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Writer's picturezackljones

First Look at a Vermi-Leachate Bacterial Community

One of the most common questions I get asked is about vermicompost leachate -- is it good or bad? Let's walk through one sample I took this summer from a worm tower I was babysitting for my neighbor while she was out of town for the winter (yes this is my life).


Bottom of worm tower where leachate sample was collected from.

What is Leachate?

First what do I mean by "vermi-leachate"? I mean the brown juice that drips from the bottom of your vermicomposter when you don't manage your moisture well like me. In the case of the worm towers you usually get some worm casting that fall through and mix with the liquid.


The Sample

From this muck pictured above, I took a sub sample using what my wife told me was our nicest champagne glass. I tried to minimize the solids, but clearly you can see a lot of suspended particles. Once you get it in the light it's actually a silky brown with no off putting odors. I had kept the worm tower through the winter where it was kept at a minimum of 45 degrees (F) and the sample was taken in the spring before it got too hot.


Half a milliliter from this glass was sampled into a syringe and frozen until I could get around to getting to the lab and extracting the DNA.


Sub sample of leachate from worm tower base.

The Bacterial Community

Before I get into this I wanted to state that I didn't think a leachate community would have many potential beneficial organisms in it because it would be too anaerobic. Most, if not all beneficial organisms are aerobic, or can at least tolerate some oxygen. However, I think you'll see I was quite wrong about this. This leachate community certainly isn't filled with as many aerobes as vermicompost is, but I would describe it as a low oxygen or microaerobic environment, and certainly not anaerobic.



Left: Leachate Bacterial Community Right: Troy Hinke's vermicompost with highlights


Diversity

Before we get into specific organisms lets look at diversity. This leachate community is less diverse than vermicompost but still more diverse than vermitea. In terms of the Shannon diversity index this community is 3.9. Most vermicompost is 5-7 and vermitea usually is less than 2. I think it's fair to say it's moderately diverse. You can refer back to Troy Hinke's vermicompost/tea/extract communities for a rough visual comparison.


Beneficial Organisms

Overall, I have seen some these organisms in vermicompost but they are present in a low abundance or not detected in all samples. Additionally, many of them are poorly understood. You may notice names on the outer circle of the graphic which are supposed to be genus level identification, end in "Family" or "Class." This means no closely related organisms has been cultured or well described and difficult to interpret.


The Saccharimonadales Order -(13%) - Phosphate Solubilization

Let's start with the most cryptic and abundant organisms, the Saccharimonadales. These organisms are thought to only live in a symbiotic or parasitic lifecycle making them hard to study. You'll see these organisms under the Patescibacteria Phylum in light green at the 1 o'clock in the krona graph above. These organisms are 13% of the leachate bacterial community. They are present in some vermicompost at low levels but were undetected in Troy's vermicompost.


You'll find Saccharimonadales at water treatment plants in activated sludge. They are known sugar fermenting and phosphate accumulating organisms. You'll also find them in soils where they have been associated with phosphate solubilization. This association has best been documented in a field trial with corn. They were so confident in this finding they put it in the title of the paper.




This paper is really interesting because they add processed sugars (fructose, sucrose, and glucose) to the soil to stimulate phosphatase activity which is linked to the increase in these organisms. They admit this probably isn't the best way to stimulate phosphate solubilization. Perhaps a more diverse mix of dissolved organic acids/sugars would?


My guess is, this leachate would stimulate phosphate solubilization because of the huge abundance of these organisms, but also because of the type of carbon in the leachate should support native phosphate solubilizing organisms at the very least. This review paper says that sugars are the most important food source for microorganisms in the soil.


Side Note on Carbon

I feel like the type or quality of carbon in vermicompost is very important to it's effectiveness and has not been well studied. The dissolved carbon like that in leachate and extracts are more bioavailable than the undissolved fraction, making it a more immediate bio-stimulant than other organic amendments. This in my opinion in why fermented compost like bokashi can be a good soil amendment, this compost has been acidified and predigested making it a readily available food source.


Bacillus Genus- 12% Nutrient Cyclers, Phytohormone Producers

Bacillus is light green, the phylum Bacilli. I've talked a lot about these organisms before as they are one of the primary plant growth promoting found in vermicompost. They are all around great nutrient cyclers, phytohormone producers, and have some disease suppression properties . What's interesting is usually there is much more diversity of other types of Bacilli not just the Bacillus genus. The Leachate environment probably selected for less aerobic species that do better in a lower oxygen environment. Does this mean they are less effective plant growth promoters? I'm not sure, but hopefully, we can better start exploring these types of questions as soon as we expand our sequencing .


