A Journey Into Soil Microbes

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In January of 2022, we took the plunge and bought a microscope with a digital camera that connects to the computer. It was a purchase to have fun with and to allow our kids to explore the microscopic world around us that we don’t get to see with our naked eye.

It originally started when we received an inexpensive microscope kit through our kids school. We all wanted to be fascinated with what we were going to explore with it, but it really didn’t work out. There was more frustration with it than there was fun.

I later began reading about soil microbes that are in the garden, compost bins, and compost teas. I wanted to learn more about this hidden world around us. Compost teas were a new thing for me to work on, but the problem was that I wasn’t sure if I was truly making the tea correctly, safely and that were producing the number of microbes these compost teas supposedly make. There are all kinds of information out there in the digital world on how to make these teas. Some people say you must do this a particular way otherwise the tea becomes unsafe. Others disagree. It is a confusing world out there.

One of the Instagram people I kind of follow (I follow her, but I don’t necessarily watch many of her reels) got a microscope herself and was talking about the microbes she was finding in her compost or soils. I also watched a couple YouTube videos and joined a webinar by Dr. Elaine’s on the Soil Food Web where she shared her setup of the microscope and talked about the importance of the soil microbes. This was the start for me into finding more interest in the soil microbes, including soil nutrients, fungi, and bacteria.

The microscope we had from the school would be horrible with allowing us to learn and see these microscopic organisms and that is why we upgraded the microscope.

Some Soil Microbes I have Found

Soil microbiology is a pretty complicated and broad topic. There is no way I will ever learn all there is currently known about this microscopic world, let alone a very small percentage of what there is out there. For the little amount I have learned to date has really fascinated me and I want to share with you what we found.

Below is a list of some of the soil microbes I have found to date. These have either come from my vermicompost (worm bins) or worm tea that I have brewed. I have not explored the compost bins yet, but when I do, I have a feeling that I will find lots of fungi because we have had lots of mushrooms grow in the bins. I should have taken the opportunity then to take samples and view them under the microscope, but I didn’t. Next time!

There are a few here that I have not had confirmed yet. I put them under the category that my gut told me based on some online research. If I am incorrect on something, please let me know in the comments below.

Algae

Most of the soil samples I have taken to date have come from my worm composting bins. Worm bins typically have moisture, sometimes more than they should depending on how well you take care of the bin. With this moisture, you are bound to have algae build up over time. You may not visually see the algae, but looking at a sample under the microscope you will mostly likely find algae spores or other forms of algae.

Bacteria

People tend to get uneasy when they hear the word “bacteria” and rightfully so. Bacteria is most known for the bad things they do such as in illness and other negative things. What some people don’t realize is that bacteria is everywhere and not all bacteria are bad. Bacteria is one of the key microbes that help break down compost and is what gives off the heat in a compost pile.

Soil bacteria is divided up into a few different groups depending on their function in the soil. Some are decomposers, which help break down dead organic matter. They break down nutrients and recycle it back into the soil for use by the plants and other organisms. Others might help with nitrogen fixation and benefit the plant or other bacteria, preventing other bacteria from taking over. Then you have the not so good bacteria that are known to be pathogens. This is just a very tree top introduction.

I have not yet been able to figure out how to identify bacteria or to truly know that I am looking at when it comes to bacteria. There is so much out there. I have found things that caught my eye, here are a couple of them:

Possible Bacteria – I have not had this confirmed yet. I am looking at the oval/rod shaped pieces. Finding other images showing shapes similar to these during my searches lead me to believe that these are a form of bacteria. This came from a sample out of my worm composting bin.

According to one source I have, this could be Streptobacilli (the chain looking thing), which indicates that this sample has moderate oxygen conditions. In the image around that chain looking thing, there is also Diplobacilli, which are considered indicators of aerobic conditions. With this information, it could be noted that this sample could be starting to go anaerobic (not good since it would mean it is oxygen deprived). I find this interesting considering this sample came from pine tree mulch that was soaking in water for about 25 hours. I don’t recall if I had an air pump in that bucket to give it air (I lost those photos on my old phone).

Cellulose

Cellulose is a substance from plants and can come from fungi and bacteria in the soil. This is typically the main source of energy for microbial activity in a compost bin (other than bacteria) and may contribute to the added heat during the composting process. I have come across a few of these in different samples from the worm composting bins. They add character to the view with their twist and turns.

Ciliate

Now we are getting to the more fascinating creatures that live in the soils.

Ciliate come in various shapes, sizes and names. A ciliate mostly identified by the cilia (plural for cilium) that are somewhat visible depending on your microscope. Cilia are the hair like pieces coming out from the organism.

You can barely see the cilia on the outer edges of this ciliate. A better camera on the microscope would allow you to see them more clearly. They move fairly quickly like tentacles. You can see the other microorganisms inside that it ate. These too move around inside it.

This is a different type of ciliate. This particular image is a screen shot of a video I took while it was moving around. Again, you can see the cilia on the upper portion of its body. This one was fun to watch move around.

Fungi

Just like there are good and bad bacteria, there are also good and bad fungi. I have seen over and over again that to easily identify good fungi is to recognize it by a few characteristics:

It should be dark in color
The septa are approximate equal distance
It should be wider than 3μm (micrometers)

1μm = 0.000001 m

These are just a general rule of thumb. Of course, this isn’t always the case as some can be a plant pathogen but has similar characteristics to those that are beneficial.

