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Chris Packham helps test cutting-edge soil sampling

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17 October 2012

Chris Packham is helping scientists to unlock the secrets of soil by unravelling its genetic fingerprint. His garden soil has had its 'DNA' sequenced in a race against the clock, to highlight both the rapid advances in DNA sequencing technology and its expanding range of uses in biological science..


Chris Packham's soil metagenomics: Biology Week 2012  

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The data unearthed which microorganisms are in the soil and what they do. This cutting edge soil analysis, known as 'metagenomics', is still in its infancy but could offer great benefits for agriculture, helping us to understand how soil works, how climate and farming can affect soil systems, and how to ensure productivity and sustainability.

Read more about the how Chris' soil was tested here:

The results

DNA was extracted from soil samples collected from five sites surrounding Chris Packham's home in Hampshire (a compost heap, mole hill, woodland, pot plant and vegetable patch) and a sixth from the John Innes Centre farm site in Norfolk.

To enable a deep exploration of the bacterial diversity, each sample was subjected to high throughput sequencing at The Genome Analysis Centre, in Norwich, which generated 150 to 200 million reads per sample and in excess of 1 billion reads in total (1,099,280,466 reads).

Over 400 bacterial or archaea genera were classified from the six soil samples. Archaea are a group of single-celled microorganisms that are now recognized as a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle.

Commenting on the results, Chris Packham said: "The diversity of organisms found emphasises the rich and complex nature of soil environments and the power of metegenomics to gain insight into the microorganisms present - even the ones at low abundance. This is a powerful tool for helping us understand soil ecosystems and it could offer big benefits for farmers and gardeners."

The sample of garden soil is ready to send to TGAC for high-speed DNA sequencing. Credit: BBSRC
Chris Packham collects a sample from his garden soil. Credit: BBSRC

Taxonomic profiling identified that Proteobacteria (which includes many of the bacteria responsible for nitrogen fixation) and Actinobacteria (which play an important role in decomposition of organic materials) were the dominant bacterial phyla in five of the six samples accounting for ~50% and ~25% respectively of the classified sequences.

The woodland sample contained, in addition to Proteobacteria (39%) and Actinobacteria (24%), high levels of Acidobacteria (28%), which are known to be associated with low pH soils.

The bacterial diversity in the compost heap and vegetable patch appeared quite similar, and may be due to the compost content of the vegetable patch.

In the pot plant, around 80% of the bacterial life appears to be made up of just three classes. This could be due lack of exposure to the outside world. A lot of potting composts are also sterilised which reduces the diversity of organisms by killing those susceptible to the sterilisation process. Also, potting composts usually contain very little soil and may thus have reduced diversity due to their input material.

The differences seen at the mole hill site could be due to the soil originating from a greater depth in the ground before excavation.

Further work to assess the extent of similarity between the taxonomic and functional properties of the samples is ongoing.

Professor Douglas Kell, the Biotechnology and Biological Sciences Research Council (BBSRC) Chief Executive, said: "The advent of genome-in-a-day technology offers extraordinary opportunities as we unravel genetic data at speeds never thought possible. Add this to the new sciences of metagenomics and we can begin to understand much more about entire communities of microbes that are key to life on earth.

"These new tools offer potentially huge benefits for future agriculture, for example, and will help us understand more about soils and the many microbes that keep crops and soils healthy and productive. It opens the doors for quick and efficient soil analysis at a genetic level."


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