Managing the Microbe Workforce – Understanding The Key Players (Part 2)

In this second installment of my soil microbe series, the focus moves from predatory fungi to protozoa. These articles are designed to increase your soil-life awareness and to inspire initiatives to harness this profound potential. If you are not driven to generate a protozoa tea after this sharing, then I have failed.

In Praise of Protozoa – The Mineral Recycling, Root-building, Earthworm Regenerators

A healthy soil houses a million protozoa per teaspoon, but numbers dwindle to below a thousand in a struggling soil. There are three main types of these relatively large, single-celled creatures and their respective distribution indicates soil type and moisture, along with the general health of the soil foodweb on your farm. The three main types of protozoa dominating agricultural soils include ciliates, amoeba and flagellates.

There are two types of amoeba, called testate and naked. Testates are encased in a rigid, chitin-based shell termed a "testa", while the naked amoeba lack that shell. The "nakeds" are essentially shapeshifters, whose enhanced fluid-like mobility enables them to explore a greater range of pore spaces. This, in turn, increases their nutrient cycling capacity.

Protozoa are found in all ecosystems, including the ocean. In the soil, they are the favorite food of the largest of the soil creatures, the earthworm.


In the soil, protozoa are largely found in the top six inches, because this is the major activity zone of the bacteria that comprise their main food. Like bacteria, they congregate around plant roots and they seek out soil moisture, which provides them maximum mobility in soil solution. During periods of drought, protozoa can form highly resistant cysts that enable them to survive in a dormant state until the rains arrive.

Protozoa largely feed upon bacteria, algae and fungi and are hugely important in the regulation of both bacteria and algae, to maintain biological balance.. In the absence of protozoa, bacterial numbers explode and this can pose problems in terms of nitrogen cycling.

In my seminars, I often cite an experience with a local ginger grower in relation to protozoa and nitrogen management. In this instance, large amounts of nitrogen were applied via irrigation but, mysteriously, there was no excess of N when tissue testing. Soil-life tests revealed massive counts of bacteria and no protozoa. This grower had regularly used methyl bromide for control of root knot nematodes, prior to adopting Nutrition Farming® principles. This nematicide gas kills much more than its target organism. It had decimated the protozoa component of his soils and the bacteria had exploded in the absence of their major predator. Bacteria are nitrogen intensive and they always eat at the table first, when feasting upon applied nitrogen. That nitrogen remains stored in their biomass until they die. The solution to this "theft" of plant nitrogen and associated inefficiency was to brew a tank full of protozoa, and apply it via fertigation. Within weeks, the need for applied nitrogen decreased by 60%! Nitrogen recycling had been reclaimed with the arrival of the protozoa.

Nitrogen, Nitrogen, Nitrogen

Nitrogen is the most abundant mineral required by plants, but most of the crop requirements of this mineral do not come from the bag. The atmosphere, and the recycling of crop residues, deliver much of the N punch (via nitrogen fixation and decomposition and recycling of plant protein). However, there is a third N stream that originates from bacteria, the most nitrogen intensive of all life-forms.

Bacteria have a 5:1 carbon to nitrogen ratio, which means that around 17% of their tiny bodies comprise pure nitrogen. That nitrogen remains in their biomass until they die, so there can be considerable gain in fast-tracking that process and recycling that lode. The terminator, in this case, is protozoa. A watermelon-sized protozoa consumes 10,000 pea-sized bacteria each day. The protozoa only requires a small percentage of the nitrogen found in the bacteria, so it spits the balance into soil solution and the plants sing "you beauty!"

The nitrogen link does not stop at this sharing of surplus N, for the benefit of your crop. This constant consumption of bacteria by protozoa is called grazing. Research has shown that grazing stimulates nitrogen-fixing bacteria, just as pruning stimulates your fruit trees. Nitrogen-fixers thrive in the presence of protozoa, so you now have greater access to free nitrogen from the atmosphere. This gift of nitrogen, in the ammonium form, helps create the desirable 3:1 ammonium to nitrate nitrogen ratio in your crop. This important ratio boosts plant resilience, reduces the need for chemical intervention and increases your farming fun.

Bacteria are more than a tiny nitrogen tank; they contain a full spectrum of minerals, which are all made more plant-available when cycled by protozoa. This cycling is termed "the microbial loop" and this has long been considered the primary benefit of protozoa in the soil. The plant feeds symbionts (like mycorrhizal fungi) and a variety of free-living beneficials, with a stream of nutrient-laced sugars. In return, the soil-life delivers multiple rewards to nurture their benefactors. It is very much a "you look after me and I'll look after you" deal.

However, this reciprocal arrangement is much more involved than was originally recognised. We are now beginning to understand new dimensions of root zone dynamics. It turns out that plant roots communicate with each other, to determine the nature of their exudates. Microbes are also constantly messaging each other and they, too, communicate with plant roots.

