Lactic Acid Bacteria (LAB) are those found in fermented foods like yogurt, sauerkraut, kimchi, and sourdough bread. These organisms are also the drivers of the Bokashi composting system and found in the EM1 liquid biological amendment as I mentioned in the last blog post.
In my mind, Bokashi and EM1 have been a somewhat controversial subject as their promoters were making bold claims about the microbial community without much evidence. I first ran into EM1 and Bokashi around 2014 when I also got into vermicomposting. I was given a Bokashi composting kit (bucket, mesh bag, and bokashi grains) by the urban worm farmer who gave me my first vermicomposting worms. He was experimenting with Bokashi composting as pre-composting step to vermicomposting (I don't recommend this).
This is a long, multipart post; Part 1 going over old bokashi sequencing data and Part 2 actually getting into lactic acid bacteria and their use cases in composting and agriculture.
Part 1: Bokashi and DNA Sequencing Data from 2014
I offered to sequence some of his bokashi composts, a few of this inoculants, teas, and vermicompost. Below is a quick overview bar chart of the samples I normally present in person. Each color in the bar chart above represents a different genus and there is no legend because there are simply just too many organisms to try to display with colors.
The main point I make with this graph is that Bokashi is simply much less diverse than especially vermicompost and most of the organisms are lactobacillus or closely related. This was actually the first vermicompost sample I sequenced and the diversity really caught my attention.
Sample Overview
I've recently asked Chris, (Aggrego Data's other half) to reprocess this data with our workflow and he also generated some custom figures like heatmaps below.
Sample Types
This graphic has the samples grouped by type along the bottom axis. The "Bokashi" samples were mostly puréed fruit with bokashi inoculant added. The "Bokashi Grain" were the EM1 or knock off bokashi inoculant grains products. The "teas" I believe were some type of bokashi liquid ferments and the "Z-bokashi" at the end was my own bokashi with kitchen scraps.
Most abundant organisms in Bokashi
The Y axis has top 20 most abundant orders of organisms in all of the samples combined. You can see at the top that Lactobacillales dominates all of the bokashi related samples. The second and fourth most abundant organisms "Rickettsiales" and "Cyanobacteria; Chloroplast" could arguably be ignored. These are actually remnants of bacteria that were incorporated into multicellular organisms, called endosymbionts. Rickettsiales evolved into mitochondria (the powerhouse of all cells in multicellular organisms) and a Cyanobacteria became a chloroplast, the organelle performs photosynthesis in plants. You'll notice these are especially elevated in the "bokashi grains". We'll look at these more closely but it's likely related to the carrier material for the inoculant organisms.
Elevated Pathogens(?) - Enterobacterales
The last thing I want to point out is the abundance of Enterobacterales which is the order than contains most of the human pathogens we are worried about. This number is quite high in nearly all of the bokashi samples, ranging from 4% and toping out at 12% in the tea. We'll take a closer look at this in some of the individual samples.
Individual Bokashi Grain Inoculants
Let's zoom in a bit to a few individual samples starting with EM1 and the other bokashi oat grain inoculants. You can scroll through all the samples below:
EM1 Bacterial Community
The first thing you'll probably notice is that EM1 is dominated by chloroplast and mitochondria sequences even more so than the bran inoculants. I'm not sure why this is because the makers of EM1 do not state what it's made with other than Lactobacillus casei and water. My guess is, it might be some kind of seaweed or algae powder which would have both of these organelles present. The amount of these cells seem to dramatically outnumber all other true bacterial cells including any lactobacillus. I have no idea if this solution was old or properly stored.
EM1 Lactic Acid Bacteria
Lactobacilliaceae is the family consisting of lactic acid bacteria (in red above) and only 2% of the total sequences. In the figure below we'll zoom in on that 2% and see it's actually comprised of 6 different genus of lactic acid bacteria.
Interestingly, none of these seem to be "regular" lactobacillus like the label claims. I don't think this really matters, but I don't know the specific differences between all these types of lactic acid bacteria.
Contaminant organisms?
