Many of my current research projects are focused on the dirt that makes the world go round. No, not the kind that a paparazzi photographer or gossip columnist would be interested in.
I am talking about soil. And I am particularly interested in the microbial communities living in soil.
Why Many Soil Microorganisms are Undiscovered Stars
Soil microorganisms are vitally important to all life on Earth. It plays central roles in processes like soil fertility, carbon cycling and nutrient cycling. They also certain to harbor novel enzymes that could be useful in everything from cleaning up pollution to synthesizing new fuels.
But despite this, we know very little about soil and it’s prokaryotic inhabitants. Although soil is estimated to contain 1,000 Gbp of microbial genome sequences per gram of soil (!), less than 0.5% of soil microorganisms have been grown in the lab and only a small portion of those have been sequenced.
Uncovering The Secrets of Soil Microorganisms
That’s why we should be rolling out the red carpet for the TerraGenome Consortium, a group of pioneers who are proposing that soil be the focus of a new global metagenomic sequencing initiative.
Metagenomic research has exploded in the last several years with the advent of next generation sequencing.
The capacity to know the exact biological content of every sample on earth is, with a lot of effort, possible. For example, large groups of scientists are focused on the human microbiome, sequencing the bacterial populations living in every crevice of the human body.
The TerraGenome Consortium aims to apply this knowhow to uncover the secret life of dirt, to deepen our understand of soil, it’s microbes and their genetic content.
Last week at ASM I had a chance to share a bottle of wine with the President of the TerraGenome Consortium, Pascal Simonet and Chair of the Communications Committee, Tim Vogel. It was a fascinating discussion about the goals of the organization, and what they need to achieve them.
Park Grass: Home of the Stars (or some of them at least)
The source of the soil has been chosen: Park Grass, Rothamsted, United Kingdom.
Information on this patch of land has been studied and the chemistry of the soil has been collected and recorded over the last 150 years. This is important because the microbial communities may be greatly influenced by factors such as pH, nitrogen content, phosphorus content, and neighboring plant life.
All of this information needs to be recorded as part of the metagenomic analysis of soils collected from any site. The chosen soil is a perfect starting point for achieving the first ever complete genetic profile of a soil. For a wonderful gallery of photos showing Park Grass and some of the work done there over the last 1.5 centuries, click here.
These Microbes Need You
But this vital effort needs your help. Prof. Vogel explained that what they need right now are researchers who are keen to get involved, to write grants and carry out pieces of the work.
The process involves extracting the DNA from soil samples then producing fosmid libraries to create a collection of clones that researchers can use in the future.
These fosmids will be sequenced using Sanger method (or next generation sequencing methods) and every genomic fragment from the soil will be stored and available for further studies.
In addition to the fosmid libraries, next generation sequencing will be performed on the isolated DNA. Scientists will need to have grant funding because of the typically large expense of this technique.
The final analysis and bioinformatics is another area where the team is going to need expertise and help. All of this data needs to be assembled and organized at one site.
The end result of this world wide effort will be a better understanding of the microbial communities that inhabit earth and what they tell us about the health of the planet and our environment.
Understanding the microorganisms in the soils around the world and at different times of the year will enable further studies on how to keep soils healthy for sustaining life for all species, including humans, even paparazzi photographers.
With the work of the TerraGenome consortium and its dedicated environmental scientists, soil will soon no longer be a black box. It will be a key to understanding what our earth needs to be happy and healthy.
Researchers are invited to join the TerraGenome Consortium. For more information, go to www.terragenome.org or read this recent editorial from the April 2009 issue of Nature Reviews Microbiology. In addition, a TerraGenome Workshop will be held at the BAGECO conference June 14-15 in Sweden. This conference will serve to bring together team leaders to discuss the key issues around the data generation, analysis, and sharing. Which sequencing platforms to use for the metagenomics portion of the study will be an area of focused discussion. Sponsorship of the BAGECO conference is still available for companies that wish to highlight their products value to the members of the consortium. Contact Janet Jansson (email@example.com) for sponsorship inquires.