The microbial community

The soil is teeming with life, but most of it is so small that we can’t see it. Combined with that, it’s hidden underground, so it presents us with a lot of challenges in looking at life in the soil. Dr. Emma Sayer is lecturer in ecology at Lancaster University. She has expertise in microbial communities and how we measure them. We’ve come here to a long term experiment at Buxton in the Peak District in northern England to talk to her about how she measures the microbial communities here and what the effects are of climate change. Emma, what would the microbial community be like here? Well, it’s quite hard to say. We know that microbial communities in the soil are incredibly diverse.

So if you just look down at one of your footprints in the snow there, then that area covers about 10 trillion microorganisms in the soil. So the diversity of microbes in the soil is really immense. And it’s quite a problem to measure this type of diversity, especially because we don’t really know what a lot of these organisms are. We don’t really have a good definition of what a species is for bacteria, for example. So the soil communities are incredibly diverse, but we don’t really know that much about them. We have really high plant diversity on these quite nutrient poor old soils, and we would expect the microbial community to sort of perhaps mirror the plant diversity.

So we have really diverse communities that are related to the different types of plants that we see in this vegetation. We have this climate change experiment behind us set up and run by Sheffield University by professor Phil Grime. Can you tell me about that? Well this is the longest running climate change experiment in the UK. It was set up in 1993, and it’s been running ever since. And over here you can see these strange metal structures. And some of them are covered with rain out shelters, so plastic roofs. And they close automatically when it starts raining. So those are summer drought treatments.

And then we also have winter warming treatments, heating cables that are buried in the soil and warm the soil during winter. And there are also irrigation treatments. And then there are several combinations. So we have irrigation and heating, and drought and heating as well. And I assume that the climate manipulations that they have here are in line with climate projections then? Yes. So you wouldn’t expect any really, really extreme changes over the long term. And this is why we’ve got summer drought and winter warming, because you wouldn’t really expect very dry winters or very hot summers, because we are in the UK after all.

And you’ve been doing work here on the microbial communities and how they’re responding to the climate change? Yes. So we’ve seen some very large changes in the community structure in the soil. So that’s bacteria and fungi. And they do seem to be responding quite strongly to the climate change treatments, especially the drought treatments. So these DNA techniques that you’re using to look at the microbial community are quite complex and rather expensive. Why is it so important to look at? Well microbial processes in the soil actually underpin or drive an awful lot of really important ecosystem functions.

So if you just think about the decomposition cycle or the brown food web, as some people like to call it, where plants grow and they produce plant material that dies off and returns to the soil. And then that’s broken down by soil organisms. And the microbes mineralise carbon and nutrients. So they take the organic matter and they turn it back into inorganic forms that plants can use. So for carbon, some of the carbon is released as CO2, as carbon dioxide, as the microbes respire, just like we do. But the nutrients that they mineralise are basically converted back into a form that plants can use and recycle.

Plants can take up the nutrients again, and that’s actually really important to a site like Buxton that has very infertile soils. And these functions that the microbial community is providing, does that provide you with some ways to measure what’s going on? Yes. So we’re going to be doing a lot of measurements of carbon dioxide, CO2. So we can use that as a measure or a proxy for microbial activity in the soil. We’re also going to be measuring decomposition processes using just little litter bags and little mesh bags that we can bury in the soil and look at how much weight of this litter is lost over time. That’s also a microbial activity.

And then we’re also going to be looking at enzyme activities in the soil. And we’re going to be doing that back in the lab. And how do you measure the enzymes? Why are they important? The enzymes give you a really nice direct measure of function. So a lot of microorganisms but also plants produce enzymes in response to resources in the soil. So this can be different forms of carbon, but also different nutrients. And for example for carbon, if you provide soil microbial communities with a nice, tasty carbon source, they will start producing enzymes to break that down so that they can use the carbon as an energy source in the soil. And how are you measuring that?

Well, we’re doing this back in the lab. You can’t really do it in the fields, because what we do is take small soil samples and we add a substrate to the soil– so something that we know these enzymes can use. And we label that substrate with a fluorescent marker. And then the measure of activity is directly related to the intensity of the fluorescence that we measure in that sample. Well thank you very much. It’s been interesting to hear about the microbial community. Thank you.