We also see Halomonas (3%) and Shewanella 1(%) as other bacteria present. EM1 is usually purported to have photosynthesizing bacteria, yeast as well as lactic acid bacteria. The Halomonas and Shewanella are likely contaminants as they can both grow in salty environments which lactic acid bacteria can also tolerate. Neither of these are phototrophic organisms or other organisms stated to be in the solution as far as I can tell.
Comparison to Other Bokashi Grain Inoculants
Aside from the differences in abundance of mitochondrial and chloroplast sequences, the knock off grain inoculants seem quite similar. They are all a combination of Lactic acid bacteria and Gammaproteobacteria consisting of Enterobacteriales, Shewenella, and Halomonas.
Bokashi Compost Bacterial Microbiomes
Below are some of the bacterial communities of the actual Bokashi compost. Aside from my own bokashi compost, these samples were taken from 55 gallon drums primarily filled with different fruit wastes with bokashi grain inoculant added.
Lactic Acid Bacteria Dominant
The red in all of the these bokashi composts are the lactic acid bacteria. You'll see the "water melon and strawberry" sample is actually 100% of a single genus of lactic acid bacteria. Because many of these are fruit based and have a high sugar content, it makes sense that lactic acid bacteria are dominating the population.
Each sample tends to have a fair amount of Enterobacterales. These organisms are usually fecal coliforms which can cause you to fail pathogen testing. I'll talk about pathogens and pathogen testing in another post, but I doubt think these organisms are truly pathogenic or something to be worried about.
Fermented Hops and Zack's Bokashi
If you look at the fermented hops, you can see some Acetobacter which turn alcohols into acetic acid. There is probably some residual alcohol in there and a bunch of yeast we aren't seeing. If you scroll over to "Zack Bokashi" this is my own bokashi composted of pretty diverse kitchen scraps if I remember correctly. This sample is also the most diverse microbial community and enriched with Bacteroidia (in green), specifically Flavobacteria (12%) and Sphingobacterium (12%). Species many from these genera have been shown to have plant growth promoting properties and are commonly found associated with plant roots. I am unsure why my bokashi has these organisms -- perhaps the more protein rich meats and cheeses selected for them or there wasn't enough carbohydrates to fully acidify the compost.
Part 2: Lactic Acid Bacteria Traits and Use Cases
Metabolism and Traits
Lactic Acid Bacteria get their name because they consume (ferment) carbohydrates (sugars like glucose, lactose, and sucrose etc.) and produce lactic acid and other organic acids. Humans also carry out the same metabolism when low on oxygen and we go "anaerobic" when working out. Remember muscle soreness is caused by lactic acid build up when there is not enough oxygen around to make energy (ATP). As shown in the overly complicated diagram below this is how sugar is broken down to generate energy with the end point being lactic acid or lactate.
These acids can dramatically lower the pH to 3-4 if enough sugars are available creating a very selective environment for growth. Lactic acid bacteria also produce a variety of antifungal and antibacterial compounds (more on this below) making it even more challenging for other types of organisms to grow. Additionality, they are salt tolerant which is why adding salt to your fermented foods like sauerkraut selects for them initially before fermentation starts. Very few other organisms can grow (like pathogens) in such a harsh environment which is why they are great at preserving food. Most lactic acid bacteria are non-spore forming but there are some bacillus species which can produce lactic acid and form spores.
Are they plant growth promoting?
Yes, based on the definition of plant growth promoting as having the ability to produce phytohormones, solubilize nutrients, reduce plant stress, and biocontrol (disease suppression) there is some evidence (limited in some cases) for all of these traits. Thankfully, there are quite a few review papers published on this exact topic, but I like Jaffar et at., 2023 and the one pictured below Lamont et. al., 2017. I'll quickly summarize them below, but they are worth a read if the topic interests you.
LAB Plant Habitat
Lactic acid bacteria can live on plant leaves and inside the roots and stems as endophytes. They tend to survive the best in high organic content soil and generally aren't found in high abundance in roots and the rhizosphere. One paper suggests that certain plants such as mulberry trees might have a special relationship with lactic acid bacteria as they are found in mulberry tree roots in geographically different locations. Overall, due to their strict diet of carbohydrates they aren't abundantly found in soils. These papers also highlight that most bokashi composts result in a lactic acid bacteria dominant community as my data agreed with.
