Video transcript: How does Chris Packam's garden grow?

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October 2012

Metagenomics and the science of a healthy soil
In Chris Packham's garden…

Chris Packham, broadcaster, author and naturalist
This is the garden of the house that I rent here in the New Forest. It's a place that is very close to my heart. I've grown up here and I very much love the ecology of this area, particularly around my home - I've got tawny owls roosting behind the barn, I've fed foxes and badgers in the garden. But these animals are just the tip of an iceberg, the very tip of an extraordinary community. And what I'm really interested in today is looking at the more fundamental building blocks of that community, and they don't come any more fundamental than the soil. And I'm going to have the opportunity to look into this soil with a degree of detail that I could never of dreamt of when I was first understanding tawny owls, badgers and foxes. Because we're going to be able to take samples from this soil and look at the DNA of all of the creatures that live in it, particular to this very area. And that for me is tremendously exciting because without all of these creatures, without the flavour of those in my garden, you couldn't have everything else. It's brilliant, absolutely brilliant.

Video shows Chris Packham looking at soil in a mole hill in his garden.

Well the soil here looks perfect but I need to expand my area of expertise, so thankfully Matt's come down from the BBSRC with all the gear. What do we need then Matt?

Matt Goode, Head of External Relations, BBSRC
Hi Chris. Well, I think we need a shovel for taking the soil sample, but first of all I need to get you to put some gloves on so you don't contaminate the sample.

Chris Packham
We don't want human DNA coming out in the soil do we?

Video shows Chris and Matt putting on gloves and collecting soil samples from the mole hill.

Chris Packham
Ok, compost heap. Here we are. It's not so much of a compost heap in fact as the dung heap. We've been putting the dung from the horses here for about the last five years. Now, plants love nitrogen. It is that that really provides them with their needs for growth and this species, the nettle, is a nitrogen fiend, and you can see the effect that its had here - it's great for butterflies, which is why I'm keen to continue it. So, I imagine if we take a sample here we're going to find a whole forna of animals which are very keen on living in nitrogen-rich soils. Label this one up as dung heap, let's be more specific than compost heap.

Video shows Chris and Matt walking through woodland.

This is an old drove way that runs down here so most of the cattle, and lots of geese apparently, were taken for hundreds of years on this very route into market in Southampton. So we could take a sample here and it might have some ancient, ancient material here.

Video shows Chris taking another soil sample from the woodland.

Chris Packham
Here we are, here's the last sample. And true to scientific practice, this is now going to be rushed off to the lab and what's going to happen to it is quite unique because we're going to be sequencing the DNA of all of the organisms that live in here. That's why we call it metegenomics. Now you see, typically, if we take a soil sample we can culture a few bacteria species and other microorganisms that are in the soil but not all of them. So what this will tell us is a complete picture of what's living in this sample, in this patch of my woodland and it will be distinctly different I suppose to what we found in the mole hill and in our dung heap. And the applied application of this is just profound because if you know exactly what is living in the soil, then you can know exactly what is best to put into it, what is best to plant in it.

Video shows footage of a seed germinating beneath soil.

Video shows the soil samples arriving at The Genome Analysis Centre.

Dr Mario Caccamo, Head of Bioinformatics, The Genome Analysis Centre
We've now received three samples from Chris Packham's house, one from the forest, one from the compost heap and the third one is from the garden. What we're going to do now is sequence the samples and when we obtain the data from the sequencing machines we are going to analyse the data and compare. We want to learn what is present in one sample and missing in the other one to fully characterise these different soils.

Researcher inside the laboratory at The Genome Analysis Centre
Right, so I've got the soil samples here and we're going to begin by seeing if we can extract some DNA from them. So the first step is to add some of the soil sample to a tube containing some particles that will help break down the soil and release the DNA. So this is just to help start break down the cell walls of the DNA to release the DNA in the solution. We then go over to the vortex mixer. So this just helps the process along a little bit more.

Researcher inside the laboratory at The Genome Analysis Centre
We've received the soil and extracted the DNA. Now there is one more step before loading those samples on a high-seq sequencer. This is a machine which transports the DNA onto what we call a flow cell.

Video shows the flow cell.

Researcher inside the laboratory at The Genome Analysis Centre
Here we have our flow cell. The soil samples are on this flow cell. You can have one soil sample per lane. We have eight lanes, eight ports at this end and eight ports at that end, and it is like eight hollow tubes with the top and bottom surface, and on those surfaces is our DNA from the soil which is clustered on the flowcell. We're now going to proceed to the machine to load it onto the sequencer.

Dr Mario Caccamo, Head of Bioinformatics, The Genome Analysis Centre
To sequence these samples, we're going to use Illumina technology, that was the technology that is available in the UK. These technologies are new, we couldn't have done this ten, fifteen years ago. In order to be able to sequence these samples, before we had to culture the organisms there. Many organisms cannot be cultured. What we can do today, with this technology, is go directly to the environment, pick the samples, put them in the machines and get the information straight away.

Video shows research analysing sequencing results.

Next generation sequencing is going to give us information about the DNA that is present in those samples and tell us the DNA of the species in those samples. Now the next step is to look into those sequences and characterise them, classify them, and understand the different species that are in the samples.

Now, healthy soil will have certain species very active and species like, for example, help with nitrogen fixation which are key for crops. There will be poorer soils that will have less presence of this bacteria, these different organisms, and we want to learn more about that in order to deal with issues around better crops, crop improvements and being able to select the right soils for the right crops.

Video shows graph of phylum levels of soil samples.

Professor Jane Rogers, Director, The Genome Analysis Centre
We've analysed around 200 million pieces of DNA and in five out of the six samples, around 70-80% of the bacteria just come from two phyla and those are bacteria that tend to be associated with the roots of the plant and also breaking down organic matter in the soil. In one sample, the woodland sample, we do see a difference and that is in the proportion of bacteria that seem to be associated with acid soil and it is known that some types of woodland are associated with certain types of acid soil, so that maybe characteristic of the woodland from which this sample was taken.

Chris Packham
These results strike me as remarkable. When you think about it, it cost hundreds of millions of dollars to sequence the first human genome and now, in a couple of weeks by using next generation sequencing, we can identify all of the microorganisms living in this soil. And the applications of this technology are simply profound. When you think about it, farmers can make precise choices about the crops they put into their soil, food security, it goes on and on. And one thing is for sure, this technology is set to expand and improve and that is really exciting.



Biology Week 2012.

This video may be reproduced in its entirety with due credit to BBSRC.

All media copyright BBSRC except seed growth and fungi footage from scienephoto.com.

Music from cinephonix.com.