8 Ways to Cultivate Beneficial Microbes (Effectively)

Increase soil microbes

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The old saying goes “feed the soil, not the plant”.  Microbes are essential for strong, healthy plants. 

How do we increase soil microbes?

To cultivate soil microbes, we can maintain soil moisture by mulching, and growing cover crops. We can feed them with sugar, compost, and add worms. We can introduce more microbes into depleted soil by growing legumes or adding a soil inoculant. And we can prevent killing them by avoiding pesticides, fungicides, and unnecessary tilling.

In this article, I will describe 8 natural ways to promote microbial growth in your soil.

What are microbes in the soil?

Soil microbes are microorganisms that are present in the soil. They perform fundamental functions such as breaking down organic residues, nutrient cycling, and stimulating plant growth. They play an important role in plant health and maintaining soil fertility.

Research suggests that a single gram of soil can contain several billions of various types of soil microorganisms.

Soil microbes are classified into bacteria, fungi, actinomycetes, protozoa, and nematodes. Each type of microbes has different roles in soil and plant health:

  • Bacteria:  they are the final stage of nutrient break-down in the soil
  • Fungi:  they live in the root zone (rhizosphere) and transfer mineral nutrients to plants, such as phosphorous and amino acids, in exchange for sugars produced by the plant during photosynthesis (a symbiotic relationship called “mycorrhiza”)
  • Actinomycetes:  although some actinomycetes are pathogens against plants, most of them protect plants against diseases
  • Protozoa:  they are large microorganisms that are consumed by bacteria
  • Nematodes:  these are microscopic worms that live around and inside plants. They eat dangerous pathogens and provide nutrients to the plant

Which microbes are beneficial for plants?

Soil microorganisms are important in the recycling of organic matter in nature (also known as “biogeochemical cycles”).

A specialized group of soil bacteria called prokaryotes perform the important function of nitrogen fixation.  They capture atmospheric nitrogen and convert it to ammonia, ammonium, nitrites, and nitrates in the soil, which is readily available for plant uptake and crucial in the formation of all nitrogen-containing nutrients, such as amino acids and proteins, and nucleic acids.

The most important nitrogen-fixing bacteria are Azotobacter, Clostridium, and Klebsiella. Other bacteria, like Azospirillum form symbiotic relationships with legumes and a family of grasses including rice, corn, wheat, oats, and barley.

Other soil microbes play an important role in pesticide degradation. They reduce soil toxicity by breaking down pesticides into less-toxic compounds, and finally to water and carbon dioxide.

For example, bacteria in the genus Pseudomonas degrade pesticides such as parathion, DDT, diazinon, aldrin, coumaphos, and endrin.  Bacteria in the Bacillus genus can degrade parathuon, diazinon, dieldrin, methyl parathion, and DDT.  Similarly, bacteria in the Alcaligenes genus degrade chlorpyrifos, glyphosate, and parathion.  And fungus such as the white-rot fungi, Fusarium, Mucor, Penicillium and Mortierella can degrade metalaxyl, pentachlorophenol, lindane, and fipronil. (Huang et al., 2018)

How to increase microbes in the soil?

Soil microbes need adequate nutrients, humidity, and oxygen to thrive. Both professional and home gardeners can encourage the growth of soil microorganisms in several ways:

1. Introduce soil inoculant

The quickest and most effective way to increase microbes in the soil is to add a soil inoculant or to introduce an external source of microbes to your soil.  It is especially useful for soil that is sterilized, baked or heat-reated (such as commercial potting mix), bare soil with no vegetation or low organic content.

The soil inoculant products generally contain these microbes:

  • Mycorrhizal fungi: these fungi increase the uptake of moisture and nutrients, especially in phosphorus-depleted soils or drought-prone soils.  It also improves soil structure.
  • Rhizobia: they are important nitrogen-fixing bacteria, and are particularly effective for garden plants like beans, peas, peanuts, and cover crops.  Inoculate legumes and other garden plants with rhizobia to boost growth and resilience, but avoid over-fertilizing.
  • Trichoderma fungi can boost root growth and plant immunity against diseases.
  • Rhizobacteria or the Bacillus bacteria can protect the plant against pathogens.

