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Plant Growth Promoting Bacteria - What exactly are they doing?

I've learned a lot while reading about all the different organisms found in vermicompost as many of them are likely plant grow promoting organisms (PGPB). As the name suggests, PGPB enhance the growth of plants meaning they help produce a higher yield, be more nutrient dense, or fend off diseases.

So what are these bacteria doing to help plants? As it turns out quite a bit -- ranging from nutrient uptake to stress reduction, plant growth hormone production and disease suppression. We are going to dig into the mechanisms of these benefits one at a time.

There are specific groups of organisms well known for promoting plant growth, mainly Rhizobia (rhiza in Greek means root). They are known known associate with legumes to fix nitrogen. However, as research in the field as progressed there is actually a large range of organisms that have plant growth promoting properties. Many of these organisms are endophytes (endo- inside, phyte- plant) which as the name implies live inside of plants. Most endophytes live inside of fine roots and can be both bacteria and fungi.

The pictures below are all arbuscular mycorrhizal fungi (AMF) present inside of roots of various plants.

Pictures courtesy of Takeshi Sentoku Twitter - @DvRiD8f52XatGLr

Functions of PGPBNutrient cycling / uptake


The most commonly known way bacteria provide nutrients to plants is through nitrogen fixation. Air is made up of about 80% N2 gas, however this form of nitrogen is not biologically available. Nitrogen fixing bacteria have specialized enzymes called nitrogenases that convert N2 gas into ammonia (NH3). Ammonia is form of nitrogen that available to plant to use. Plant roots (usually of the legume family including clovers, soybeans, alfalfa, lupines, and peanuts form nodules (seen below) that attract and host nitrogen fixing bacteria.


Phosphorous is another macro nutrient needed by all plants. In some soil types such as clay there is a lot of phosphorous present but like nitrogen gas it is not biologically available. It is bound up in mineral complexes with iron, aluminum, calcium and manganese. In order to make the phosphorus available to plants they need to solubilize these minerals. Phosphorous solubilizing bacteria produce small organic acids which bind, or chelate, the metals attached to the phosphorous molecule. The phosphorous is then unbound and available to the plant.

Some bacteria can also produce enzymes known as "phosphatases." These enzymes react with organic phosphorous. "Organic" in this case means carbon based as opposed to mineral bound. Basically, they can cut the phosphorous out of decaying biological material so it can be taken into the bacterial cell and used.


Iron is needed by plants for photosynthesis, and as we just discussed it can be bound in mineral complexes in soil. Bacteria produce and excrete special molecules called siderophores which bind specially to iron (in Greek siderophore means "iron carrier"). When these molecules bind to iron it makes the iron available to both the bacteria and plants. Below is a depiction of how three siderophores bind to an iron atom.

Quick Nutrient Summary

The term "nutrient cycling" get thrown around a lot, but is rarely explained in any detail. So if you ever hear bacteria or fungi help with "nutrient cycling," these are examples of what they are talking about. Essentially, a nutrient needed for life is locked up in some way and needs to be freed to continue in its cycle. Plants and bacteria work together to make this happen. Plants feed beneficial bacteria carbon made from from photosynthesis and in return bacteria provide nutrients to the plant that it cannot easily access.

Plant growth hormones (Phytohormones)

There are a few different classes of plant hormones but the main ones you'll hear about in relation to plant growth are auxins, gibberelins, and ethylene. Interestingly, many root associated bacteria have evolved to produce these hormones to help their plant partners.


The primary auxin hormone is called indole acetic acid (IAA) and is usually the active ingredient in rooting compounds. As you might guess, auxins promote root growth but also flower formation and fruit growth. If your a farmer looking to increase crop yield, these benefits cannot be overlooked.


Gibberellins are another class of plant hormones that can also be produced by bacteria. They play a role in seed germination, stem elongation, and flowering. While not research has gone into biological seed coatings, gibberellin producing organisms might be the next big thing in organic seed treatment.


