Microbes: Starting in the soil

15 January 2019

Interview with

Giles Oldroyd, University of Cambridge


Hands holding soil


We’re beginning our microbial journey in the soil. Soil isn’t just a source of water and minerals for plants; it’s a whole ecosystem teeming with microscopic life. And some of these microbes form special relationships with plants that enable them to grow in places - and produce yields - they otherwise couldn’t. These include so-called nitrogen-fixing bacteria.

These bacteria can grab nitrogen from the air and turn it into a form that works as a fertiliser. But only some plants have the genes that enable them to team up with these microbes so they can benefit from this effect. So scientists at Cambridge University’s Sainsbury Laboratory are exploring whether they can move the genes from plants like peas, which can do this, into plants like barley that currently can’t so we can reduce the amount of fertiliser these crops need. Hannah Laeverenz Schlogelhofer went armed with a shovel to meet Giles Oldroyd to find out how...

Giles - I'm going to dig up this plant that's just growing. You can see the roots that havegrown down into the soil and this is the interface where the plants are forming these beneficial associations with microorganisms. In this handful of soil there's gonna be billions of bacteria. It's a very very rich environment for microorganisms. There's lots of fungi, lots of bacteria, a lot of them are saprophyds - they’re just living off the decomposition of the soil. But some of those microorganisms are very specialised to associate with plants.

Hannah - Microorganisms can feed plants two essential nutrients. Fungi can provide phosphates and bacteria can provide nitrogen. A special group of bacteria called Rhizobia have the ability to turn nitrogen from the air into ammonia

Giles - Only a few species of plants - the legumes, that’s peas and beans - associate with nitrogen fixing bacteria and the plant roots grow down into the soil. They find the bacteria that are living in the soil and then attract those bacteria into their roots and the bacteria colonise the roots of the plant and then do the nitrogen fixation inside the roots of the plant.

Hannah -  In agriculture, rather than relying on bacteria in the soil, fertilisers are used to provide crops with the nitrogen they need. But fertilisers are used in huge quantities and have major environmental impacts...

Giles -  It washes into our rivers and streams and oceans and seas and causes major problems to biodiversity and aquatic systems. It also results in a lot of nitrogen pollution in the atmosphere. When you spray the soils with these nitrogenous fertilisers some of it is converted to gaseous forms of nitrogen, called nitrous oxide, and they're incredibly potent greenhouse gases. They’re about 35 times more potent as a greenhouse gas than carbon dioxide. Agriculture in total accounts for about 30 percent of greenhouse gas emissions globally and a lot of that is coming from nitrogenous fertiliser application.

If we can reduce that amount of nitrogen fertilisers that are applied then we address the problems with water pollution but we can also address some of the greenhouse gas emissions from agriculture. There's a huge potential here to bring the power of soil microorganisms into agriculture for the acquisition of nitrogen and phosphorus

Hannah - Only legumes can form associations with nitrogen fixing bacteria. However by transferring this ability to other plants, this might change in the future. Specific genes can be isolated and taken out of legume plants, like peas. Once isolated a naturally occurring process called bacterial gene transfer is used to put the genes from legumes into barley.

Giles - We have those engineered barley plants. We're just in the process of working out which plants express those genes well and then we're testing all the effects of having transferred those genes into barley and so in two years time, if you come back to me, I hope I have a much better answer as to what the implications of this engineering is.

Hannah - We then slipped on some lab coats and went to take a look at these genetically engineered barley plants.

Giles - We're now down in the bowels of the Sainsbury lab where we grow all the plants and these are genetically modified plants. We have to do it in a very tightly controlled environment so  there's no escape of seed from any of this environment.

We can go into the growth room now and you can see there is a lot of barley plants growing here. So these are genetically modified plants that are carrying some of these genes from peas that we hope will transfer this nitrogen fixing symbiosis.

Hannah - And they just look like normal barley plants.

Giles - Yup. So that they're very normal barley plants, they behave just like a normal barley plant. They're just carrying a few extra genes from peas that will affect how they associate with the bacteria in the soil.

Hannah - Why is it really noisy in here?

Giles - It’s so noisy simply because we have to control the heat. So we've got a lot of airflow moving in here.

Hannah - Is that what’s spraying in from the ceiling?

Giles - The spraying in is just controlling humidity. We're trying to create the optimal environment for these barley plants to grow by doing so using lights and humidity and air control.

Hannah -  To escape the noise and humidity we headed back to Giles's office. The genetically engineered plants hold huge potential to reduce our reliance on fertilisers and harness the nitrogen fixing abilities of microbes. But when will the crop be ready to grow in the field?

Giles - It is very hard for me to put a timeframe on it because if we're right in our assumptions right now, then it’s actually very few genes, then I would say there's probably a 10 year window but we are working with the unknown. It's the nature of science, there are no guarantees.

Hannah - And like with any new technology potential safety concerns also need to be considered.

Giles - Right now we don't have those crops right. So we don't have the ability to test the safety concerns but it is something that we have to definitely consider. It would be a major trait that you're putting into cereals. And so we'd have to consider the safety implications for both the environment and for human health. But I think that right now the potential of this technology, particularly the potential of the technology to reduce agricultural pollution, is so great that we really have to crack on and do it. Acknowledging that those risks exist and doing what we can to mitigate those risks


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