Chloroflexi Phylum (12%) - Relatively Unknown

Overall it's hard to interpret these organisms (they are the teal color in the krona). You notice that all of the organisms end in "class" or "family" and the names are a bunch of weird letters and numbers. This means they are candidate classes of organisms that haven't been cultured and are poorly understood. We do see them in vermicompost but usually only around 1% of the community.


JG30-KF-CM45 Family

I can say that JG30-KF-CM45 Family has been associated as a key indicator of tobacco growth under low chemical fertilization (Shen et al., 2023) and a few studies have seen it associated with the rhizosphere of plants such as tobacco.


KD4-96 Class

The KD4-96 Class is the other major group of organisms under Chloroflexi. I see a few papers calling them plant growth promoting organisms, but none of them have a citation to back that up. One paper has this Class of organisms correlated with increased maize yield after soaking the seeds in a Rhizobium solution.


Azoarcus Genus (4%) Nitrogen Fixers

This group of organisms is really interesting. All species of this genus are known nitrogen fixers, with some species being isolated from grasses and rice. I'll leave you with some quotes from some of the literature on them.


Electron scanning microscope image of Azoarcus rhizosphaerae (Lin et al., 2014) https://doi.org/10.1007/s10482-020-01401-w)

"In this strictly respiratory bacterium, transcription nifHDK gene and N2 fixation occur only under nitrogen-limiting and microaerobic conditions." (Patel et al, 2023)"


"Azoarcus spp. with its ability to colonize and fix nitrogen in graminaceous [grasses] crops offers exciting possibility in sustainable agriculture practices, as most of the staple food crops of the world belong to Gramineae family which cannot form nodules (Chauhan et al., 2015) .


It's still unclear if all species of this genus can be root associated, but these organisms seem to be rare and are of special interest as grasses cannot form root nodules like legumes to recruit nitrogen fixing bacteria. Crops like wheat and hay could be grown without or less synthetic nitrogen which could have a huge impact given the global scale of these crops.


Actinobacteriota - (25%) Anti Fungal

Now jump to the red part of the graph, Actinobacteriota. For vermicompost I usually look at the sub-class Actinobacteria which can be up to 25% of the community. In this leachate sample, Actinobacteria are only 4% and instead we have more novel less understood Classes of organisms such as Solirubrobacterales and Acidimicrobiia. I will focus on the organisms that are well identified.


Ilumatobacter - (4%) - Antifungal and Nitrogen Cycler Associated with Biochar

This organism has been seen to be enriched in bamboo roots with high disease resistance (Kachor et al. 2024) In a study done on soils with continuous cropping of tomato plants, Ilumatobacter was the number one indictor genus of fusarium inhibition. This fact is shown in the figure below, where the red bars indicate a significance difference in fusarium wilt inhibition. I should also say the paper concluded that "Vermicompost was the most effective organic fertilizer to suppress Fol [Fusarium] in long-term continuous tomato cropping soil."

Note on Fusarium Wilt
Our tomatoes getting hit hard with Fusarium Wilt this year.

Fusarium Wilt is a soil fungal disease which affects many different types of commercial crops and can cause up to 100% yield loss. It is considered a threat to global food security, causing 100's of millions of dollar in losses. It's also something we are dealing with in our tomato plants in our garden this year after growing tomatoes in the same plot 4 consecutive years.


Ilumatobacter Associated with BioChar Application

Ilumatobacter also seems to be associated with biochar or activated carbon application. This study on Pak Choi (or Bok Choi) they found a 3% biochar application was the most effective and stimulated the growth of Ilumatobacter. These organisms were specifically associated with Pak Choi health.


Maybe charging biochar with leachate might be an effective tool to fight soil borne diseases? Maybe the deep pore structure of biochar provides a more protected habitat for these types of organisms. (Shout to Nick Sorg At Back to Earth Vermicastings who first suggested this idea to me)


Solirubrobacter- (6%)-Keystone Species

This genus of organisms is globally ubiquitous in soils and rhizospheres of plants of all different types and considered a keystone species. These organisms contain broad genetic diversity allowing them to be adaptable making them attractive for soil amendments (Jara-Servin et al., 2024). Their direct role in plant growth promotion is questionable but some species have recently been found to produce phytohormones and solubilize phosphorus(Ajinde et al., 2024) .


