What if Small Scale Farmers in Sub Saharan Africa Could Create Effective Fertilizer in their Backyards?

My idea to utilize anaerobic digestion, microalgae and bacteria to make this a reality.

Rachel Lee
20 min readJan 24



Fertilizer prices have risen 30% since the start of 2022 because of the ongoing war in Russia and Ukraine [1]. (Russia produces 23% of global ammonia, 14% of urea, 25% of nitrogen and 21% of global phosphate fertilizer. [2] Since the beginning of the war, Russia has halted all exports of fertilizer).

Farmers and food producers around the world are suffering from a fertilizer deficit of 20%. Because of this global shortage of fertilizer, researchers are predicting that throughout 2023, global crop yields will decrease by 15% [3].

And this decrease in crop yields will impact countries already below the poverty line hardest. The world’s most vulnerable countries will be hit the hardest with high fertilizer prices.

With limited access to fertilizer, smallholder farmers will not plant as much as they’d normally be able to grow. This will dramatically decrease local access to food, pushing countries to turn to expensive imports.

Africa Fertilizer Watch predicts that crop yields in Sub Saharan Africa will decrease by 21% in 2023 [4]. If this happens, an estimated 2.04 million people will not have food [5].

“All signs point to 2023 looking even worse on an acute level, on a chronic level, and in terms of malnutrition. The numbers we’re seeing across the board at every level are increasingly concerning

That is actually terrifying. Catherine Maldonado, the senior director of food security at Mercy Corps says that 2023 is set to be the worst year for poverty and hunger since the 2000s. [6]

It makes me sick to think that poverty has been (very) slowly decreasing each decade, and now, one year could erase years of poverty alleviation and push millions of people into famine and extreme poverty.

This graph:

Our World In Data

has been slowly going down from 1983 to 2020. And now in 2023, all research and data predicts that this line will shoot back up to the 1980s level.

The question that has been burning on my mind lately is how can we prevent these grave predictions from turning into reality?

And I don’t have the correct answer to this. In fact, I don’t think that there is one correct answer to this question.

But what I do have is a crazy idea (that could very well not work for many reasons) to address the fertilizer crisis in Sub Saharan Africa.

Decentralizing fertilizer manufacturing

Sub Saharan Africa is currently suffering from a fertilizer deficit of over 20% compared to availability before the Russia-Ukraine war. [7]


Because Russia has halted all exports of fertilizer.

Why is this a problem?

Because Russia and Belarus produce over 30% of the world’s fertilizer. [8]

So what if we decentralize this system? Instead of one country producing a large majority of one of the most important agricultural resources, we create a system where each farmer can produce their own fertilizer? (And this system is good for the environment unlike current fertilizer manufacturing which accounts for 2% of global greenhouse gas emissions [9])

The body of research about alternatives to the Haber Bosch process (process that creates fertilizer) is a field called organic fertilizer. Which is fertilizer derived from organic sources, unlike chemically manufactured synthetic fertilizer that the world runs off.

Why organics haven’t caught on at the commercial level is simple: efficiency. Organic fertilizer doesn’t increase yields to the degree that synthetics do.

So the criteria for this decentralized fertilizer manufacturing system to replace synthetics in Sub Saharan Africa is:

  • Produced locally, which is the premise of decentralizing fertilizer production.
  • Environmentally sustainable, both the manufacturing process must be sustainable, but also the long term affect of the fertilizer on the soil and surrounding ecosystems health must be positive. (No run off that causes dead zones, decreased nutrient content of soil and greenhouse gas emissions.)
  • Cheap, so fertilizer is easily accessible to the poorest of small scale farmers.
  • Effective, this one is the easiest to understand. The fertilizer must be just as good as synthetic fertilizer.

These are the four buckets that I will use as criteria to access an alternative to the status quo of fertilizer production. If the alternative doesn’t check all four of these boxes, it is not an effective solution in my mind.

Fertilizer from trash

My proposal of a solution to tackle the fertilizer crisis in Sub Saharan Africa is based on anaerobic digestion, which is a multi-billion year old process that turns organic waste into biogas.