Nutrient Solubilization
LABs can solubilize nutrients such as phosphorous and calcium through organic acid production. This benefit is primarily driven by their primarily fermentive metabolism resulting in organic acid production.
Some isolated species have also shown the ability to fix nitrogen and produce siderophores to solubilize iron, but I don't think these abilities are broadly distributed within lactic acid bacteria. Composts inoculated with EM1 showed greater nutrient uptake when applied to various crops, but it is attributed to an of a increase speed in organic waste degradation not directly due to the presences of LAB.
Plant Biostimulant Traits
Some lab strains have been shown to produce the plant growth hormone indole acetic acid (aka auxin or IAA) and gibberellin. I don't think this is where these organisms generally excel, but if you look at the review paper you'll see examples of previous studies showing evidence for plant growth stimulation.
Biocontrol Properties
Disease prevention or delayed onset is where, in my opinion, LAB have the potential to shine. Taken directly from the review paper, Lamont, et. al., 2017: "There are three known mechanisms by which LAB acts as a biocontrol agent; through the production of antimicrobial compounds, reactive oxygen species, and bacteriocins; by excluding pathogens by pre-emptively colonizing plant tissues vulnerable to infection and by altering the plant immune response."
Use Cases
Bokashi Composting
Bokashi composting is the addition of lactic acid bacteria with a grain inoculum usually which ferments your food. I think it works better with high carbohydrate foods like bread and fruits. After a few months of acidification, the predigested food scraps are usually buried in dirt to finish the process. Personally, I would rather save my fruits and veggies for my worms. However, I am thinking about starting a bokashi compost bucket for breads and sweets since we don't feed those to our worms and they usually go down the sink.
Soil amendment
As I just mentioned, burying mature bokashi compost is the most common way to add bokashi in your garden or farm. In my mind, this is going to add some nutrients to the soil and attract a lot of native worms and other macro and microorganisms which will rapidly consume the predigested food scraps. Maybe in the end it mostly turns into worm castings anyways? You would also be adding a fair amount of acidity into the soil which depending on your soil conditions might be a good thing. These acids can help solubilize minerals unlocking, phosphorus, calcium, potassium, and other trace elements from the soil especially in mineral rich and carbon poor soils.
In most soils, I wouldn't expect the lactic acid bacteria or any yeast to really survive with the exception of high organic soils or artificial soils like coco coir. However, I would expect their addition and all of the organic acids, exopolysaccharides (EPS), and other metabolites to boost the native soil community. As a soil amendment, I don't think the benefit is really dependent on the survival of the lactic acid bacteria which is usually the biggest criticism of biological amendments.
Interestingly, when I was discussing this with my wife (born in Lithuania), she said her grandma and aunts would ferment old breads in a bucket and add it to their cucumbers and other garden plants. It seems at least in some parts of the world, fermentation as a soil amendment was cool before it was branded and bottled.
Case Study - Terra Flora Soil Works
I wanted to highlight Andrew Couzen's Instagram account Terra Flora Soil Works. Andrew operates a small farm and uses both bokashi and vermicompost as soil amendments. In the video below you can see he uses bokashi to top dress tomato plants after transplanting with vermicompost. As we'll discuss below he also uses lactic acid bacteria to suppress and delay powdery mildew onset.
Foliar Powdery Mildew Suppressant
LAB has been repeatedly shown as an effective means of biocontrol of powdery mildew and other foliar pathogens. Other compost teas have also shown these effects as well, but it is thought that acid production from LAB especially, prevents fungi from growing. It's also been demonstrated that spaying leaves with milk or whey has a similar effectiveness in preventing powdery mildew likely because native lactic acid bacteria colonize it and acidify the leaves.
I think that's about all I have to say about EM1 and lactic acid bacteria. There are definitely some great use cases for them as a soil conditioner and biocontrol agents. If you have any questions or additional insights about these topics please comment below!
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