Septa are the dark lines you see in the fungi shown in the image below. These septa separate the hypha into segments or compartments. Just like everything else, these septa serve a purpose in various types of fungi, but not all fungi have septa.

Here is a piece of fungi that clearly shows a nice dark color with pretty equal spacing of septa.

To give you an idea on the size of these fungi stands (Hyphae), the diameters are usually between 4 and 6μm and the human hair is on average between 70 and 100μm.

Fungi can have multicellular (having multiples cells) or unicellular (having singular cell). As a gardener, you may have heard of Mycorrhizal fungi. If not, go look at the ingredients on a bag of good soil and you may find it in there. Mycorrhizal fungi have branching hyphae, making them multicellular.

Nematodes

I don’t know the exact number of species there are of Nematodes, but doing a quick search online, there appears to be between 40,000 and over 1,000,000 species. Some are parasitic, even in humans and other animals. Nematodes are a round worm. For soil, there are a few types of Nematodes that we can categorize just to make things much more simplistic. The most common are:

Bacterial feeding
Fungal feeding
Predatory
Root feeding
Plant parasites

Not all nematodes are good for the garden. Some will kill your plants and others will help break down organic matter. You can buy beneficial Nematodes for your garden as a natural pest control for pests in the soil and occasionally some above ground.

How do you identify these? It has something to do with their mouth parts, but because I am still learning about these, I am going to stop there and just share with you a few that I have found. Most of the samples I have taken usually have one or two of these guys.

This is a Bacterial Feeding nematode and it can be identified by the mouth, which you will see closer in the image below.

This is the mouth of the bacterial feeding nematode.

This is the rear end of the nematode. One source says it releasing the nutrients in plant available form (aka…pooping). I don’t know if this is 100% accurate but it sure looks like it. The diagrams I have found on the biology of nematodes show the anus where the line and depression are shown at the top rear of this nematode. Maybe those small specs are the releasing of the nutrients and I mistook the large darker clump at the very tip being the waste.

The round thing shown here is called a bulb pump, or metacorpus. Bulb pump because it is round and pumps (That’s how I remember the name of this organ). This is an organ that pumps the food (nutrients) up and down the esophagus.

Rotifers

I don’t know much about these little guys yet, but they are really cool to see. I have only found a couple of these in my samples. You don’t want to have a lot of rotifers and ciliates in your bin. If you have a lot of them, it could be an indication that your bin is going anaerobic.

Rotifer kind of squished (shortened) up.

Up close image of the mastax. The mastax is the dark part in the middle. This is basically the jaws and in a video I have you can see it pumping or chomping. It is pretty cool.

Photosynthetic Bacteria Spores inside a dead Rotifer. You can still see the mastax.

This is another type of rotifer. They are like slinkies as they move. They squish up and then shoot forward by extending their bodies.

Testate Amoebae

Testate Amoebae are another microorganism that I have seen a lot of but don’t know much about yet. These are a single-celled organisms and I believe they have a hard shell around them. The shell is called a test (testate). These are different than the naked amoebae, which don’t have a test.

This one is cool looking to me because it appears that you can see part of the test (shell). I could be wrong about that, but that is what is looks like to my untrained eye.

Yeast

Yeast are a type of fungi and are single cell, so technically this category should go under the fungi but I will keep it here.

Others I Have Not Yet Identified

There are many other microorganisms in the samples I have taken from my worm bins that I have no idea they are even there. There is a lot here to learn and I don’t expect to come close to learning it all. But as I do find things, I post the photos and videos on a couple different Facebook groups where people seem to be very helpful and knowledgeable with these microorganisms. As I learn more about them, I expand my notes and keep looking for more.

What Are The Benefits to This?

For one, you get to learn about a whole new world of living organisms, ones you don’t get see with your naked eye. There are very few that you might be able to see, such as the nematodes, but that is a very rare occasion.

Two, you can get an idea on the quality of your soil by knowing what is living in there.

Three, knowing what is in your soil could help you determine why your plants may not be thriving.

Do You Want To Do This Yourself?

This is a fun little side hobby to go along with composting, vermicomposting, and gardening. You too can do this if you have a microscope. A computer to hook up a camera really helps so you can take pictures and video, but it isn’t absolutely necessary. I have used my cellphone with the camera up to the eye piece of the microscope and have taken pictures and video and honestly, the quality was a bit clearer than the camera that came with the microscope.

After a lot of research on what type of features you need in a microscope to properly view soil microbes, I came across this one that I use and would recommend: OMAX – 40X-2500X LED Digital Trinocular Lab Compound Microscope with 5MP Camera and Mechanical Stage – M83EZ-C50S. It has everything you need to perform these tasks of viewing soil microbes. If the 5MP camera isn’t good enough for you, you can always upgrade it, but I find that the provided with this microscope is descent enough quality, otherwise, you will be spending much more money on something better. If comes with free software for the camera.

Here is our son using the microscope and viewing it on the laptop.

Conclusion

There are many, many more microbes out there and I am sure that I have come across some that I didn’t even know I was looking at. This is just the beginning of this journey for me and I will share more with you as I learn and discover more.

Rick Simper has various hobbies, including woodworking, metalworking, composting, and gardening. He is an Architect full time and uses these hobbies to get away from the busy week of Architecture.