Glycomyces - (4%) - Plant (especially wheat) associated

Scanning electron microscope image of Glycomyces phytohabitans (Xing et al, 2014) https://www.nature.com/articles/ja201440

Glycomyces is the last of the Actinobacteria we are going to talk about. This is another fairly "novel" genus of organism. These organisms are aerobic and, like most actinobacteria, are filamentous. Interestingly, most of the literature around them relates to new species being isolated from wheat roots, both from the rhizosphere and from the inside of the roots and stems meaning they can be endophytes or live inside of plants.

While many species seem tightly associated with plants I don't see any research on any specific plant growth promoting properties. A recent 2024 paper calls this genus plant growth promoting, but I can't find a specific reference to back this up. Definitely more research is need around these species and how they interact with plants/wheat.


Flavobacterium- (4%) - Primary Plant Growth Promoter

These organisms have been observed to have many plant growth promoting properties. Kolton et al. states they represent a significant fraction of root- and leaf-associated microbiomes in a broad range of plant species. 34/44 flavobacterium isolates were able to solubilize inorganic phosphorus and all isolates were able to produce the plant growth hormone auxin (Soltani et al. 2010). Wheat yields increased 15% compared to the control when one strain of Flavobacterium was applied (Rahmani et al. 2016). Overall great organisms to have in your vermicompost or liquid extract and could likely be useful in a foliar or soil application.


What's Not in Leachate?

It's also important to consider what's not in leachate. Notably, there is zero trace of anything "bad" like pathogens or anaerobic organisms.


Pathogens

First off and probably most importantly we are not seeing any sign at all of any potential pathogens. Most certifiers and regulators looks at "fecal coliforms" which fall under the Enterobacteriaceae Family. These organisms include E. Coli, Klebsiella, Enterobacter, and Citrobacter. We see nothing even remotely relate to these organisms. This is a little surprising for me because these organisms tend to prefer lower oxygen environments (like the human gut). We see some of the coliforms in vermi-teas sometimes but the leachate environment for some reason is not suitable.


Anaerobic Organisms

I see zero evidence of any strictly anaerobic organisms that are very oxygen sensitive. Examples of all the organisms I identified were either aerobic or micro-aerophilic.


Bottom Line

Based on this one sample, vermi-leachate seems like it would work best as a soil drench. Nearly every well identified organism has potential plant growth promoting function especially related to nutrient solubilization. Some of these organisms are seemingly rare but valuable. Vermicompost or this leachate seem useful in the fight against soil borne diseases such as Fusarium Wilt. Charging biochar might be beneficial to create a "home" for some of these organisms in the soil.


You might have noticed that "wheat" was mentioned a lot as many of these organisms have been isolated from this crop. Perhaps this community might have an outsized effect on grasses. Doing a seed soak with leachate or applying it at planting would be an interesting experiment.


I want to talk more in the future about carbon and more specifically dissolved organic carbon. It might be just as beneficial if not more so than the microbiology of the sample in some cases.


Remaining Questions

Are all leachate communities similar to this one? I think the type of community that forms is dependent on the compost it's coming from. This vermicomposter I would say was very mature with all levels containing near finished vermicompost. Would a thermophilic or less mature vermicompost have a different community or be more anaerobic, I think it's possible.


Can we replicate these communities just by leaving vermicompost in water without aerating but just having passive oxygen diffusion?


Does this community have a distinct use case vs tea or extract?


Hopefully we can start to explore some of these questions in the future.


Please comment or ask any questions below!

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3 Comments


Permaculture Gardens
Permaculture Gardens
Oct 18

Wow! This is amazing! I feel like I've learned so many new things in one blog post/analysis. I love that you found a paper saying vermicompost is anti-fusarium! I guess it's really a good thing that I decided to study compost tea from vermicompost instead of any other. Thank you so much for sharing!

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Dan Lonowski
Dan Lonowski
Oct 07

This is an eye-opener Zack! Our assumptions about leachate being predominantly anaerobic seem to be unfounded. Although it may not be ideal, it is apparently not so bad. The comparison to properly brewed, aerated vermicompost tea will be interesting to know more about.

And the champagne glass was a good choice!

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zackljones
zackljones
Oct 11
Replying to

Thanks Dan! The results were surprising to me too. Hopefully we get some more leachate samples soon to see how conserved this community is between different types of compost

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