My idea is to create household size anaerobic digestors out of tubular film to turn on farm agricultural waste, food waste and human waste into digestate, which will be further processed with cyanobacteria into a nutrient rich, organic fertilizer.

What is anaerobic digestion?

Anaerobic digestion (AD) is a process where bacteria breaks down organic matter (like agriculture waste, manure, and food waste) without oxygen. The bacteria used in anaerobic digestion are acidogenic bacteria.

I like to think about AD as sophisticated composting — it is essentially a more effective process to convert all organic waste matter into usable products. You chuck large amounts of organic waste into the system, and after a month of bacteria breaking down the waste, you are left with biogas, a renewable energy.

This all happens in large reactors with high pressure like the image bellow:

Anaerobic digestion plant in Oregon source

But AD can also happen in large plastic films (essentially long bags), like the image bellow. This method of AD is called tubular film.

Tubular film digestors on a dairy farm in California source

There are two temperatures which the AD process can operate at. The first is the mesophilic method which happens at 35–40°C, and the second is thermophilic which happen at 55–60°C. Thermophilic is only used in a large commercial AD plant because of the high amounts of energy needed to maintain the high temperatures. Mesophilic is used for smaller scale plants.

There are 4 steps in the AD process:

  1. Hydrolysis: the acidogenic bacteria in the reactor break down the organic feedstock into smaller macromolecules by turning carbohydrates into sugars, lipids into long chain fatty acids and proteins into amino acids.
  2. Acidogenesis: the acidogenic bacteria absorb the macromolecules into their cells and use the new energy to create intermediate volatile fatty acids (IFAs). IFAs are short chain mono-carboxylate compounds which are a precursor to producing biofuel. During this process of creating IFAs, ammonia is produced (most important element to create fertilizer).
  3. Acetogenesis: the acetogenic bacteria convert the VFAs into acetate, producing hydrogen as a by product, and the fatty acids into propionate.
  4. Methanogenesis: the methanogenic bacteria convert the acetate and propionate into methane, concluding the AD process. [10] [11]

This entire process take around 30 days.

And the product that we are left with is biogas, a renewable energy that can be used for electricity, heating and cooking. Biogas is comprised of 60% methane gas and 40% CO2 gas. [12]

Digesting 1 ton of food waste through anaerobic digestion produces approximately 300 kWh of energy, enough energy to power 4 incandescent lightbulbs for 10 hours. [13] Anaerobic digestors can also be hooked up directly to stoves (called a biogas stove) so the biogas can be used for cooking as it is being created.

Biogas stove design

The unwanted waste

In the case of fertilizer, it is not the biogas we are interested in. The biogas can be transformative for families who previously had little to no access to energy, and even just the daily amount of biogas produced is enough to transform a family’s living conditions.

Water can now be properly boiled preventing diseases, meals can be cooked faster speeding up the cooking time for the women, wood doesn’t need to be cut down for a cooking fire which saves time for women, the house can be heated, lights can be used at night. All these things are game changing for families living in poverty. [14]

But for fertilizer creation, we are interested in the by product of the AD process: digestate.

There are two parts of digestate. The solid fraction (left) and the liquid fraction (right). The solid part contains most of the phosphorus, and the liquid part contains most of the nitrogen. [15]

Digestate is a nutrient rich slurry which is usually thrown out in streams and rivers.

But this makes no sense to me? Why would you throw out a useful, nutrient dense compost which could act as a fertilizer?

And the reason why digestate is thrown out is quite simple: it’s not that effective. It provides the soil with beneficial nutrients and bacteria, but not the same concentrated chemical formula in synthetic fertilizer that increases yields.

The solution to this is quite straight forward. We must find a way to make digestate as good as synthetic fertilizer.

