Unearthing the soil's microbiome

What lives in the soil?
16 June 2020

Interview with 

Jacob Malone, John Innes Centre, Norwich


Hands holding soil


Before we start tunneling into the planet though, let’s first consider what’s directly beneath our feet. Across most of the Earth’s surface, that’s soil, which sustains the plants and trees we see growing everywhere. But invisible to the naked eye, and buried within the soil itself, is an enormous community of microbes, without which most things could not grow. Jake Malone is from the John Innes Centre in Norwich, and he spoke to Katie Haylor...

Jacob - I guess soil is a mix of two main things. One of these is minerals: things like clay or sand or stones. But the other very important part is decomposed organic matter. So it's mainly plant matter which has decayed. But what we're really interested in - or at least my lab is really interested in - within the soil are all of the different microorganisms that live there. As well as tiny insects and worms and things like that, you'll also find thousands of different species of fungus and bacteria. They're all interacting and fighting with one another and communicating with one another. And that's what gives soil its really special characteristics.

Katie - The soil has a microbiome, just like we have a microbiome then?

Jacob - Yeah, that's true. There are thousands of different species of fungi, and bacteria, and other microorganisms which live in the soil. And they're all competing with one another, and communicating, and interacting with other things in the soil like plants. So what you'll find is soil pathogens, for example, fungi and bacteria that will try and kill plants; but you'll also find bacteria that will fight them off, or fungi that will fight them off, and try and protect the plants in order to benefit from having it in the soil. And you find some interesting types of bugs, like symbiotic bacteria such as rhizobia or arbuscular mycorrhizal fungi, which are a type of fungus which provides nutrients to plants exchange for carbon, which comes from the plant roots.

Katie - So it's a trade-off, then? There's a relationship going on here.

Jacob - Absolutely, yeah. What you find is that most plants will secrete a large amount of their fixed carbon - so the carbon that they take from the air as carbon dioxide - they secrete that into the surrounding soil. And the reason they do this is to attract these microorganisms, which will benefit them. In the case of the symbiotic microorganisms like rhizobium or these mycorrhizal fungi, they will be providing something that the plants can't get easily, such as fixed nitrogen or fixed phosphorus, things like that. And in return they will be taking sugars directly from the plant roots. The plants, I should say, don't normally want to do this. They'll do it if it's advantageous to them. But if you have a farming system and you supply, for example, a lot of nitrogen or lots of phosphorus to the soil artificially, then the plants will actually suppress the relationship with the microorganism, and they'll say, "okay, I don't want to do this, it's costly for me, and I don't need to because I have this fertiliser". So the plants are quite clever in that respect.

Katie - In general, how are our soils doing? Do we have enough soil to grow the amount of food that we need?

Jacob - That's a good question. We don't have enough soil in Britain. About... I should say about 70% of the soil in Britain is currently used for agriculture.

Katie - Wow. 70% - that sounds like quite a lot.

Jacob - It is a lot, yeah. Apart from some areas of upland and some forests, and about 10% of built over land, most of England certainly is given over to farmland. That doesn't provide enough food to feed everyone; and I should also say that, certainly in recent years, the quality of soil has been degrading. The reason for this is intensification of agriculture. And this has led to things like the compaction of soil, from driving large tractors and other vehicles over it; soil erosion from removing hedgerows and other landscape features that prevent erosion; and also the contamination of soil, for example with microplastics or with chemicals. The addition of things like phosphorus and nitrogen to the soil has also degraded it to some extent.

Katie - What can be done about that? Because it doesn't really sound that sustainable. Is that a fair thing to say?

Jacob - I think it is a fair thing to say. Although there is a lot we can do. I think one of the absolute best things we could do is more sustainable land management going forward. So for example, if you plant trees around the sides of fields, it's been shown to reduce erosion and also to increase crop yields within those fields. And a lot of what we're doing - a lot of what we're trying to study at John Innes and elsewhere - is how we can intelligently manage and sustainably manage farming practices going forward. And I tend to be an optimist. I think we're learning a huge amount. And I think people are a lot more aware these days of the importance of soil, and the importance of keeping and managing soil sustainably.

Katie - So on that then... how do scientists like yourself study the microbes in the soil in order for us to make - if we're talking about, say, crops - as much food as sustainably as possible, where do the microbes come in?

Jacob - Well we're studying microbes in lots of different contexts. For example we might look at what microbes are present in a field, or we might look at what do those microbes do. We can look at what proportion of... for example, what proportion of a particular type of microbe is present; and what does it do, what molecules does it produce, is it good for a plant or bad for a plant. And we can also study - and we are studying - how different plants interact with these microbes. So what molecules are they putting out to attract to the bugs, which bugs do they attract, how important is this, and how does that interact with different soil types to lead to sustained plant growth.


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