Video transcript: Chris Packham's soil metagenomics: Biology Week 2012

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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, you couldn't have everything else.

Video shows Chris taking a 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. 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 researcher in the laboratory 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 garden, from different places, different sites in the garden. Now what we want to do is to sequence directly the samples and obtain information about the species and organisms that are really alive in that soil. 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 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.

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

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