Goal: make digestate as effective as synthetic fertilizer

Digestate checks 75% (3 out of 4) of the boxes for an alternative to current fertilizer production. Digestate is:

  • Produced locally: The majority of anaerobic digesters are large scall production factories. My idea is to decentralize this by implementing small scale, home anaerobic digestors which can run off the waste (food waste, human waste, agricultural waste) that one family produce. The images below give you an idea what small scale digesters look like:
(From left to right), Sistema.bio AD system in Kenya, Household AD system in Southern India, HomeBiogas system in the Democratic Republic of Congo
  • Environmentally sustainable: AD produces zero emissions, compared to the 1.87 tons of CO2 produced per 1 ton of ammonia during the Haber Bosch process. [15] Not only is the production sustainable, but the application of digestate results in 96% less runoff than synthetic fertilizer, which would solve the dead zone problem. [16] And finally, digestate also increases soil health and quality long term by providing an array of nutrients and organic matter (like bacteria), which is polar opposite to synthetics which suck all nutrients from the soil and decrease soil health long term. [17]
  • Cheap: The only costs of small scale AD is the upfront cost of the digester, which varies depending on the size of the digester. The average cost for a 9ft by 4ft design is $300–600 USD. (We will come back to price because my idea will make this cost much lower because of the material I propose to build the digester out of and the design I have created to control pressure.)
  • Effective: This is the check box that digestate doesn’t check. Digestate is not as effective as synthetic fertilizer. This is the main problem that my idea is addressing.

My idea to increase effectiveness of digestate

My idea has a few different layers: the material of the digester, pressure pockets and digestate processing unit.

Material of digestor

Most smaller scale digesters are concrete or brick domes like the images below:

But this concrete is expensive; a circular digester with a 10 feet diameter costs $2200 to build and install, which is unaffordable to most small scale rural farmers in Sub Saharan Africa. [18]

These concrete digestors are called fixed dome digesters, where 75% of the total volume is for the slurry and the remaining 25% is for biogas storage. Fixed dome digesters are usually built underground or partially underground like the images above, which increase the price by roughly 20% since a large hole must be dug in the ground. [19]

The alternative to the fixed dome digester is a floating drum digester which is made of a steel gas tank. This steel gas tank adds an additional $400+ USD onto the construction cost of the digestor, making it an expensive and unattractive option.

Left: fixed dome digestor system design, Right: floating drum digestion design

My idea is to simplify these two designs into a less complicated, cheaper and just as effective design.

Instead of using concrete and steel, I propose that using tubular film, a thick and durable plastic, could provide the same optimal environment for the bacteria to digest the waste, while being much cheaper.

The system looks something like this:

My design idea

The beauty of this design is that it is extremely simple, and very customizable. The inlet (where the waste goes in), outlet (where the liquid digestate comes out) and biogas pipe (where the biogas comes out) can be constructed to fit the wants and needs of the family.

The best part of using tubular film is that the construction cost plummets from $2200 to less than $250 USD. [20]

Pressure pockets

The two most important elements of anaerobic digestion are temperature and pressure. A steady temperature is easy to achieve because the black tubular film attracts heat from the sun.

Pressure is a little harder to achieve. In a commercial plant, pressure monitors and turbines are used to maintain a pressure of 5.0 mBar.

But a much simpler way to create steady pressure is with weight. So in my tubular film anaerobic digester design, I have added simple pockets on both sides of the tube which rocks can be placed in. These rocks will add weight to the digester to create the pressure needed for the AD process.

Visual I created of the pressure pocket design on the tubular anaerobic digestor

This pressure will ensure that the AD process is efficient and quick and processing the waste into digestate and biogas.

Digestate processing unit

Here comes the big problem point of my idea: digestate isn’t that efficient.

Digestate checks all the boxes (cheap, small scale, environmentally sustainable) except efficiency.

What I mean by efficiency is digestate’s effect on crop yields. Synthetic fertilizer increase crop yields by over 60%. [21] Digestate on the other hand, increases yields by 3%. [22] With this low efficiency, it’s hardly worth it to even use digestate.

To make digestate an actual alternative to synthetic fertilizer, it must be in the same effectiveness range as synthetic fertilizer.

So the main work and research for my project has been about the effectiveness of digestate — how to make it as good as synthetics. But before I share my research on the topic, we need to understand the limiting factors of digestate.

