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| Heidelberg,
Thursday 21 April 2005 |
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Whale bones and farm soil Sequencing biodiversity |
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![EMBL researchers Dr. Christian von Mering [back], Dr. Peer Bork [front]](../../../../../images/press/press05/press21apr05s.jpg) |
| EMBL researchers Dr. Christian von Mering [back], Dr. Peer Bork [front] |
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Press
Release 21 April 2005 [PDF]
[Deutsch]
Scientists use metagenomics to characterize the invisible life in various environments Instead of sequencing the
genome of one organism, why not sequence a drop of sea
water, a gram of farm soil or even a sunken whale
skeleton? Scientists at the European Molecular Biology
Laboratory [EMBL] in Heidelberg and their US
collaborators have done just that, and the result is a new
appreciation for the rich diversity of life that exists in the
most unlikely places [Science, April 22, 2005].
Bacteria make up the greatest mass of life on earth
by far and play a crucial role in the lives of all
other organisms. But scientists have only touched
the tip of the iceberg when it comes to identifying
bacteria – 99% of species cannot be grown
by standard techniques in the laboratory. The emerging
field of 'metagenomics' is rapidly giving researchers
a view of how diverse microbial life really is.
Instead of analyzing the genome of a specific organism,
scientists sequence the DNA from environmental samples
such as the ocean or soil. For the first time, this
gives them a clear picture of the diversity of life
in these habitats.
"These studies were simply not possible before," says
Peer Bork, the EMBL scientist responsible for the data
analysis in the project. "And future applications for this
type of technology are endless, from giving farmers
insight into their soil to fighting bacterial contamination in
hospitals to characterizing microbes in a patient's mouth."
In the current study, Bork worked with EMBL scientist
Christian von Mering and US collaborators to analyze two
very different samples: whale skeletons from the bottom
of the ocean floor and soil from a farm in the USA. Sunken
whale skeletons are a lipid-rich nutrient source that can
foster the growth of a flourishing ecosystem that contains
specialized bacteria, whereas soil is an example of a
complex microbial environment that can contain more
than 3000 distinct species [most of them bacterial] in a
half-gram sample.
The scientists started by sequencing hundreds of
thousands of genes from each sample Æ the DNA
equivalent of about 50 complete bacterial genomes. This
data was then complemented by two recently published
data sets from studies on surface water and on acidic
underground mine water, enabling for the first time a
comparative study of life in four different habitats.
From the genes in each environmental sample, scientists
constructed a 'functional fingerprint' of each habitat.
These fingerprints revealed that the way in which each
bacterial community had adapted to different
environmental conditions was reflected in its genetic
material. Different classes of genes were found to be
specifically enriched in each environment, for example
enzymes that break down plant material in the soil sample
or photosynthetic genes in the surface water. Apart from
known genes, the scientists also found many new
environment-specific genes whose function was not
previously known. Often, they could predict their broad
functional class from the gene's location in the DNA
fragment. In soil, for example, many novel genes were
predicted to be involved in DNA repair and in the
biosynthesis of antibiotics.
"Although only a limited number of pieces of the puzzle
have been revealed through the many thousands of
fragments of DNA from different organisms, they are
sufficient to capture differences between the communities
from genome sizes to lifestyle," Bork says.
This type of approach could provide more information
on environments about which little is known –
permitting estimates of the nutrient supply in the
soil or pollution levels in the sea. The data may
also be used as the starting point for estimating
the total number of species on earth, as well as
the number of cellular processes that make life
so complex.
Source article
Comparative metagenomics of microbial communities
S. Tringe, C. von Mering, A. Kobayashi, A. Salamov, K. Chen, H. Change, M. Podar, J. Short, E. Mathur, J. Detter, P. Bork, P. Hugenholtz, E. Rubin
Science. April 22, 2005.
For copies, please contact the AAAS Office of Public
Programs
Tel: +1 202 326 6440, E-mail: scipak@aaas.org.
Press Contact
Trista Dawson
EMBL Press Officer, European Molecular Biology Laboratory,
Meyerhofstrasse 1, 69117 Heidelberg, Germany
Tel: +49 [0] 6221 3878452
E-mail: trista.dawson@embl.de |
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