Bacteria are a vital part of soil and the health of plants, so it is no wonder that there is a lot of talk about keeping soil bacteria healthy, increasing their numbers, having the right kimnd of bacteria, and so on. It only makes sense that if bacteria are important for plants, gardeners should (a) know more about them and (b) learn to manage them properly.

Unfortunately, along with good practical information, you will also find quite a few soil bacteria myths. The one I’d like to discuss today deals with the idea that you can figure out which type of bacteria you have. Armed with this information, you can then manage the populations to increase the ones that are most beneficial for your plants.

Soil Bacteria and Dr. Elaine Ingham

Dr. Elaine Ingham has become synonymous with the Soil Food Web. Her teachings include many good ideas about keeping soil healthy. She is a proponent of compost, and adding organic material to soil. She promotes the idea that microbes in the soil are very important for developing good soil structure.

Unfortunately, Dr. Ingham then takes these ideas to a ridiculous extreme. She recommends gardeners should look at the microbes with a microscope, and with this device, they will be able to identify the various bacteria in soil. Once you know which bacteria you have in your soil you can take steps to manage the herd, and increase the right ones which would make the growing conditions more favorable for your plants. She goes on to suggest that different plants need different populations of bacteria and gardeners can learn to customize their soil.

Here is a quote from the advertisement for one of her courses where a full day is dedicated to identifying microbes: “Get the necessary training to identify the bacteria, fungi, protozoa, and nematodes that drive the health and well being of our plants” (ref 1, Soil Foodweb with Dr. Elaine Ingham).

I have no problem with the idea that microbe types in soil are important, and that their ratios might change over time, and that such changes influence plant growth. This is all very true.

What I have a problem with is the idea that anyone can control this situation in a quantitative way. To do this you need to be able to identify the current bacterial types that you have, and then influence their populations to make them more suitable for you plants.

Note: Added March 28, 2016. A couple of comments left at the end of this post said that Dr. Ingham does not promote the identification of species. I now think that is correct.

The commenters can’t imagine where I got such an idea. So I went back and looked at a lot of the promotion from Dr. Ingham, and looked at several online videos. In every case she talks about the ‘identification of microbes’. In the video she clearly differentiates between various types of bacteria, and nematodes and talks about the importance of identifying these various types, and how this can be learned using a microscope. Clearly she expects you to do much more than just count total bacteria and total nematodes as one commenter said.

From her web site: “we will develop a wider and wider base of knowledge as more people encounter all the myriad of organisms that exist in soil.  Which in turns leads to a better understanding of what exactly is in different soils, in different climates, and with different organic matter and plants.” Sounds like a lot more than just counting bacteria, fungi, protozoa and nematodes!

The Soil Food Web also talks a lot about ‘increasing diversity’ of microbes. If you don’t know which species you have how can you know that your methods are increasing diversity? You can’t, which would lead a reader to think they are doing much more than just counting total bacteria.

I think this is a case of misleading the reader/viewer about her courses. I don’t think it is intentional.

What about the rest of this post? If identification of species is not the goal, are the comments still valid? I think they are. The post is mostly about gardeners using the information gained from the microscope.

I have just finished reviewing the book Teaming with Microbes, a gardeners Guide to the Soil Food Web and they say the following about using a microscope “when it comes to the microorganisms, we will be the first to admit that you will not be able to determine precisely what is in your soil, even with a powerful microscope.“ This comment comes from two strong proponents of the Soil Food Web, Jeff Lowenfels & Wayne Lewis. I agree with their conclusion.

Bacteria in Soil

Bacteria in soil carry out some very important functions. Some are nitrogen fixers which convert the nitrogen in the air, N2, into ammonia, nitrite and eventually nitrate, so plants can use the nitrogen. The decomposers are a large group of bacteria that decompose organic matter. This process releases nutrients for the plants and improves soil structure.