The following are the 8 most popular soil inoculant products we have reviewed. Read this article to learn why we recommend 3 of them and the criteria you should consider in selecting a good inoculant.

Soil Inoculant


Editor's Pick

1. Great White

Great White Premium Mycorrhizae 4 oz


●     2 microbe types (14 species of mycorrhizal fungi, 2 species of Trichoderma)

●     highest concentration


●     Pricey

●     No Bacillus

Editor's Pick

2. Mikrobs

Mikrobs - Microbial Superpack for Living Soil. Revitalize Plants (8 Oz)


●     3 microbe types (4 strains of mycorrhizae, 3 strains of richoderma, 4 strains of bacillus)

●     High concentration of Trichoderma and bacillus

●     Macronutrients and growth hormone

●     Good value


●     Low concentration of mycorrhizal fungi

3. Real Growers Recharge

Real Growers Recharge - Mycorrhizae Instant Compost Tea/Soil Microbes for Plant Growth - 16oz


●     3 microbe types (4 strains of mycorrhizae, 2 strains of Trichoderma, 4 strains of Bacillus)

●     High concentration of Trichoderma and Bacillus

●     Key macronutrients


●     Low concentration of mycorrhizal fungi

●     Pricey

●     Available only in large formats (at least 16 oz)

4.  MYCO+ 

Bloom Booster and Yield Enhancer for Plants - Big, Heavy, Healthy Harvests, For Use In Soil and Hydroponics - Concentrated Phosphorus and Potassium - Flower Fuel 1-34-32, 20,000g


●     2 microbe types (4 strains of mycorrhizae, 1 strain of Trichoderma)

●     Macronutrients

●     Good value

●     Available in small packages (7 oz)


●     Low concentration of microbes

Best Budget Inoculant

5. Myco Bliss

Myco Bliss Powder (2lbs) - Mycorrhizal Soil Inoculant for Plants - Highly Concentrated 5-Strain Inoculant - Mycorrhizae Rooting Powder Improves Nutrient Uptake & Water Retention


●     1 microbe type (5 strains of mycorrhizal fungi)

●     Acceptable concentration of microbes

●     Cheapest and best value (for big bag)


●     Contains only mycorrhizal fungi


DYNOMYCO Premium Mycorrhizal Inoculant - Root Enhancer/Stimulator - Mycorrhizae for Plants - Concentrated Mycorrhizal Inoculant - Supreme myco strains - Treats up to 68 Plants! (340 g / 12 Oz)


●     1 microbe type (2 strains of mycorrhizal microbes)

●     High concentration of microbes


●     Contains only mycorrhizal microbes

7. Mikro-Root 

Mikro-Root, Trichoderma Fungi for Healthier Root Management. Solubilize Fixed Phosphate in The Soil to be readily Available to Plants (2 oz)


●     To supplement soil lacking in Trichoderma


●     Contains only Trichoderma

●     Pricey

8.  Botanicare Hydroguard

Botanicare Hydroguard Bacillus Root Inoculant, Quart


●     High concentration

●     Liquid form for hydroponics


●     Contains only Bacillus

●     Only 1 strain of Bacillus

●     Short shelf life of 6 months

2. Feed with sugar

Sugar is the food for microbes and sugar can be used as a “fertilizer” to boost the number of microbes in soil and accelerate the decomposition organic matter in soil.

A study shows that adding molasses to compost teas of fish and kelp can increase the population of bacteria and fungi by 10 times (Shrestha et al., 2011).

Another study also shows that mixing 1 tbsp of molasses with about 4 cups (1 liter) of water and using that as a foliar spray in growing water spinach resulted in an almost 8% increase in the yield of water spinach, compared to not applying it at all (Bethe et al., 2017).

