The answer to the problem of feeding the growing global population may be microscopic.

By Wendy Zukerman.

Feeding the world with microbacterial agriculture

An Australian wheat field.
Credit: Totajla

It was a remarkable affair. Early in Earth’s history, bacteria embedded itself deep inside certain cells, forming an intimate liaison that has lasted throughout time. The adventurous bacteria were safer in their new residence, and the cells got a very powerful source of energy. The bacteria could convert sunlight and carbon dioxide into sugar, hence providing their hosts with the power of photosynthesis. This partnership ultimately spawned the evolution of plants. Now scientists are looking to harness the intertwined evolutionary history between microbe and plant once more. They want to use it to help solve one of humanity’s greatest challenges.

It is predicted that by 2050 there will be nine billion people on Earth. To feed the growing masses we may need to boost agricultural yields by more than 70 per cent. But we’re running out of tools to help us.

Without sacrificing biodiversity, there’s little new arable land left. Water resources are limited. Plant diseases and weeds are slowly becoming resistant to pesticides. And in the developed world, we can’t dump any more fertiliser on our plants – rather than producing more food, the phosphorus and nitrogen is leaching into groundwater. Rising salinity, soil erosion and extreme weather will make the task of producing food ever more difficult.

To stave off hunger, scientists – along with the multibillion-dollar agriculture industry – are looking to exploit the very life forms that gave us plants. An interesting array of bacteria, as well as fungi and viruses, has recently been discovered living in, on and around plants. Collectively known as the plant microbiome, these beasties provide plants with nutrients, kill diseases and even pump out hormones spurring crops to grow. After decades of killing bugs through pesticides and fungicides, we are coming to understand we need them. Forget the green revolution – microbiologists are starting a microbial revolution.

In 2013, an ambitious report entitled “How Microbes Can Help Feed the World”, written by the American Academy of Microbiology, argued that the microbiome was a largely untapped resource that could fuel a new wave of agriculture. They set a goal to increase agricultural output by 20 per cent in 20 years, using 20 per cent less fertiliser. Could microscopic bugs really achieve this feat?

Farmers have known for some time that certain bacteria and fungi help plants grow. Perhaps most famously, bacteria colonising the root of legumes can fix nitrogen, so converting unusable gaseous nitrogen into a form plants can feed on. Before there was an industrial way to fix nitrogen, much of our agriculture depended on these tiny microbes. Similarly, it’s well known that microscopic fungi partner up with plant roots, fashioning long threads that reach deep into the soil to help plants access nutrients, minerals and water. But, according to Keith Clay, a professor of biology at Indiana University, this is “the tip of the iceberg – there’s another world out there”.

New technology has changed the game here. In a gram of soil there are about 10 billion bacterial cells, with up to 10,000 different species of bacteria. Until relatively recently, we could only study a fraction of these bugs – the few that would grow on laboratory culture. This meant that entire families of life, such as fungi that live inside plant cells, were invisible to scientific understanding. Clay says these bacteria are critical to plant health “and almost none of these have been isolated or described”.

Rather than futzing around with agar plates, scientists now analyse microbes through their genes. “DNA technology has meant that we can move forward in this world,” says Ian Anderson, a professor of molecular ecology at Western Sydney University. “Having the whole genome sequence tells us what that organism does and what it has in its arsenal to survive.”

Through these experiments scientists have found an incredible connection between plants and their microbes. Plants ooze “come hither” chemicals to attract beneficial microbes. “They’re basically saying, ‘It’s really nice over here, come live with me,’ ” says Dr Cathryn O’Sullivan at the CSIRO. Arabidopsis plants, for example, secrete an acid to recruit probiotics that help them fight infections. Exploiting this relationship is hoped to reduce the need for pesticides in agriculture. Small experiments have already found that inoculating crops, such as rice, with the right bacteria could protect them from disease.

Meanwhile, other bacteria can boost agricultural output. Pseudomonas, which live in the soil around a plant, make hormones goading roots to grow. In one trial, inoculating wheat with a cocktail of these bugs over two years increased yields by more than 30 per cent. Another bacteria, Burkholderia, has been shown to ramp up rice production. O’Sullivan wants to use these plant steroids to inspire crops to grow during drought. “There is a lot of potential here,” she says.

And in the furiously hot soils of Yellowstone National Park, where temperatures reach 70 degrees Celsius, one hardy plant survives: panic grass. This super power comes from a curious ménage à trois between a fungus, which has infected the grass, and a virus living inside the fungus. It’s believed that the two organisms work in cahoots to flick on a stress response in the plants, enabling them to live in the toxic heat. Researchers are looking to exploit this threesome to grow crops in extreme environments, perhaps by inoculating corn and rice with the microbes.

With the right cocktail of bugs, we may be able to use less fertiliser, such as phosphorus and nitrogen. Plants need these elements to grow, but there is a limit to how much of the stuff we can chuck onto crops. Phosphorus, for example, reacts with iron, aluminium and calcium in soils, rendering it solid and hence largely useless to plants. Certain strains of bacteria and fungi can pump out enzymes that turn phosphorus into a soluble form that crops can use. Already, glasshouse experiments have found that tomato and wheat that are infected with particular concoctions of bacteria need less fertiliser to produce the same yield.

Unravelling and exploiting this hitherto invisible world of microbes is expected to soon become big business. Already, Novozymes – a company that develops microbial fertilisers and pesticides – sells a strain of the fungus Penicillium bilaii under the banner JumpStart, which the company says helps the plant to use phosphate from soil. Agribusiness giant Monsanto, which calls the microbial space a “new opportunity”, recently aligned with Novozymes. Last year, the alliance announced it was already in the midst of conducting research in 170,000 field trial plots across the United States, a figure it expects to more than double next season. Bayer, Syngenta and DuPont are also in the microbial game.

The tricky thing will be taking these small, but promising, experiments into the farmyard around the globe. “There is a big step from the pot to the field,” says O’Sullivan. “You have to make sure that it’s safe.” After all, bacteria that are beneficial in controlled quantities in a pot could turn bad if they dominate their new environment. Mass producing microbes and shipping them internationally may also prove to be problematic and unsafe.

And there’s another concern. We are uncovering a new ecosystem here, one whose complexity has been compared to the complex food web of herbivores, predators, scavengers, plants and pollinators that sits above the ground. Introducing a new cocktail of microbes into a world we don’t fully understand may be unwise. On the other hand, we’ve probably fouled much of this minuscule community with fertilisers and pesticides already. And soon, as a species, we’ll be getting hungry.

This article was first published in the print edition of The Saturday Paper on Sep 19, 2015 as "Yield of dreams".

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Wendy Zukerman is a science journalist and host of the Science Vs. podcast.