Ethylene is a gas that, contrary to the previous hormones mentioned, promotes plant death or senescence. It is produced when plants are stressed or near the end of life and causes leaves to droop and curl. It is also used as a ripening agent for fruits like green bananas. Bacteria don't produce this but can break it down to lower a plant stress response as you'll find out in the next section.

Stress Reduction

Plants face a wide range of problems which cause stress including drought, high salinity, and soil contaminates such as heavy metals. As mentioned in the previous section, plants produce ethylene in response to these stressors. Some bacteria are able to alleviate stress by breaking down ethylene with an enzyme called 1-aminocyclopropane-1-carboxylate deaminase or just (ACC) for short. I think of this as similar to adding ice on an injury to reduce swelling. Conveniently, many of these bacteria that produce this stress relieving enzyme are themselves also drought or salt tolerant making them the ideal counter part for plants in arid regions. As noted in the figure below auxins and gibberellins also help plants regulate and recover from stress.

Heavy metals such as Arsenic, Zinc, Copper, and Lead can also cause stress to plants. Bacteria help reduce this stress by transforming the metals into less toxic forms or even taking up the metals and storing in their cells. While not directly related many of these bacteria have also shown promise in remediating polluted soils.

Disease Resistance

The final topic I want to talk about is disease resistance. This topic is probably the most complex because their are many mechanisms and involves interplay between microbial communities and plants. Firstly, just the presence of beneficial microorganisms can help the plant by simulating its immune system and competing for space and resources around the roots. This passive protection is difficult to quantify directly, but essentially just having a microbial community associated with plant roots creates a first barrier of protection from invading organisms.

A more direct form of disease protection comes from organisms that produce antibiotics and antifungals. The most well known types of bacteria that produce a range of antibiotics are the filamentous organisms the Actinobacteria. One genus alone, Streptomyces (found in some vermicompost), has had a huge impact on human medicine. Species from this genus have had a huge impact on human health producing antibiotics used to fight TB, leprosy, cancer, typhoid fever, and methicillin-resistant Staphylococcus aureus (MRSA) just to name a few.

Demonstrating how Streptomyces is preventing the spread of a cucumber fungal disease on an agar plate.

The agricultural importance of these types of organisms is just as big. A recently published paper actually suggested that Actinobacteria might be the most promising candidates for plant inoculants as they contain all of the previously talked about beneficial plant growth promoting properties. Several commercial formulations of different Streptomyces already exist as general biocontrol agents or specific fungicides.

As always any questions or comments please ask away.

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Permaculture Gardens
Permaculture Gardens

Hi Dr. Jones, You answered my question about the PGPRs on the Vermicompost Tea blog in this blog. Thanks!


Hi Zack,

I'm really just a layman fascinated with vermicomposting and the microbiology of soil. But I wanted to let you know that this blog has quickly become one of my favourite reads and I'm really looking forward to following your work going forward.

I wanted to ask your advice - I've read a lot about the right moisture content levels of a vermicomposting setup. I've seen some experts keep their moisture content as high as 80% (advised in "The Worm Farmer's Handbook"), but many other well-known pros say between 40 - 60% is best. My anecdotal experience has been that drier seems to be better, so I'm inclined to agree with the 40 - 60% range. I also feel…

Zack Jones
Zack Jones

Hi Sean,

Thank you for the kind words, I really appreciate it! As far as moisture content goes, if you look back at this post, you'll notice that moisture levels are about 50% to 70%. One producer had a moisture level of 45% but said they felt that was too dry. What I've heard is that higher moisture (70%) is better for breeding and lower moisture (50-60%) is better for composting. The more water your compost bin has the less oxygen and more anaerobic (no oxygen) areas you'll have. This can slow down bacterial and fungal degradation of your compost. Another factor is that most or really all beneficial plant growth promoting bacteria are aerobic (oxygen loving). While I don'…

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