The most common way of adding sugar to soil is to mix 1 tablespoon of molasses to every 4 cups (1 liter) of compost tea, fish and kelp, or a liquid soil inoculant. This would help increase microbial population and help with plant growth.

3. Grow legumes or a cover crop

Grain legumes (peanuts, soybeans, cowpeas, fava beans) and perennial and forage legumes (sweet clover, vetches, alfalfa) can increase microbial population in soil because they grow in a symbiotic relationship with nitrogen-fixing microbes.

Studies have shown that an acre of grain legumes can fix up to 250 lbs (113 kg) of nitrogen per year (Flynn & Idowu, 2015).

The plants are capable of fixing their own nitrogen and thus you don’t need to apply nitrogen fertilizer when growing legumes, or only very lightly when grown in sandy or clay soils with low-organic matter

Similarly, perennial and forage legumes, like sweet clover, vetches, and alfalfa can fix 250 to 500 lbs (113 to 226 kg) of nitrogen per acre.  Because of their nitrogen-fixing properties, legume cover crops are used to “fix” farmland naturally that are low on nitrogen due to the previous harvest.

Tip for gardeners: Grow legumes in crop rotation to replenish nitrogen to land previously harvested

4. Add worms

Earthworms can build a microbial population in soil because they propagate microorganisms in their gut.

They digest and recycle organic matter into the soil and make nutrients easily available to microorganisms.

They also create a healthy environment for bacterial and fungi growth as they loosen up compacted soil and make it more aerated, release plant-available nutrients and improve carbon dynamics (Medina-Sauza et al., 2019).

Tip for gardeners:  Increase the number of earthworms in your garden by adding compost or compost manure which is an important food source for earthworms.

But, do not add them to pots or your container garden if the pot is smaller than 16 inches (40 cm) in diameter because earthworms can eat plant roots when there is a limited supply of their preferred food in small pots.

5. Add compost

Compost can increase microbes because it is rich in carbon, nitrogen, and nutrients for soil microorganisms.

Compost is organic material which is decomposed from animal manure, kitchen waste, and plants.

Vermicompost is organic waste decomposed by earthworms, red wrigglers or white worms and has more nutrients than compost, making it ideal for vegetable gardens.

Tip for gardeners:  Add compost to your garden or pots, or mix it into the top layer from time to time to boost plant growth and resilience.

6. Mulch and keep soil moist

Humidity is one of the important factors in the population of soil microorganisms.

Studies suggest that the number of bacteria and fungi began to soar particularly 3 days after rainfall, and after 10 days the bacteria population increased by 50 percent more (Borowik et al., 2016).

Similarly, prolonged periods of drought kill soil microbes. The microbe population starts to drop 14 days after drought (Meissner et al., 2015). Their population increases again after rewetting, although there is a lag after rewetting and the lag period increases with the duration of the drought.

Tip for gardeners:  Increase soil moisture by watering, especially a slow drip system for a large outdoor area.  Also, try to trap or retain moisture by adding landscape fabric, plastic mulch, organic mulch or ground vegetation.

7. Avoid pesticides, herbicides and fungicides

Chemicals such as pesticides, herbicides, and fungicides are extremely toxic and kill not only pests but can also kill good soil microorganisms.

Although fungicides and bactericides are designed to kill certain types of fungi and bacteria, repeated use will kill beneficial microbial life, affecting the entire soil ecosystem.

A review of more than 400 published studies, comprising more than 2,800 experiments and 285 pesticides, has proven that pesticides can harm beneficial organisms in more than 70 percent of cases (Donley & Gunstone, 2021).

The review has shown that pesticide-intensive agriculture is the leading factor in the major decline of soil microorganisms. The use of pesticides is the most significant driver of soil biodiversity loss in the last decades.

8. Avoid unnecessary tilling

Tilling should be avoided for healthy soil to not disturb the fluffy aerated structure of the soil.

The natural structure of healthy soil has pores between soil particles and tunnels created by worms and dead plant roots. These pores and tunnels store oxygen, which is crucial for microbes.

