Soil Microbes: What Our Soil Biology Test Revealed
Most people judge soil by what grows in it. We wanted to look a little deeper, at the soil microbes themselves: the fungi, bacteria and other microscopic organisms that play a central role in breaking down organic matter, cycling nutrients and supporting plant growth.
So we sent samples from three areas of our property in the Macedon Ranges, Victoria, to a laboratory for a soil biology test. One area represents our starting point, one is a three year old tree system, and the third is a two year old, no dig, chemical free flower patch.
The headline result was striking. Total fungal biomass was approximately 11 times higher in the tree lines and 14 times higher in the flower patch than in our baseline sample. But not everything improved.
Some measures changed very little, while others still point to areas we need to work on. Before getting into the numbers, an important qualification is needed. These are single samples taken once from one property. This is not a controlled scientific trial, so the results cannot tell us exactly what caused each change. They are a snapshot of what is happening on our land and, importantly, a useful baseline for future testing.
What are soil microbes?
Soil microbes are living organisms that are too small to see without a microscope. Along with slightly larger soil organisms, they form what is often called the soil food web, a network in which organisms consume one another and break down organic materials, helping release nutrients that plants can use.
The main groups measured in our test were:
Bacteria: Single celled organisms involved in breaking down simpler forms of organic material and cycling nutrients.
Fungi: Organisms that grow as long threads and are particularly important in breaking down tougher materials such as wood and helping bind soil particles together.
Protozoa: Single celled organisms that consume bacteria. As they do so, they release nitrogen into forms that plants can access.
Nematodes: Microscopic worms, some of which feed on bacteria or fungi while others interact with plant roots.
Mycorrhizal fungi: Fungi that associate with plant roots and exchange resources such as nutrients and water with the plant.
How we tested: a soil health test that measures biological activity
Most conventional soil testing focuses on chemistry, including things such as pH and nutrient levels. A biological test asks a different question: what living organisms are present in the soil, and in what quantities?
Our samples were collected on 9 September 2026 and analysed by AgPath, who have been fantastic to work with. The laboratory reported the measurements per gram of dry soil, allowing the three samples to be compared on the same basis even if their moisture content differed when collected.
At the time of writing, we are still waiting on the chemistry results from these samples. This article therefore focuses on the biological results only.
Our three sampling areas
The Baseline
We wanted a section of the property with relatively few regenerative interventions to provide a reference point for comparing both the current system and future results.
We selected the inter rows between the tree lines. Other than some decompaction work, these areas have not been actively managed as part of the regenerative project.
Tree lines
A three year old food forest system (Project Genesis) with an established swale network. Samples were taken from between the trees.
Flower patch
A two year old, no dig flower growing area. Approximately 5 to 10 cm of compost is added each year, using either compost made on site or imported mushroom compost, and crops are planted directly into the beds.
The area is drip irrigated and managed intensively as a market garden. Compost is added to the surface rather than incorporated into the soil, and the beds are otherwise left undisturbed. Apart from the initial tilling required to establish the area, it has not been cultivated.
Our soil test results, side by side
The table below contains the measurements reported by the laboratory. Measurements shown as µg/g represent millionths of a gram of organism per gram of dry soil. Measurements shown as #/g represent the number of organisms counted per gram of dry soil.
Measure | Baseline | Tree lines | Flower patch |
Total fungi (µg/g) | 44.33 | 485.59 | 614.92 |
Total bacteria (µg/g) | 51.67 | 30.03 | 60.25 |
Active fungi (µg/g) | 10.81 | 8.06 | 9.80 |
Active bacteria (µg/g) | 1.35 | 1.51 | 2.81 |
Actinobacteria (µg/g) | 0 | 0 | 5.28 |
Flagellates (#/g) | 224.83 | 113.92 | 2,555.85 |
Amoebae (#/g) | 101.24 | 850.73 | 788.84 |
Ciliates (#/g) | 0 | 8.88 | 19.21 |
Nematodes (#/g) | 0.11 | 0.35 | 0.27 |
Nitrogen cycling potential (kg/ha over 3 months) | under 6 | under 6 | under 28 |
Mycorrhizal fungi (% of roots) | 1 | 1 | 0 |
Looking at the full dataset, a clear pattern emerges. Fungal biomass and several groups of organisms associated with nutrient cycling increased substantially, particularly in the flower patch.
At the same time, some measures remained low or showed little improvement.
What improved: soil fungi, protozoa and nematodes
Fungi showed the largest increase
Total fungal biomass increased from 44 in the baseline to 486 in the tree lines, or about 11 times higher.
In the flower patch, it increased to 615, approximately 14 times the baseline level.
This was the largest change recorded in the entire report.
There are plausible reasons for this pattern. Soil that remains covered and relatively undisturbed, particularly where perennial plants are established, is commonly associated with greater fungal development. Tillage can physically break fungal networks apart, so reducing soil disturbance may favour fungal growth over time.
However, our results cannot prove that reduced disturbance was responsible for the increase. There are several differences between the three areas, including vegetation, age, irrigation and management.
Protozoa also increased
Amoebae increased to roughly eight times the baseline level in both the tree lines and flower patch.
The flower patch also recorded approximately 11 times more flagellates than the baseline.
Because protozoa consume bacteria and release nitrogen as part of that process, increases in these organisms can be associated with greater nutrient cycling within the growing system.
Nematodes increased
Nematode numbers also moved in a positive direction, reaching around three times the baseline level in the tree lines and approximately 2.5 times the baseline in the flower patch.
The absolute numbers are still relatively small, so this is something we want to keep monitoring rather than treating one result as a definitive trend.
