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Chris Packham helps scientists unearth soil’s secret ‘DNA’ to mark Biology Week

24 September 2012

  • Soil 'DNA' could hold clues to growing better crops
  • Rapid advances in DNA sequencing paves the way for cutting edge soil sampling
Chris Packham collects a sample from his garden soil. Credit: BBSRC

Chris Packham collects a sample from his garden soil. Credit: BBSRC

Chris Packham is helping scientists to unlock the secrets of soil by unravelling its genetic fingerprint. His garden soil will have 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.

Samples of soils from Chris' garden, and the surrounding area in the New Forest, will be sequenced in under 1 week to reveal genetic data from the microbes they contain. The data will unearth which microorganisms are in the soil and what they do. This cutting edge soil analysis is only a reality due to the rapid speed at which genetic data can now be gathered. The technique 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.

The soil samples were collected by Chris Packham at his home in the New Forest in Hampshire and have been rapidly transported to The Genome Analysis Centre (TGAC) in Norwich where the sequencing process provides the genetic data in under a week. The data will then be analysed with results presented during Biology Week (13-19 October 2012). Chris took samples from different sites around his home, including the garden lawn, a dung heap and nearby woodland. TGAC scientists will extract, sequence and analyse the DNA and compare the different qualities of the different samples.

Chris Packham said: "I heard of the human genome project, and the recently released tomato genome, but the idea of decoding the genetic information of the bugs in my garden soil is astounding… and in just a matter of days! Soil is teeming with microscopic life, whether it's bacteria, fungi or invertebrates, and this new tool is a powerful way to study the tiny microbial worlds that are essential to life on earth. I can't wait to see what beneficial bugs are lurking in my back garden."

Professor Jane Rogers from TGAC said: "Obtaining genetic data from an organism used to be a laborious process but with the latest technology a project that would have taken years now takes just one week.

"Thanks to advances in DNA sequencing, whole genomes, the entirety of an organism's genetic information, can be sequenced in a matter of days - and it is getting faster. In the next few months, we will have the capability to sequence a genome the size of the human in 24 hours. This amazing capability has huge benefits for bioscience.

The sample of garden soil is ready to send to TGAC for high-speed DNA sequencing. Credit: BBSRC

The sample of garden soil is ready to send to TGAC for high-speed DNA sequencing.
Credit: BBSRC

"Rapid collection of genetic data is not only useful for studying individual organisms, we're also beginning to analyse genetic samples from environments, like a soil sample, so that researchers can better understand how the microorganisms within them work. This will provide a new way to monitor the effects of fertilisers and climate on soil and contribute to more sustainable agriculture for the world."

Looking at DNA on this broader scale is referred to as 'metagenomics' and will provide information that can help to decide how the soil should be managed and optimised. By analysing a soil sample scientists can discover the DNA sequences of the microorganism that it contains. Some of the sequences act as identification tags for different organisms or functions. Comparing these tags against a database identifies which organisms are in the soil and what they do. This cutting edge technique will use experimental analytical systems and new approaches to testing soil samples in a bid to improve our understanding of the bugs beneath our feet.

Considering the vital role that soil plays in cleaning our water, cleaning our air, and helping to produce our crops, these types of data are essential to help address major issues like food security and climate change. This approach could benefit farmers in the UK and across the world, as well as policymakers, conservationists and even gardeners.

This type of analysis has previously been too time consuming to use outside of large research projects but recent advances in technology have meant that genetic data can be returned very quickly, and the technology is getting faster still.

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."

Mark Downs, Chief Executive of the Society of Biology, said: "Biology Week will highlight the world-class bioscience that goes on in the UK - everything from neuroscience to dolphin science. This kind of soil science is cutting edge and also shows us how quickly we are improving DNA sequencing technology. The speed of sampling to results is simply mind blowing.

"At a human level the potential benefits are significant, helping us monitor health and change life styles to help ameliorate potential problems."

While unlocking the raw data is getting faster, the analysis and understanding still takes time. Scientists at TGAC will be analysing the results to deliver preliminary information in time for Biology Week.

About TGAC

The Genome Analysis Centre (TGAC) is a specialist in genomics and bioinformatics, focusing on the interpretation of DNA sequence data to enable and drive advances in food, health and environmental bioscience in research and industry.

TGAC receives strategic funding from BBSRC and is a centre of UK National Capability, committed to applying genomics knowledge to advance scientific knowledge and promote economic growth.

Advances in next-generation sequencing - TGAC currently deploys the latest advanced high-throughput sequencing for the UK bioscience community allowing whole genome analysis of bacteria in a day and larger genomes, e.g. human, in less than one week. The next technology will enable such larger genomes to be sequenced in approximately 24 hours, "Genome in a Day".

This new technology will be one of the most accurate next-generation sequencers offering unprecedented speed and flexibility while producing high quality data.

About Biology Week

The first ever Biology Week will take place on 13th-19th October, organised by the Society of Biology. Events around the country will give everyone the chance to learn about biology, the science of the 21st Century. A Biology Week launch event will take place in the Houses of Parliament on Wednesday 17th October. http://www.societyofbiology.org/biologyweek

About Society of Biology

The Society of Biology (www.societyofbiology.org) is a professional body for bioscientists - providing a single unified voice for biology: advising Government and influencing policy; advancing education and professional development; supporting their members, and engaging and encouraging public interest in the life sciences.

About BBSRC

BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.

Funded by Government, and with an annual budget of around £445M (2011-2012), we support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.

For more information about BBSRC, our science and our impact see: www.bbsrc.ac.uk.
For more information about BBSRC strategically funded institutes see: www.bbsrc.ac.uk/institutes.