Why is digestate not effective?

There are a few reasons why digestate sucks compared to synthetic fertilizer:

Nutrient form

The NPK (nitrogen, phosphorus, potassium) in synthetic fertilizer is water soluble, which means that the nutrients are immediately available to plants. This is a major reason why synthetic fertilizer is so effective — less than 24 hours after being applied to fields, the roots already have access to the nutrients. [23]

Digestate, on the other hand, contains NPK bound to other elements, which prevents the nutrients from being up taken by the plant. Nutrients in digestate take up to 6 months to be absorbed by plants.

This is what is called the release rate of fertilizer. Synthetic fertilizer has a fast release rate. Digestate has a slow release rate.

The release rate of fertilizer determines how efficiently plants take up nutrients: the faster the release rate, the higher the efficiency. The slower the release rate, the lower the efficiency. [24]

Nutrient concentration

Synthetic fertilizer is created to have the highest amount of nutrients possible, to deliver plants high highly concentrated nutrients in a usable form.

For example, urea and ammonia have a nitrogen content of 46% and 34% nitrogen respectively. Phosphorus fertilizers like monoammonium phosphate (MAP) and diammonium phosphate (DAP) have phosphorus concentration of 11% and 18%. And potassium chloride (KCl) has a potassium content of 8–14% potassium. [25]

The micro and macro nutrient concentration of digestate is almost laughable compared to synthetics:

1–3% nitrogen, 0.5–2% phosphorus and 0.5–2% potassium. [26]

(It is important to note that digestate does contain other micro nutrients that many synthetic fertilizers don’t, like calcium, magnesium, zinc, copper, iron as well as important bacteria and organic compounds that synthetics don’t have.)

The rest of the digestate is made of organic matter like cellulose, lignin, hemicellulose, and a lot of water.


Every batch of synthetic fertilizer is the same — farmers buy a bag of fertilizer knowing exactly how many nutrients are contained in the fertilizer and how much to apply to fields.

It’s impossible to have this consistency with digestate. Every batch of digestate is different depending on the temperature outside, pressure in the digester, feedstock used, kind of waste and reaction time inside the digester. [27]

This makes it super hard for farmers to know how much digestate to apply to fields. One batch may have a high nutrient content so farmers only need a small amount , but the next batch may be mainly water and therefor farmers will need much more.

And the list doesn’t stop there. I could keep going and mention the different kinds of synthetic fertilizer that are available for different kinds of plants (granular, liquid, gaseous), or the low amount of hard metals which makes synthetic fertilizer so great.

And because of all these advantages of synthetic fertilizer over digestate, digestate is just thrown out or used as a soil amendment. Roberta Pastorelli and her team at the Research Centre of Agriculture and Environment examined this exact problem, and concluded that because of the low effectiveness of digestate, it will never been used to replace fertilizer:

“Overall, digestate is a good source of organic matter and nutrients that can be used as a soil amendment to improve soil health and reduce the use of synthetic fertilizers. But never a replacement to synthetic nitrogen fertilizer.” [28]

Using digestate has been shown to decrease the use of synthetic fertilizer by 40%. [29] This is great, but it isn’t awesome.

What would be awesome is if we could further process digestate to solve the three key problems that limit digestate effectiveness I listed above (accessible nutrient form, high nutrient concentration and consistent nutrient profile.)

Conventional digestate processing

In the large commercial anaerobic digestion plants, there are three processes used to increase nutrient content: Liquid separation, evaporation, reverse osmosis.

Liquid separation and reverse osmosis both filter out the water in digestate so only a thick, nutrient dense portion of the digestate is left. Evaporation evaporates the water so the remaining material is the thick, nutrient dense digestate (most of the nutrients in digestate are in the solid portion, not the liquid).

All three of these systems happen in large plants at very high temperatures and high pressures, which means these processes are not feasible for small scale home digesters in Sub Saharan Africa.

Picture of KUMAC digestate processing plant that uses reverse osmosis. This is obviously not a small scale operation. source

So we need a way to increase the nutrient content of digestate on a small scale.

