Teaming with Microbes – A Close Look, Part 1

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Robert Pavlis

Teaming with Microbes, A Gardeners Guide to the Soil Food Web was reviewed in an earlier post Teaming with Microbes – In-depth Book Review. In this post I would like to delve into some of the contents of the book in more detail and provide a different perspective on the soil food web. A gardener can learn a lot by looking at these topics in some detail.

Teaming with Microbes - A Close Look, Part 1
Teaming with Microbes – A Close Look, Part 1

Teaming with Microbes – A Close Look

Items in quotes are taken from the book. In some cases the quotes have been shortened to make the concepts easier to understand but as much as possible I have used the same wording as found in the book.

Fertilizers Kill Microbes

“Fertilizers (commercial) are salts; they suck the water out of microbes”

It is true that the majority of commercial fertilizers are salts – things like urea are not salts. The nutrients used by plants to grow, like nitrate, phosphate and potassium are also salts, or more correctly ions of salts. When the salt fertilizers dissolve in water they form ions.  The fact is that there is absolutely no difference between the ions from commercial fertilizer and those from organic sources. This has been discussed in more detail in What is Organic Fertilizer?

The idea that fertilizer sucks out water out of microbes is wrong but it is based on some science. Osmosis is the movement of water, through a membrane, from a source of low concentration to one of high concentration. If the microbe finds itself next to water with a very high solute (ie fertilizer) concentration, higher than itself, the microbe might loose some water. But fertilizer will dissolve in water and form a fairly low concentrated solution, except maybe right next to the fertilizer pellet. Fertilizer does not suck water out of microbes in the soil.

Plant Science for Gardeners by Robert Pavlis

Phosphate in Soil

“phosphate, an anion, stays in solution and is easily leached away by water. It is often missing in soils”

“phosphorus, when applied as a fertilizer, becomes unavailable to plants in seconds”

The above two quotes seem to contradict one another – P (phosphorus) can’t stay in solution and at the same time be unavailable to plants?

Phosphate (PO4) is NOT very soluble in water and it sticks to soil. Because of this it moves through soil very slowly – a centimeter or two a year. Phosphorous (P) exists in soil in both a soluble form and an insoluble form. The insoluble form quickly sticks to soil and represents the majority of P in soil. As plants and other organisms use the soluble form of phosphorus, more of the insoluble form is released from soil as the soluble form.

Although it is true that P is locked up in soil quickly it is also true that it is released slowly to the soil solution for plants to use over time.  So adding commercial phosphate fertilizer is similar to adding organic material – both release the P slowly over time.

The total phosphorus level in most soils is high. In fact several US states have now banned lawn fertilizer containing any phosphorus because the soil already has lots. Adding too much compost is making some organic soils toxic because the P accumulates in soil and sticks around much longer than other nutrients.

How Much Phosphate Is Too Much?

“Use NPK values below 10-10-10 so fungi will not be killed with excess phosphate.”

This sounds like good advice, but it isn’t.

High phosphate levels will kill fungi – that part is true. However, suggesting that P levels below 10% (the middle number in 10-10-10) are OK is incorrect because it does not take into account existing P levels in the soil. If existing levels are already toxic, adding anything above 0% will harm soil and fungi. To understand this better have a look at All Tomatoes Need The Same Fertilizer.

Some organic farms are adding too much compost. The nitrogen gets used up, leeches away or is converted back to N2 gas. The phosphorus remains in the soil and builds up to toxic levels. The amount of phosphorus you should add to your soil depends on the current level in the soil – not some arbitrary formula.

Different Forms of Nitrogen

“ammonium (NH4) is converted to nitrate (NO3) by nitrogen fixing bacteria. This process happens in alkaline soil conditions”

There are three key forms of nitrogen of interest to gardeners; nitrogen gas (N2), ammonium (NH4) and nitrate (NO3). N2 can’t be used by plants, but the other two forms can.. Decomposition of organic matter produces mostly NH4, but also some NO3.

Microbes in the soil convert the NH4 to NO3. This nitrification process is carried out by nitrifying bacteria, NOT nitrogen fixing bacteria, as claimed in the quote. Nitrogen fixing bacteria convert nitrogen gas (N2), to ammonium (NH4) and other nitrogen containing organic molecules that plants can use.

The nitrification process is influenced by temperature, moisture, aeration, pH, and other environmental factors. Contrary to the quote, the rate of nitrification proceeds most rapidly at neutral pH (ie pH = 7) and declines as soils become excessively acid or alkaline (ref 1).

This latter fact is important in the soil food web theory, because the gardening rules depend very much on a plants preference for either NH4 or NO3, as well as a preference for acidic or alkaline soils. If NH4 is converted to NO3 at neutral pH instead of alkaline pH, a significant part of the soil food web rules for gardening are no longer valid.

Worm Castings Contain High Levels of Nutrients

“Vermicastings are seven times richer in phosphate and ten times more potash … than soil. “

Vermicastings are worm castings – ie worm poop. Although this quote is correct, it is misleading.

Most of the nutrients in organic matter are in the form of large molecules which plants can’t use. The digestive process in worms breaks down the large molecules and releases the nutrients in a plant usable form. When labs measure the nutrients in soil or worm castings they are only measuring the soluble forms that are available to plants, ie the nutrients.

