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Could advanced microbes really replace artificial fertilizer?

July 31, 2018

The emergence of synthetic biology offers the potential to engineer microbes to help us grow crops without the need for artificial fertilizer.

We are all more than just a single being. In fact, our bodies contain more bacteria than human cells. A cornucopia of microscopic organisms live both on and inside us, providing vital services that are essential for our survival.

This is, of course, not a uniquely human quality – all animals and plants share their existence with a similar multitude of microorganisms. This ecological community of interdependent organic entities is called a microbiome.

Some plants, such as soybeans, have microbiomes that include special bacteria, usually living in their roots that can take the nitrogen from the air and convert it into essential nutrients necessary for their host to grow. Most living organisms, however, have not evolved with this ability.

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Why farms need fertilizer – for now…

Almost 80% of Earth’s atmosphere is nitrogen but for the majority of plants and animals, it is unusable in this form. Most plants get the nitrogen they need to grow from substances in the soil, and animals by eating those plants (or other animals).

This creates a challenge for farmers around the world. To meet the ever-growing demand for food, farmers need to use synthetic fertilizers to top up the supply of nitrogen and other nutrients in the soil so they can continue to grow and harvest crops to meet the world’s food needs.

“Synthetic nitrogen fertilizers are absolutely critical to growers worldwide, and are probably used on 90% of agricultural production,” says Mike Miille, chief executive of Joyn Bio, a new joint venture between Bayer and Ginkgo Bioworks. “If you took that away then you would see production of these crops drop to very low levels – or possibly cease altogether –because they simply wouldn’t have the nutritional intake they need to grow.”

So important are artificial fertilizers to sustaining global agriculture, it is estimated that almost half the world’s human population exists because of them. That's about 3.6 billion people currently on earth that have artificial fertilizers to thank for their existence.

But this comes at a price.

The process of converting nitrogen gas from the atmosphere into nitrate compounds, the Haber-Bosch process, is costly and very energy intensive. It consumes 1-2% of the world’s energy supply and about 3% of global natural gas production. It is also responsible for about 3% of all CO2 emissions. Synthetic fertilizer also cannot be dosed precisely – and the excess run off is damaging to the environment.

“Synthetic fertilizers have a lot of benefits, but also a lot of consequences to their use,” says Maya Almaraz, post-doctoral research fellow at the University of California Davis. “When we apply nitrogen fertilizers to crops only about half the nitrogen that we use goes into the crops that we eat and the other half is often lost to the environment.”   

So is there a way to cut the use of nitrogen fertilizer by mimicking the microbes that help fulfil some plants’ nitrogen needs?

"By using these beneficial microbes, we hope to reduce the impact on the environment and offer the grower the chance to be more sustainable both economically and environmentally."

– Mike Miille, CEO of Joyn Bio

Building microbiomes

Over the past decade, the cost and time it takes to analyze, sequence and edit DNA has fallen precipitously. This has helped give rise to a new industry, one that seeks to program cells like a computer scientist would program a computer – synthetic biology.

“Biology runs on digital code in the form of DNA. In every organism – you, me, the plants outside – there is a code that can be read out that tells that organism the things that it can do. Fundamentally what Ginkgo does is make changes to that code to allow cells to do new things,” says Jason Kelly, co-founder and CEO of Ginkgo Bioworks.

This ability to enable microscopic organisms to do new things is at the center of Joyn Bio’s mission to develop a sustainable alternative to synthetic nitrogen fertilizer.

This new joint venture is focusing on analyzing the beneficial microbes that already fix nitrogen from the air for plants such as soybeans and peanuts to understand the genes and pathways involved. The intention is to find ways to create similar microbes to help crops like corn, wheat and rice extract nitrogen from the air, radically reducing the need for synthetic fertilizer.

“At the crux of what we are trying to do is use microbes to significantly reduce the amount of fertilizer that growers need to put out there,” says Miille. “By using these beneficial microbes, we hope to reduce the impact on the environment and offer the grower the chance to be more sustainable both economically and environmentally.”

If this new company is successful, then just as people take probiotics to improve their gut health, our major crops could soon well be benefitting from similarly ‘friendly’ microbes. And in doing so help meet our growing demands for food in a more environmentally sustainable way.

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