There are a few options out there that attempt to do this:

  1. Feedstock — using a nutrient rich feedstock like veggie scraps and manure could increase nutrient content of the digestate (verse a less nutrient dense feedstock like wood chips or plant stalks).
  2. Adding supplements — adding enzymes or bacteria chosen specifically for breaking down compounds to release nutrients. Or adding a compound like lime to neutralize the digester and maintain a healthy pH could also increase nutrient content.

But non of these options significantly increase nutrient content.

Because of this, I have been researching other more effective ways to increase nutrient content of digestate, and I have landed on microalgae-bacteria consortium.

My proposal: microalgae-bacteria consortium

A microalgae-bacteria consortium is a combination of microalgae and bacteria that can be used to improve the nutrient content of digestate. Microalgae and bacteria have the ability to degrade organic matter and release nutrients, which can make the digestate more nutrient-rich.

Here’s how it works:

  • Microalgae are photosynthetic organisms that grow rapidly and use carbon dioxide, light, and other nutrients to produce biomass. They can also absorb and convert dissolved nutrients into plant-available forms (like the nutrient form that synthetic fertilizer is in).
  • Bacteria are microorganisms that can degrade organic matter and release nutrients. They can also convert dissolved nutrients into plant-available forms.
  • When microalgae and bacteria are grown together in a consortium, they work together to degrade organic matter and release nutrients. Microalgae produce biomass and release dissolved nutrients, while bacteria degrade the biomass and release more nutrients. (It’s a synergistic relationship between the microalgae and bacteria!) [30]

Quantitative metrics: what the numbers say

There’s some amazing research out there showing that adding a kind of microalgae bacteria consortium to digestate can improve the nutrient content of digestate.

Marta Franchino et al. found that processing digestate with a Chlorella vulgaris and Bacillus sp. consortium resulted in increased phosphate content by 10%, increased ammonium content by 3% and increased nitrate content by 17%. [31]

P. Foladori et al. found that a consortium of Scenedesmus sp. and Enterobacter sp. increased nitrogen content by 13%. [32]

And Kristina Weimers et al. found that the phosphorus content increased by 21.8%, sulfur increased by 21% and nitrogen increased by 30% when digestate was processed with a Chlorella vulgaris and Pseudomonas sp. consortium. [33]

By averaging out each nutrient increase, I found that using a microalgae bacteria consortium increased nitrogen content by 30%, phosphorus content by 10% and potassium content by 9%.

Which equals a total increase in nutrient concentration by 49%.

That is massive.

It is enough of a nutrient increase to put digestate in the same ball park as synthetic fertilizer.

With microalgae bacteria consortium, the final NPK content of digestate would skyrocket from 1–3% N to 31–33% N, from 0.5–2% P to 10.5–12% P and from 0.5–2% K to 9.5–11.5% K.

And when you compare these numbers to the average synthetic fertilizer at 34–46% N, 11–18% P and 8–14% K, the new digestate is pretty darn close.

It’s crazy that something as simple as algae and bacteria can produce such a massive improvement in nutrient content.

How exactly does Chlorella vulgaris and Pseudomonas sp. work?

Let’s zoom in closer to the microalgae bacteria consortium. The consortium I have chosen for my idea is Chlorella vulgaris and Pseudomonas sp.

Chlorella vulgaris and Pseudomonas sp. under a microscope | source

Chlorella vulgaris is a type of microalgae that absorbs and converts dissolved nitrogen into plant-available forms.

Pseudomonas sp. is a type of bacteria that degrades organic matter and releases nitrogen, phosphorus, and potassium.

Together, these microorganisms work together to break down the NPK in plants and convert the nutrients into a usable form that is immediately available to plants. Chlorella vulgaris will absorb and convert dissolved nitrogen into plant-available forms, and Pseudomonas sp. will degrade organic matter and release more nitrogen, phosphorus, and potassium. [34]

Putting everything together (literally)

It’s easy to think that throwing a bunch of microalgae bacteria consortium into the digester will increase nutrient content.

