys inform the science just as much, if not more, than the sequencing. We just try and turn a bunch of anecdotal evidence into something a little more scientific.

  5. Thanks Steve for always providing such great content and thank you Zack for your research and data. I’ve enjoyed reading your analysis on core microbiome, different factors affecting the microbial community, and other info on the Vermi-Microbiome Project. Keep up the good work and count me in, if possible, for the next round of testing

    1. Hi Matthew,

      Thank you for following along with the project blog… I’m still a bit of novice when it comes to scientific communication compared to Steve. Glad to have you in for the next round!

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