The flower patch showed the broadest improvement
The flower patch showed the strongest overall pattern of improvement.
In addition to the changes above, it recorded approximately double the active bacterial biomass of the baseline, a much higher estimate for nitrogen cycling, reaching up to 28 kg per hectare over three months, compared with less than 6 kg in the baseline.
It also recorded the presence of actinobacteria, which were not detected in the other samples and are involved in breaking down more resistant organic materials.
Taken together, these results suggest that the flower patch is developing a more biologically active and functionally diverse soil environment, although repeated sampling will be needed to see whether these differences persist.
What did not improve: soil bacteria, active microbes and mycorrhizal fungi
Soil bacteria changed very little
Total bacterial biomass in the flower patch was slightly higher than the baseline, at 60 compared with 52.
The tree lines, however, recorded 30, a little over half the baseline measurement.
This creates an interesting contrast. The baseline contained slightly more bacteria than fungi, whereas the newer systems now contain substantially more fungal biomass than bacterial biomass.
Based on the measured values, the tree lines had roughly 16 times more fungal biomass than bacterial biomass, while the flower patch had about 10 times more.
That shift is worth watching as the systems continue to mature.
Active microbes remain low
The report also distinguishes between total and active organisms.
Total measurements tell us how much biological material is present. Active measurements provide an indication of how much biological activity was occurring at the time the sample was collected.
Our active fungal measurements were slightly lower in both newer areas than in the baseline, while active bacteria remained low across all three samples.
So although there is substantially more fungal biomass in the newer systems, only a relatively small proportion of that measured biomass was active at the time of sampling.
This is one of the clearest reminders that a biological result is not simply a matter of more being better. The different measurements tell different parts of the story. I am yet to discuss with the lab what these results mean, and practically, how we can adjust our operations to make our soil more healthy.
Mycorrhizal fungi still need attention
Mycorrhizal colonisation remains one of the clearest areas for improvement.
Only 1% of roots were colonised in the baseline and tree lines, while no colonisation was recorded in the flower patch. Given the substantial benefits the mycorrhizal network provides plants (such as enhanced nutrient uptake, increase water absorption, and resiliance to stress, pests and disease), I am keen work towards this improving as I believe this will significantly improve crop productivity on our farm.
Are our ciliate numbers too high?
Based on the laboratory's stated limits, no. Ciliate numbers were within the relevant ranges in all three samples.
Ciliates are one type of protozoa and can increase under conditions where oxygen availability is limited, such as prolonged waterlogging or compaction. For that reason, higher numbers can sometimes provide a useful warning signal.
Our measurements increased from zero in the baseline to 8.88 in the tree lines and 19.21 in the flower patch.
Importantly, ciliates represented less than 1% of the total protozoa in each sample, with flagellates and amoebae making up the majority.
The tree lines are the area we will keep an eye on because that result sits relatively close to the laboratory's stated limit for that system.
How to interpret results from a biological soil test
If you have a biological analysis carried out on your own property, a few principles can make the report much easier to understand.
Start with the units. Different organisms may be reported by weight or by count. Comparing numbers only makes sense when the units are the same.
Separate total from active. A high total measurement does not necessarily mean that a large proportion of the organisms are actively functioning at the time of sampling.
Read laboratory targets in context. Target ranges may vary depending on what the soil is being used for. In our report, different benchmarks were provided for pasture, fruit trees and herbs, meaning the same measurement can be interpreted differently depending on the system.
Look for trends rather than one off scores. A single sample is a snapshot. Comparing different areas can be useful, but repeating a test from the same area over time is even more informative when you want to understand how a system is changing.
Know what the test does not measure. A biological analysis does not replace chemistry testing for nutrient levels, pH or organic matter. Those are separate measurements and become particularly useful when interpreted alongside biological data.
What we are doing next
The next step is to look at these biological findings alongside the chemistry report once it arrives.
We will also discuss the results and possible amendments with the laboratory before deciding what changes, if any, should be made to our management approach.
For us, the most important part of this process is not chasing a single perfect number. It is building a long term dataset that helps us understand what is happening on the property and whether our management decisions are moving the system in the direction we want.
We plan to repeat biological testing annually, ideally under comparable conditions, and share the results here as the project develops.
That means future posts will be able to show not just where the soil started, but how it continues to change over time.
Common questions
What is the difference between a biological soil test and a standard soil test?
A standard soil test generally focuses on chemistry, such as pH and nutrient availability. A biological test looks at the organisms living in the soil. The two approaches measure different things and can be used together to build a more complete picture.
Why did the fungal biomass increase so much?
We cannot say with certainty from one set of samples.
The tree lines and flower patch have both experienced substantially less soil disturbance than the baseline area, and both have maintained plant cover. Those management differences are consistent with conditions often associated with increased fungal development.
Is one test enough to judge soil health?
No.
A single test gives you a snapshot of conditions at one location and one point in time. It becomes much more useful when you can compare similar samples over multiple years and, ideally, combine biological measurements with chemistry and observations from the property itself.
Want to understand your own soil?
At Ecologic Solutions, we design sustainable gardens, farms and productive landscapes using methods such as permaculture and regenerative principles.
Our work ranges from suburban backyards and home gardens through to acreage properties and farms across Victoria, with remote design support also available.
Every site is different. Water movement, soil, slope, aspect, vegetation, climate and how you want to use the land all influence what a practical regenerative design looks like.
Whether you are starting a productive garden, redesigning an existing property or looking for a more regenerative approach to farm management, we can help you understand the opportunities within your site and develop a practical path forward.
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