Bacterial pathogens cause diseases in plants. We don’t really want them around, but they are part of nature and play an important role. Normally, the good bacteria out compete the pathogens, and keep their numbers low enough so they don’t cause a problem.

Find out more about the bacteria found in compost at Compost Microbes – Good for the Soil?

Bacteria Species in Soil

How many species of bacteria exist in soil? You would think the question would have a simple answer, but the honest truth is that scientists don’t know. Most species of bacteria have not been identified which means no one knows how to identify them.

Estimates range between 2,000 and 8.3 million species of bacteria per gram of soil (ref 2).

Identifying bacteria is so complicated that the experts use approximation techniques to figure out the number of species. It is impossible to sit down in front of a microscope and figure out which species you have. For a glimpse at how soil scientists try to estimate bacteria communities see reference 3 .

A study (ref 4, Toward a Census of Bacteria in Soil) compared soil from Alaska and Minnesota and used computer models to identify species of bacteria because doing real identification was impossible. They found several thousand species, and 20% were endemic. So the soil bacteria from these two regions were quite different from one another.

The bottom line is that no one is able to identify bacteria species by looking at a soil sample. If the experts can’t do it, gardeners can’t do it – even if they take Dr. Ingham’s course.

Types of Bacteria

OK, so you can’t identify soil bacteria at the species level, maybe you can identify them as ‘classes’ of bacteria?

You can certainly see some bacteria cell structure under a microscope, and you can form classes of bacteria based on physical structure; rods, spheres, spirals etc., but that does not really tell you anything useful about which ones you want in the garden.

You can’t differentiate aerobic from anaerobic bacteria, based on physical appearance. You also can’t differentiate between beneficial and pathogenic bacteria. Identifying a bacteria as belonging to one or the other of these classes is critical to Dr. Ingham’s methods for the management of soil bacteria, and especially for the creation of compost tea.

You can count the number of bacteria you see, but I don’t know how accurate that is for a soil sample.

The average gardener can learn very little about the bacteria in soil by looking at a soil sample under a microscope.

Professional Labs

Let us assume that I have convinced you that you can’t identify the bacteria yourself. You then have the option of using one of the labs Dr. Ingham recommends on her web site, to do this identification for you.

Here is what one of them says “Complete Food Web Test (done by SFWNY) – Quantifies total and active bacteria, total and active fungi, and presence/absence of protozoa” , ref 5 Soil Foodweb Inc – Identifying Organisms. Your results will give you 4 numbers plus a yes/no for protozoa! Remember this is a ‘complete’ test, but it does not provide any information about the identification of bacteria. Odd – maybe the testing lab never took Dr. Ingham’s course??

So even the recommended professional labs don’t try to identify species, aerobic vs anaerobic, or even beneficial vs pathogenic.Why? It’s too complicated.

Managing Bacteria in Soil

The idea that someone can take a light microscope and find out critical information about their soil bacteria is ridiculous. You can certainly see bacteria, and you might be able to count some of them. That information is not very useful.

Even if you could get the information, what would you do with it? I don’t see how you would know which bacteria you should grow for each of your plants? No such table exists. How does this change for each plant you own? Nobody knows. We don’t even know which bacteria live in your soil!

Adding more organic matter will increase the number of bacteria – you don’t need to measure them to know this. Bacteria automatically increase in numbers when you supply a food source. Having active bacteria in soil is a good thing even if you don’t know which species you have. You don’t need a microscope.

In this discussion I have focused on bacteria in soil, but all of the comments also apply to bacteria in compost tea. Except for counting bacteria, a microscope will not help you to qualify your compost tea herd. Besides, there is no current evidence compost tea works any better than just compost.


  1. Soil Food web with Dr. Elaine Ingham;
  2. Pyrosequencing enumerates and contrasts soil microbial diversity;
  3. Empirical and Theoretical Bacterial Diversity in Four Arizona Soils;
  4. Toward a Census of Bacteria in Soil;
  5.  Soil Food web Inc – Identifying Organisms;
  6. Photo source: Filter Forge