But that would never work.

The anaerobic digestion process is extremely sensitive, any change in the bacteria levels, pH, pressure or temperature will ruin the final biogas and digestate.

And this is where the research usually stops for using microalgae bacteria consortium in digestate processing — since the bacteria consortium can’t be added directly into the digester, it seems like a brick wall that can’t be worked around.

My idea is to add an additional processing unit onto the traditional anaerobic digester design. A visual of my idea is below:

Visual I created of my AD digester design with the digestate processing unit

Both the reactor (long tube on the left) and the digestate processing unit (small tube on the right) will be made of tubular film for the reasons we went over above.

Digestate processing unit

As the digestate is created in the main reactor, a slight decline in elevation will push the digestate out of the main reactor and into the adjacent digestate processing unit.

The main reactor houses the anaerobic digestion bacteria, but the digestate processing unit houses the microalgae-bacteria consortium: Chlorella vulgaris and Pseudomonas sp.

The digestate will spend on average 30 days in the digester, which is the time it takes AD bacteria to break down organic waste into digestate. [35] The digestate will then spend another 20–25 days in the processing unit for the Chlorella vulgaris and Pseudomonas sp. to release nutrients from the biomass and convert them into a form usable to plants. [36]

Now the great thing about this system is that digestate isn’t just produced every 50 days and then you harvest it and are left with bags of digestate.

Instead every day digestate is produced based on the amount of fertilizer fed into the system.

The amount of digestate produced per day is 30–40% of the total volume of feedstock and water fed into the system that day. [37] So depending on the amount of fertilizer a farmer needs, they can adjust the amount of waste they put into the digester.

This is the same for the biogas production — biogas will be produced each day which can be used immediately for cooking, heating or light. 60–70% of the total volume of the feedstock and water fed into the system is turned into biogas.

I am personally super excited about this idea because it checks all the boxes:

Produced locally CHECK. Pushing down the technology of AD which usually happens in massive commercial reactors to small scale home digesters, allows individual farmers and families to have a constant supply of biogas and digestate.

CheapCHECK. The entire system including materials, labor, bacteria and operation costs equal out to $300–600 USD. Compare this to the money small scale rural farmers in Sub Saharan Africa spend on fertilizer a year ($20–120 per hectare of land per year) and money spent on energy for farming and living ($60–150 per month), it quickly becomes clear that an AD plant is cheaper in the long run. It provides consistent fertilizer and energy for families at a low cost. [38]

Environmentally sustainable CHECK. The AD process releases practically no emissions, requires no transportation and uses organic materials. The production process is sustainable, and the final digestate is considered an organic fertilizer which is much better for the soil and surrounding bodies of water compared to synthetic fertilizer.

EfficientCHECK. Using microalgae bacteria consortium in a digestate processing unit can increase overall nutrient content by 49%, putting it almost on par with synthetic fertilizer.

This could be revolutionary.

Access to fertilizers and a constant source of energy are two of the biggest problems small scale farmers face.

Fertilizer is essential to maintaining high crop yields and ensuring farmers will have a bountiful final harvest. Energy is essential for not only farm equipment, but life at home. Access to energy is a game changer for the entire family, freeing up time for women who collect firewood, providing constant cooking potential, and allowing families to work into the night.

I wanted to end with words from the World Bank:

“The world’s ability to quickly realign energy and fertilizer supply chains in ways that leave room for poorer farmers will be one of the determining factors in the length and severity of the food crisis in Africa and the displacement of rural populations already under pressure from climate change.” [39]

Fertilizer is the most important commodity for farmers. A system which puts the powers of this commodity in the hands of the farmers who need it most, will allow these farmers to prosper.

Livelihoods will improve, yields will increase, people will be lifted out of poverty.

This is the crazy future that I dream of, and I can’t wait till this future comes to life.

I’m Rachel, a 16 year old biotech lover, ultra runner and podcaster. Check out my other work and connect with me:

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Rachel Lee

I’m a 16 y/o biotech lover, podcaster and ultra runner using biotech to improve agricultural productivity in Africa.