If healthy soil is tilled, it breaks up and collapses the natural structure of the soil, leaving only fine particles of soil stacked on top of each other.  In such a case, tilling would actually compact the soil, instead of loosening it.

Also, tilling can kill earthworms, reducing their population and diversity in the soil.

However (and this is important), tilling is still necessary when the soil structure is not healthy, i.e. compacted and water-repellant that water pools on top and cannot penetrate.  In such a case, mechanically breaking up the soil such as by tilling or lawn aeration would help revitalize the soil by letting oxygen and water flow into the soil.


Billions of microbes exist naturally in the soil.  In most cases, we don’t actually have to do anything in particular to make them grow, other than providing a good environment for them to grow.  To do this, we need to make sure the soil does not dry out by mulching and growing cover crops.  

We can give them a boost by giving them food (sugar, such as molasses) and adding compost.

For soils that are depleted, we can introduce more microbes by growing legumes or even adding a microbial inoculant.

For sterilized soils such as potting mix, we can give them a jump start by using a soil inoculant to introduce an external population of microbes.

Finally, we need to prevent killing them by avoiding the use of any forms of pesticides, herbicides, and fungicides, and avoid any unnecessary tilling. 

Happy gardening!


Here’s Why Sugar Can Fertilize Soil (With Recipe)

Can Tilling Kill Earthworms? (What You Should Know)

Top 3 Inoculants for Plants: More Than Just Mycorrhizae

Proven Ways To Fix Hydrophobic Soil (Organically)


Bethe, L.A., Salam, M.A., Fatema, U.M. & Shakil Rana, K.M. (2017). Effects of molasses and compost tea as foliar spray on water spinach (Ipomoea aquatica) in aquaponics system. International Journal of Fisheries and Aquatic Studies 2017; 5(3): 203-207

Borowik, A. & Wyszkowska, J. (2016). Soil moisture as a factor affecting the microbiological and biochemical activity of soil. Plant Soil Environ., 62 (6), pp. 250-255

Cox, J. & Reid, G. (2005). How to encourage soil organisms. State of New South Wales Department of Primary Industries.

Donley, N. & Gunstone, T. (2021). Pesticides Are Killing the Organisms That Keep Our Soils Healthy. Scientific American.

Flynn, R. & Idowu, J. (2015). Nitrogen Fixation by Legumes. Guide A-129. College of Agricultural. Consumer and Environmental Sciences. New Mexico State University.

Hayat, R., Ali, S., Amara, U., Khalid, R. & Ahmed, I. (2010). Soil beneficial bacteria and their role in plant growth promotion: a review. Annals of Microbiology.

Huang, Y., Xiao, L., Li, F., Xiao, M., Lin, D., Long, X. & Wu, A. (2018). Microbial Degradation of Pesticide Residues and an Emphasis on the Degradation of Cypermethrin and 3-phenoxy Benzoic Acid: A Review

Hoidal, N. (2021). Should you add microbial soil amendments to your garden? University of Minnesota Extension

Medina-Sauza, R. M., Álvarez-Jiménez, M., Delhal, A., Reverchon, F., Blouin, M., Guerrero-Analco, J. A., Cerdán, C. R., Guevara, R., Villain, L. & Barois, I. (2019). Earthworms Building Up Soil Microbiota, a Review. Red de Ecología Funcional. Instituto de Ecología A.C.. Xalapa, Mexico.

Meisner, A. Rousk, J. & Bååth, E. (2015). Prolonged drought changes the bacterial growth response to rewetting. Soil Biology and Biochemistry, Vol 88, pp. 314-322

Shrestha, K., Shrestha, P., Walsh, K. B., Harrower, K. M. & Midmore, D.J. (2011).  Microbial enhancement of compost extracts based on cattle rumen content compost – Characterisation of a system. Bioresource Technology. Vol 102 (17), Pp. 8027-8034

Wagner C. S. (2011). Biological Nitrogen Fixation. Nature Education Knowledge 3(10):15

Carol Chung
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