It is a veritable facebook frenzy beneath our feet and this new understanding highlights several things. Soil biology now appears more important than chemistry, and one wonders how we could have developed a world of agricultural "scientists" schooled only in chemistry. We must surely now question the "science" behind constantly compromising this complex creation with dumbed-down nutrition, acids, salts and toxic chemicals. When we truly understand this inextricably interrelated system, what agronomist in their right mind could recommend a biologically bankrupt strategy like chemical fallow? The definition of science is "adherence to natural laws and principles". Where in Nature do we see naked soils? Nature abhors a vacuum and it is anti-science to create one!

There are diverse impacts from this complex messaging and quorum sensing. For example, this messaging maze directly determines the amount and composition of the sugar gift. It is not a simple reciprocal exchange, as was previously thought.

Root zone architecture is also impacted by this interplay, and it turns out that protozoa are key players in this all-important root development.

Root-building Microbivores

Mycorrhizal fungi provide a vast tag-on of fine fungal filaments that can expand the original root surface area manifold. However, protozoa have a different impact. They are major architects of root structure and development, creating much more branching and associated root surface area, particularly in grasses, cereals and sugarcane.

As I have mentioned, the plant is constantly releasing glucose-based exudates to stimulate soil-life, and the microbial carnival created by this windfall means that there are many times more microbes in the root zone than in surrounding soil. The microbivores that feed upon this abundance also arrive in numbers. There are 30 times more protozoa immediately beside the root, than found in root-free soil just centimetres beyond.

It is now understood that this feeding frenzy is of tremendous benefit to the host plant.

Of the three main members of the protozoa family, flagellates are the smallest. They propel themselves through soil solution by flapping their whip-like tails (flagella). Amoeba are the second largest and they lumber through the soil by pouring their body into leg-like structures called pseudopods. Ciliates are the largest of the group and they zip through soil solution via multiple paddle-like, hair structures (cilia), enabling a rush toward prey or a rapid departure from predators.

protozoa flagellates amoeba cilates

Left to Right: Flagellate, Amoeba and Cilate

There are signaling techniques used by both positive and negative players to trigger plants to direct carbon for additional root structures. Root root knot nematodes, for example, direct plants to build the root galls that house them, while nitrogen-fixing bacteria conduct their plant partners to create their nodule homes. Protozoa also utilise this messaging strategy, but they use key hormones as the medium for the message.

Protozoa boost roots in three ways. Firstly, they can release auxins, hormones renowned for their root and leaf stimulating capacity. It is the amoeba that specifically generate this root-enhancing response. If you can encourage amoeba to flourish in the rhizosphere, or introduce them with a protozoa tea, there is a major root-building reward.

The second form of root stimulation also involves auxins but, in this case, they are not produced by protozoa. In 2002, Bonkowski and Brandt conducted research with watercress seedlings inoculated with protozoa. They observed five-fold increases in lateral root branching of young seedlings, but were able to demonstrate that this dramatic hormonal response did not come directly from the protozoa. Instead, the grazing of bacteria by protozoa stimulated the production and release of auxins from the bacteria, in response to their "pruning". The larger roots, in turn, produce more exudates, the feeding bacteria and their protozoa predators both benefit, and your crop thrives.

Finally, in this concert of mutualistic interrelationships, the protozoal pruning also stimulates nitrifying bacteria which, in turn, increase nitrates in the root zone. Nitrate nitrogen acts as a signal for lateral root elongation.

The nitrogen impact associated with protozoa, then, is truly profound. These important organisms recycle ammonium nitrogen from the bacteria they consume and stimulate nitrogen-fixing organisms to provide a further supply of nitrogen in the ammonium form, from the atmosphere. Finally, they trigger nitrifying bacteria to create the nitrates required to help achieve the desirable 3:1 resilience ratio between ammonium and nitrate nitrogen.

The Top Ten Protozoa Pointers

  1. Flagellates dominate in drier, less disturbed soils, while ciliates multiply in irrigated, bacterial-dominated, cultivated soils.

  2. Soils can have high numbers of protozoa or bacteria-eating nematodes, but not both, as they compete for the same food source.

  3. Protozoa can speed the decomposition of organic matter by boosting bacterial activity.

  4. The on-farm brewing of a protozoa tea can be boosted if you feed them up with bacteria – i.e., add a bacterial tea to the lucerne tea on the first day of the brewing process (see the protozoa tea recipe below). Protozoa double in numbers every two hours when provided with their favorite food (bacteria).

  5. Protozoa feed selectively on bacteria and, in this manner, they have a major impact on the composition of the bacterial biomass. This impact appears to be highly desirable, hence there can be great benefit in restoring protozoa numbers.

