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Best Garden Helpers Ever: Bacteria in Soil (and Other Microbes)

Published: February 24, 2022
Black soil in a hand. Soil bacteria help plants and trees access the nutrients they need in the soil.
An active population of beneficial soil bacteria an improve any plant's ability to absorb nutrients. Photo Credit:

Probiotics are good for us humans. At least that’s what we learn from the media these days. Articles online tell us that probiotics – also known as “helpful bacteria”- improve digestion and boost our immune systems. These tiny, living microscopic organisms are found naturally in fermented foods or you can buy probiotic supplements in your local health food store.

But do fruit trees need probiotics? What about other edible plants and herbs? In recent years, scientists have been learning that there is also helpful bacteria in the soil. These little organisms can help your plants in many ways:

  • They can help plants access phosphorus in the soil (which is often tightly bonded with other minerals and inaccessible to plants). Phosphorus is a nutrient that is important for root growth.
  • They can convert nitrogen gasses in the tiny pores of the soil into water-soluble nitrogen that our plants can absorb. Nitrogen powers leaf and branch growth.
  • Bacteria in soil also helps break down organic matter, releasing minerals that your trees and plants need for good health.
Do you have enough beneficial bacteria in your soil to keep your plants healthy? Find out by watching this video.

how does bacteria in soil help our trees and plants?

There is still a lot of mystery around how bacteria in soil functions. But what we do know is that these beneficial microorganisms love to consume sweet stuff in the soil. Their favourite food sources are high energy carbon sources like sugars.

Well, it’s lucky for us growers that fruit trees and other plants can be messy. They take in liquid nutrients through their roots through osmosis. But often some of the sugary energy they produce through photosynthesis seeps out from their roots into the soil.

If there are helpful bacteria in the soil near the roots of your tree, they can gobble up the sugary carbs your tree roots release and they’ll live, eat more and more, multiply, and then die. And when they decompose, they release those nutrients back into the soil – but this time it’s in a form that is more accessible to your plants. So now the plants will be able to enjoy the benefits of that phosphorus, the converted nitrogen, and the minerals they didn’t have access to before.

Scientist in blue gloves holding a teaspoon full of soil.
There are over a billion soil bacteria in just one teaspoon of healthy soil.

How do you know if your soil has a diverse population of beneficial soil bacteria?

A teaspoon of healthy soil will have over a billion bacteria in it. These organisms are so tiny that most of them can't even be seen with a microscope. So how do you know if your soil has a good population of soil bacteria and other microbes that can support your plants and trees?

According to the Soil Conservation Council of Canada you can find out pretty easily. In their "Bury Your Briefs" or "Soil Your Undies" campaign, they encourage farmers and other growers to evaluate soil microbe activity by burying a clean pair of 100 percent cotton underpants in the soil.

In this video excerpt, learn why Canadian farmers are burying their briefs to find out more about beneficial soil bacteria and other organisms in their soil.

The idea is to leave the cotton undies in the ground for a month or two. If your garden has plenty of healthy soil bacteria and other organisms they will break down the cotton fibres. After a couple of months, you can dig up the pants. If you have a lively and healthy population of soil bacteria, the cotton will be fully composted and all that you will find is the waist elastic.

Want to do this test in your garden? You can download the Soil Your Undies Protocol here.

Man holds decomposed underware. All that is left is the waist elastic. Soil bacteria broke down all of the cotton fibre.
Canadian farmer Blake Vince digs up his briefs to find that all that remains is the waist elastic. This shows that the population of soil bacteria and other microbes is actively breaking down organic matter in the soil. Photo credit: Blake Vince.

You can learn more about soil bacteria and the "Bury Your Briefs" campaign in this hour-long podcast. The interview features University of Guelph experts Cameron Ogilvie, Knowledge Mobilization Coordinator and Kari Dunfield, Canada Research Chair in Environmental Microbiology of Agro-ecosystems.

how to activate friendly bacteria in the soil

Some soils have been overworked or heavily disturbed and that can deplete the popluation of soil bacteria and beneficial microorganisms. So how can you feed and activate the existing bacteria in the soil? Here are some ideas:

  • Add compost to your garden annually. Each time you are also adding beneficial soil bacteria. And the organic matter in the compost also feeds the existing microbes in your soil.
  • Avoid tilling the soil. Tilling breaks up the aggregates, or clumps of soil, that protect soil bacteria and other microbes. Tilling also destroys beneficial soil fungi which has a symbiotic relationship with plants and trees.
  • Grow a wide range of plants in your garden. You can do this through crop rotation or by using cover crops. Each type of plant helps to support different types of microbes so crop diversity will help support a diverse population of soil bacteria.
Susan Poizner spreading compost around the roots of a fruit tree. Compost and rotted manure help increase the population of helpful soil bacteria and other beneficial microbes.
Mulching with compost can help increase the population of beneficial soil bacteria. Compost tea, if aerated correctly, can boost those populations as well. Photo Credit:

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Products that feed soil bacteria

There are lots of interesting products that you can use to feed the existing population of microbes in your soil including:

  • Compost tea
  • Molasses
  • Humic acid
  • Liquid fish emulsion

The goal in applying these products is to get them deep into the soil where they can be used by the soil bacteria (and fungi) that live there. Some are diluted and sprayed onto the soil. Sometimes products like these can be mixed together (with the molasses and liquid fish emulsion, for example, feeding the living bacteria in the compost tea). Whatever you try, always follow the manufacturer’s instructions.

Earth Alive grows out bacteria on a petri dish in the lab to measure the microbial density in their biofertilizer product. Each spot on the dish is a “colony” that grew from a single spore; by counting the number of colonies, the technician can determine how many bacteria were in the original sample. Photo Credit: Earth Alive.

bio-fertilizers are designed to boost helpful bacteria populations in soil

Today scientists are also trying to find ways to supplement the soil bacteria population. They do this by isolating the most active and energetic microbes in the soil and then developing them into soil amendments.

One such company is the Quebec-based company Earth Alive Clean Technologies. Taking soil samples from healthy, fertile soils, they isolated the different types of microbes they found living in those soils and screened them to see which were the most active strains of helpful bacteria. The strains chosen were those that were best for increasing crop productivity.

This type of organic bio-fertilizer is added just once a year at the beginning of each growing season for best results, according to the producers. Earth Alive's Soil Activator is one of their products designed for home growers.

bacteria and your fruit tree fertility program

If you have one fruit tree in your yard, or a number of them in your orchard or community garden, this is just one tool of many that you can use to help give your trees a boost. But what is most important is that you fulfil your tree’s fertility needs. You can learn all about that in my online course Unlocking Soil Potential. My goal is to simplify all aspects of fruit tree care so we can all successfully grow these trees – not just the experts!

After all, organic fruit tree growing doesn’t have to be difficult if you know what to do!

*This site contains affiliate links to products. We may receive a commission for purchases made through these links.

Susan Poizner

Director, Fruit Tree Care Education Online
Susan Poizner is an urban orchardist in Toronto, Canada and the author of Grow Fruit Trees Fast, a fruit tree care guide designed for new growers who want to grow organic fruit trees successfully - and quickly! She is also the author of the award-winning fruit tree care book Growing Urban Orchards. Susan trains new growers worldwide through her award-winning fruit tree care training program at and she teaches fruit production in person at Niagara College in Ontario. Susan is also the host of The Urban Forestry Radio Show and Podcast and an ISA Certified Arborist.

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