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WasteMINZMay 7, 2025 12:00:00 AM5 min read

The microbiology of compost - it's alive!

You know that compost is a great source of nutrients for plants - but did you know it’s alive? 

This International Compost Awareness Week, take a moment to consider all the hardworking microbes beneath our feet, in our farms and gardens and in our compost piles.

As well as nutrients, compost adds beneficial microbiology to the soil. Good compost contains a huge range of beneficial microorganisms/microbes, including bacteria, fungi, protozoa and nematodes.

microbiology1 - mature compostA maturing compost pile. Image credit: Kate Walmsley, Kaicycle. kaicycle.org.nz 

Under our feet is the soil food web, a busy tangle of life and death that keeps nutrients moving through growth and decomposition. There are nematodes - tiny worms - that feed on bacteria, releasing the nutrients from the bacteria into the soil in plant-available form. There are fungi which partner with plant roots, increasing the plant’s access to water and nutrients, and get fed by plant sugars flushed through the roots in return. More familiar soil organisms, like earthworms, eat the smaller creatures. There are bacteria which are farmed by plants, being fed plant sugars and then absorbed through the roots and “milked” of specific nutrients, before being released back into the soil to repeat this "rhizophagy cycle" which was only discovered recently.

microbiology2 - the soil food webImage credit: Paula Harkes, A leap towards unravelling the soil microbiome

Turns out we still have a great deal to learn about how soil works. But it’s becoming clear that the mutualistic relationships (beneficial both ways - a type of symbiosis) between plants and soil microbes are critical to soil health, as well as plant immunity and disease suppression. Our industrial food system has largely side-stepped this highly evolved symbiotic system, replacing natural nutrient cycling with high doses of plant-available nutrients in synthetic fertiliser. This leads to the soil food web shutting down and soils degrading and eroding over time, while herbicides, pesticides and fungicides are increasingly needed to control plant diseases that are symptoms of nutrient and biology imbalances. Monocropping, or growing vast stretches of one plant, aggravates these problems.

microbiology3 - maize silage crops

Maize silage crops. Image credit: country-wide.co.nz/south-island-maize-delivers

The Soil Food Web approach, created by Dr Elaine Ingham, focuses on restoring the microbial biodiversity in soil to grow plants and nutrient dense food without the use of synthetic fertilisers, herbicides or pesticides. It starts with using microscopy to understand the microbes in the soil, and identify what microbes are missing or what ones might be causing problems. Then, a program is devised to attain the ideal soil microbe populations for the specific plant to be grown. Different plants/crops thrive in different microbial conditions; for example, some plants like soil with similar bacterial and fungal levels, while others, such as tree crops, prefer fungi-dominated soil.

To attain these ideal conditions, high-quality compost with a biodiverse range of beneficial microbes across bacteria, fungi, protozoa and nematodes is used. The compost may be directly applied to soil, or brewed into extracts/teas to boost microbe levels.

 The following images are taken from samples of compost, showing some examples of the main beneficial microbes that, if present in high enough numbers, indicate a healthy compost micro-ecosystem.

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Photo credit: Cory Hope, Certified Soil Food Web Lab Tech. cory@jhdltd.co.nz
Compost credit: Glenview School, Porirua

In the above image, the green arrow is pointing to a beneficial bacteria and the orange arrow is identifying some beneficial fungal hyphae. Both the bacteria and the fungi play a crucial role in decomposing organic matter and extracting micronutrients from mineral particles, such as clay. The compost was made from food scraps mixed with a carbon source - such as arborist mulch - in an approximate ratio of 1:1, with the compost temperature peaking between 55°C and 75°C.

 

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Photo credit: Cory Hope, Certified Soil Food Web Lab Tech. cory@jhdltd.co.nz
Compost credit: PaeCycle community composting, Paekākāriki

The yellow arrows in this image show two different types of beneficial protozoa -  testate amoebae - indicating some diversity in the protozoan population. All beneficial protozoa consume bacteria and sometimes fungi, enabling natural nutrient cycling. The compost was made from food scraps mixed with a carbon source in an approximate ratio of 1:1, with the compost temperature peaking between 55°C and 75°C.

 

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Photo credit: Cory Hope, Certified Soil Food Web Lab Tech. cory@jhdltd.co.nz
Compost credit: Te Hiko Centre for Community Innovation, Cannons Creek, Porirua.

This image shows a beneficial bacterial feeding nematode in action. Bacterial feeding and fungal feeding nematodes, alongside protozoa, are crucial elements of the Soil Food Web as they consume bacteria and fungi and release plant-available nutrients into the soil which feeds the plants; this is natural nutrient cycling.

 

microbiology7Photo credit: Rebecca Swan
Compost credit: City to Farm, Hibiscus Coast

This image was taken during a “Microscopic Journey to the Centre of your Compost” course by Growing Point. The next course begins May 20th. It shows the presence of long strands of beneficial fungi that have branched. This indicates a mature compost that has had minimal disturbance, allowing the fungal hyphae to grow long and branched and thick in diameter. The compost is made with food scraps collected from commercial businesses using a Bokashi method with biochar and is then dug into a banana swale, allowing it to finish composting in situ.

 

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Photo credit: Rebecca Swan
Compost credit: Untangled Landscapes, Redvale

The above image is from a sample of compost made using the Johnson-Su method, and shows good levels of diverse beneficial fungi and less bacteria, indicating it will likely have a high fungal:bacterial biomass ratio - ideal for tree crops. This would be expected from a Johnson-Su process, which is left to mature for a year undisturbed, allowing the fungi to grow. The long undisturbed maturation period also causes the bacterial population to decrease, as the food sources for the bacteria are used up and protozoa are hard at work eating 10,000 bacteria every day.

If you’re a composter, why not consider doing some soil microbiology testing to see how the quality of your compost could be improved even further?

Written by Kate Walmsley, Cory Hope and Rebecca Swan


 

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