  6. A soil that contains unusually high numbers of ciliates is often compacted and anaerobic. The use of gypsum and humic acid, in this instance, can improve both soil structure and protozoa balance.

  7. If a soil hosts large numbers of visible algae on the surface, this can often be indicative of a lack of protozoa.

  8. Protozoa can consume pathogenic organisms, including both bacterial and fungal disease organisms. They are an often unrecognised, protective component of a fully-functioning soil ecosystem.

  9. Protozoa are the favourite food of earthworms. When you repopulate your soil with a protozoa tea, the earthworms arrive in force. These "intestines of the soil" decompose organic matter four times more efficiently than standard decomposition. Their poo is an unparalleled natural fertiliser. They deliver calcium to the soil, via glands that produce calcium carbonate. Earthworms aerate, particulate and remineralise the soil, and they also incubate a unique range of beneficial bacteria in their gut, which can not be accessed from elsewhere.

  10. Protozoa are also an important food source for beneficial nematodes and microarthropods. Good nematodes are important for recycling minerals, while the microscopic insects shred organic matter down to a more manageable particle size for bacteria and fungi to decompose. The soil foodweb functions to deliver food and suppress disease only when all components of the food chain are present.

Making Your Own Protozoa Inoculum

I hope that you are now motivated to consider the production of your own protozoa tea. It is a simple and highly effective strategy that could benefit many of us. In fact, I intend to start one for my research farms this weekend. The equipment required is basic and inexpensive. It might involve a 20 L home brewing kit (The Life Force® Microbe Brewer™) for the advanced home gardener. On the farm, it could involve a 200 L brewing station (The Brewstar 200™), or a 1000 L shuttle set up to multiply microbes.

NTS microbe brewing units

The two NTS units mentioned above are ideal because they involve aeration from bubblers rather than venturis and impellers. These systems allow the addition of lucerne hay (the starter inoculum) directly into the tank. If you are using a brewer with a pump and venturi, then you will need to isolate the lucerne (alfalfa) to avoid clogging the pump. This involves placing the hay in a homemade teabag (a piece of shade cloth with a drawstring) and dangling the teabag into the tank during the brewing process. Organic lucerne (alfalfa) hay is jam-packed with all three forms of protozoa because it has such a high nitrogen component. The perfect compost has a 30:1 carbon to nitrogen ratio. Lucerne hay also has a 30:1 C:N ratio and that is one reason why it is the best known garden mulch.


Here is the 200 L recipe for a protozoa tea that will successfully inoculate two hectares with a productive protozoa workforce:

200 L Protozoa Tea Recipe

  1. Add 180 L of water to your NTS Brewstar 200™ unit (or a similar brew kit) and activate the bubbler.

  2. Now add 2 L of LMF™ (Liquid Microbe Food), 2 L of Dominate-B™ and 2 kg of compost (preferably vermi-compost).

  3. Brew this bacterial tea for 24 hours.

  4. Next, add your lucerne (alfalfa) as a protozoa inoculum, at the rate of 1.5% (i.e., 3 kg of lucerne hay per 200 L).

  5. At this point you will also need to add more food to the brew, as the multiplying bacteria have consumed the original offering. Add 2 L of fish fertiliser (Nutri-Sea Liquid Fish™) and 2 L of molasses to the tank, to feed your protozoa army.

  6. Now brew the protozoa tea for a further two days before applying at a rate of 100 L per hectare. It can be fertigated or boom-sprayed on the soil.


We have found that the initial creation of a 24 hr bacterial tea, with the microbe food, creates a massive bacterial food source for the protozoa when they are introduced. Dominate-B™ is included to ensure that the tea is completely bacterial-dominated, as opposed to multiplying other organisms found in the initial compost inoculum. The lucerne is only introduced after day 1, in a 3-day brewing process. The protozoa reproduce every two hours in the presence of this bacterial soup and favoured protozoa food (fish and molasses). If you own a microscope, you can view the protozoa-packed end product. The completed brew should be applied to the soil within 24 hours.

Dominate-B, Nutri-Sea Liquid Fish and LMF from NTS

In Conclusion

Soil biology has been largely ignored in ten decades of extractive, chemical agriculture. Just as we are now awakening to the enormously important roles of the human biome, we are also recognising the vast complexity and productivity of microbial ecosystems in the soil. We cannot continue to ignore this world beneath our feet because it directly impacts our profitability, our farming pleasure, our health, and the ongoing viability of our planet. Protozoa are an integral part of this interconnected puzzle and if we can ensure their proliferation we maximise nutrient cycling, nitrogen management, root health, earthworm activity and disease management. Let me know how your protozoa tea performs.

To go back to Part 1 of this article, please click here.

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