Worm castings are high in nutrients because worms are efficient digesters, not because they increase the total potential of nutrients in the soil. Without worms, the microbes would produce just as many nutrients – they are just a bit slower at the process.

In fact the gut of a worm is full of bacteria, and it is actually the bacteria that are doing much of the digestion. Worms are just a convenient place for the microbes to live and they chew up the organic matter into small pieces making  digestion by bacteria more efficient.

In the end, the amount of nutrients your soil gets with or without worms will be the same. Worms just speed up the process. Is that a good thing for a garden? It is not a good thing for our natural woods – but that is another story.

Browns and Greens in Compost

“Brown items contain carbon. Green items contain easier-to-digest bacterial foods and are good nitrogen sources. Brown material consists of difficult-to-digest lignin, cellulose and tannin.”

Assuming the material going into compost is plant material or manure, almost none of it contains ‘carbon’. You might have some carbon if you throw in wood ashes.

Browns and Green contain a lot of chemicals that contain carbon, like sugars, and starch, but these are quite different from carbon, which is extremely inert. The molecules containing carbon in both brown and green material will be almost the same because decomposition has not started yet. Both contain lignin, cellulose and tannin. Lignin, for example is an important part of cell walls – it is responsible for things like plant stems, and structure in leaves. Since both green and brown stems/leaves have structure, they both contain lignin. Since greens and browns both contain the same carbon containing molecules they are equally difficult to digest.

Microbes need nitrogen in order to grow and multiply. Greens have more nitrogen allowing the microbe populations to grow faster. More microbes means faster digestion. It is the nitrogen that causes green material to compost faster, not any differences in internal organic molecules.


For more on this review see Teaming with Microbes – A Close Look, Part 2.


  1. Plant and Soil Sciences – Nitrogen as a Nutrient;


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Robert Pavlis

I have been gardening my whole life and have a science background. Besides writing and speaking about gardening, I own and operate a 6 acre private garden called Aspen Grove Gardens which now has over 3,000 perennials, grasses, shrubs and trees. Yes--I am a plantaholic!

5 thoughts on “Teaming with Microbes – A Close Look, Part 1”

  1. Hi Robert,

    Jeff Lowenfels along with Elaine Ingham have a yahoo group called Compost Tea. They would be happy to answer any questions and have answered mine on several occasions. I even asked Dr Ingham why the earthworm seems to be left out of the Soil Food Web diagram which she had a big hand in designing and I was told because the USDA wanted it so. The earthworm should actually be front and center when you are discussing soil in its relationship to agriculture and in the diagram.

    The earthworm is as important or even more important than pollinators in putting food on your table. Many species of earthworms besides their ability to suppress soil borne diseases of plants hang around the root ball zone making the nutrients of their castings easily accessible to plants. There are a few species of microbes that develop symbiotic relationships with plants but earthworms stay in close proximity and benefits from the plant products of respiration without being detrimental to the plant’s growth. Lumbricus rubellus is a species very beneficial if hanging around the root ball. Earthworms and their digestive tract make nutrients at a larger proportion more readily available in plant friendly forms in organic garden settings than conventional fertilizers and the reason why organic numbers on organic fertilizers are so low and yet provide more than enough nutrition for the plants

    One should have as many earthworms while having several species in their soil to ensure healthy and productive soil. My motto is if you don’t have earthworms gardening with you, you are gardening alone and doing all the work and not reaping all that you could.

    My grandmother in her garden in New Brunswick, Canada used wood ash from her stove to side dress root vegetables, carrots, beets and turnips which I think made them much more sweet tasting.

    I think Jeff’s second book Teaming with Nutrients would be a better read for the NPK perspective. Teaming with Microbes is more of a primer to begin to garden microbiologically and an excellent beginning in learning to steward the soil and tools to increase the healthy microbiology, for me anyway

    All plant material has a carbon to nitrogen ratio, if it is that below 30:1 it is considered a green and over is considered a brown.

    Please take a look at Mulder’s Chart as bad things happen when there is an overabundance of an element (nutrient). Some will lock out others and the need for a soil test is never more evident than with an overabundance.

    • Earthworms are an invasive species here and before they were introduced in North America plants grew just fine. I am not at all convinced they are that important to a landscape garden.

      Statements like “Earthworms and their digestive tract make nutrients at a larger proportion more readily available in plant friendly forms in organic garden settings than conventional fertilizers” are not correct. Earthworms can’t create nutrients so they don’t make them available “in larger proportions”. they can make them available sooner, but they don’t make more. they certainly don’t provide more, or make them available quicker than synthetic fertilizers.

      Wood ash is not recommended for gardens.

  2. Robert, you mention adding wood ash to compost as a carbon source in the article above. I have access to large amounts of wood ash. What is your opinion on using wood ash in compost or in the garden?

    • Wood ash contains P and K as well as other nutrients. It has no nitrogen. Because it lacks nitrogen is is not a very good fertilizer unless another form on nitrogen is added.

      It also has a high pH. If you soil is very acidic, it would be a good addition. If it is slightly acidic or alkaline I would not use ash since plants prefer slightly acidic pH.

  3. Mr. Pavlis. Thank you very much for your wonderful writing. It is a comfort to me to understand a bit clearer the mechanisms of soil chemistry and not be fooled with the gimmicks.


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