A method for observing the soil Nitrogen cycle in action


I had been developing a coir based organic plant growth medium for a couple of years and was getting fairly good results. However I wanted to know exactly what the actual nutrient levels in the mix were so I had a sample tested by a professional soil testing lab. The test was fairly expensive but it provided a comprehensive set of results. What surprised me was a high ammonium content and practically no nitrate.

Naturally occurring and ubiquitous nitrifying bacteria convert ammonium to nitrite and then to nitrate. I came across a research paper from the late 1940s which described a nutrient medium for growing nitrifying bacteria. Many of the ingredients in the medium are commonly used as fertilizer including ammonium sulfate, epsom salts and calcium carbonate (lime). My idea was to try growing nitrifying bacteria on a substrate such as vermiculite and add that to the mix.

After a couple of months working with a 5 gallon bucket of solution, an aquarium air pump, some fertilizer and vermiculite I did get a conversion of ammonium to nitrate.

In order to detect the presence of nitrate in the bucket I obtained some nitrite-nitrate test strips from a store that sells aquarium supplies. It was also necessary to keep track of  the pH and ammonium content. The pH paper I was using was hard to read so I did some googling for something better. I didn’t want to invest in an electronic pH meter at the time and found a Canadian company, Indigo Instruments, that sells some very nice pH strips and also Ammonia, Nitrite-Nitrate, and Phosphate test strips that have a much wider test range than the strips from the aquarium store.

It turned out to be a lot of work and didn’t seem to produce a noticeable difference in plant growth.

How it evolved

After abandoning the idea of growing nitrifying bacteria on vermiculite I started using the pH strips to test batches of coir mix. One day, out of idle curiosity,  I dipped one of the nitrate strips in some of the soil extract I was testing for pH. To my great surprise it showed a high level of nitrate! Apparently what had happened with the sample of mix that was tested by the lab was that it did not have enough time for the nitrogen cycle to progress to where there was a detectable level of Nitrate. It was a very fresh batch.

I started testing batches of mix for pH, Nitrite, Nitrate, ammonium and occasionally Phosphate. One day I thought it might be interesting to graph the test results but soon discovered that there wasn’t enough data to make a decent graph. I mixed a fresh batch of medium and began testing every two days.

Some results

As time went by a data graph began to show some interesting trends.


  • First, the Ammonium (Black line) started to increase after just one day. This is probably due to soil microbes (ammonifiers) breaking down the organic Nitrogen source in the mix which originally consisted of protein.
  • As soon as there is some ammonium present, bacteria of the genus Nitrosomonas, begin to proliferate and start oxidizing the ammonia to Nitrite (red line). Nitrite is toxic to plants and can increase to dangerous levels in a short time.
  • Fortunately the next step in the nitrification process starts up very quickly. Bacteria of the genus Nitrobacter begin to proliferate in the presence of Nitrite and oxidize the Nitrite to Nitrate (green line) which is a primary plant nutrient along with ammonium.

The two oxidation steps that convert ammonium to Nitrate also release hydrogen ions which make the soil solution acidic and the pH drops accordingly. The bacteria that are responsible for nitrification are sensitive to pH and are less active at low pH. The drop in pH that results from nitrification appears to bring the process into a state of equilibrium and the pH as well as the level of Nitrate in the soil solution stabilizes.

There is a drop in Nitrate after reaching an early peak that would be toxic to most plants. This is probably due to the fact that the overall microbe population in the soil uses much of the nitrogen for their own growth. Those microbes also require a source of Carbon for building the molecules that form their bodies. The majority of soil organisms are heterotrophs and use “labile” carbon sources in the soil.

Providing the proper level of bio-available carbon (Carbon-Nitrogen Ratio, C:N) is a means of controlling the level of dissolved Nitrogen in the soil solution.

The test strips I use are considered qualitative even though they give results in parts per million. They do provide enough resolution for useful and consistent data. As of this writing I have graphed the process in three batches of mix and have gotten very consistent results. Each data set takes about a month to complete.

What I learned

Organic gardening literature often talks about the rate at which organic fertilizers  release nutrients. I have found this information to be quite unreliable and have not seen any mention of the source of this information. The main Nitrogen source I am currently using is feather meal a low-cost, high Nitrogen fertilizer, which is listed as slow release, taking up to 6 months to break down. According to the data I have collected it releases most of it’s Nitrogen in about 10 days or so. This is consistant with research from the University of California-Davis. Researchers found that feather meal and blood meal (considered quick release) release Nitrogen at close to the same rate.

It is not a good idea to plant into a freshly mixed batch of grow medium. The early increase in soluble nitrogen compounds to toxic levels can damage plant roots. As a rule of thumb you should wait at least two weeks after mixing the ingredients. This may take even longer when temperatures are low. I have heard this before but now I know why.

How the test in done

For s detailed description of the testing procedure see the related post Measuring Changes in Soil Nitrogen.


  1. Dan,

    Thanks for the mention & link to indigo instruments. We sold our domain indigo.com recently & the link will go cold soon.

    Could you update it to “indigoinstruments.com/test_strips/”?

    Every link helps us.

    Thanks for your time.

  2. […] an attempt to stimulate nitrification in an organic plant growth medium. See the post “A method for observing the soil Nitrogen cycle in action” for more information and some test […]

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