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| Heidelberg, 2 February 2007 |
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| Investigating the invisible life in our environment
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Researchers Peer Bork and Christian von Mering at EMBL Heidelberg. |
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A new comparative metagenomics method provides insights into the
evolution of the smallest beings on Earth
Press
Release 2 February 2007 [PDF]
Microorganisms make up more
than a third of the Earth's biomass. They are found in water, on
land and even in our bodies, recycling nutrients, influencing the
planet's climate or causing diseases. Still, we know surprisingly
little about the smallest beings that colonise Earth. A new computational
method to analyse environmental DNA samples, developed
by researchers at the European Molecular Biology
Laboratory [EMBL] in Heidelberg, now sheds light on the microbial
composition of different habitats, from soil to water. The
study, which will be published in this week's online issue of the
journal Science, also reveals that microbes evolve faster in some
environments than in others and that they rather rarely change
their habitat preferences over time.
Studying microorganisms has proven very difficult in the past,
because most naturally occurring types do not grow in the lab.
The rapidly growing field of environmental DNA sequencing,
called metagenomics, now helps to overcome this problem.
Instead of analysing the genome of a specific organism, scientists
sequence all the DNA they find in environmental samples, ranging
from seawater to soil. They collect vast amounts of sequence
fragments, which contain genetic information of thousands of
species forming communities that colonise a certain habitat.
"We have developed a new and very precise method to classify the
microbial communities that are present in a given sample,"
explains Peer Bork, joint coordinator of the Structural and
Computational Biology Unit at EMBL. "We first identify informative
DNA sequences in a sample and then map them onto the
tree of life, a phylogeny of organisms with sequenced genomes, to
find out which microbes are present and where yet unknown
species fit into taxonomy and evolution."
In this way, Bork and EMBL alumnus Christian von Mering classified
microbial communities present in four very different environments:
ocean surface, acidic underground mine water, whale
bones from the deep sea and farm soil.
"Most of the DNA we found fits into the evolutionary ancient
parts of the tree of life, which means that the organisms are probably
not close relatives of the species sequenced and known so
far," says von Mering, who carried out the research in Bork's
group. "Our novel method complements current classification
attempts based on individual RNA molecules and also has additional
unique features. It allows us to gain insight into the evolution
of microbes in the context of their habitats."
Comparing the datasets from different environments, the
researchers discovered that microorganisms evolve at different
speeds depending on their habitat. While organisms at the ocean
surface evolve fairly rapidly, soil microbes only change slowly
throughout evolution, perhaps partly due to long dormancy phases
during winter.
In collaboration with Phil Hugenholtz and Susannah Green
Tringe from the Joint Genome Institute in Walnut Creek,
California, Bork and his colleagues also investigated whether
habitat preferences of microbes have remained the same throughout
evolution. "It turns out that most microbial lineages remain
loyal to a certain environment for long periods of time, only very
few are able to adapt to different lifestyles," Bork says. "This tells
us that it is not easy to enter a new environment and compete
with the established communities in it, which contradicts the
longstanding belief that every microbe can potentially live everywhere."
To investigate the invisible life on our planet further, samples of
many different environments are being collected and analysed.
Metagenomics experiments generating enormous amounts of
data and new computational methods extracting meaningful
information from it will provide a much better understanding of
biodiversity on Earth in future.
Source Article
C. von Mering & P. Bork et al., Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments, Science
Express, 1 February 2007
Press Contact
Anna-Lynn Wegener
Press Officer
EMBL Heidelberg
Tel: +49 6221 387-8452
Email: wegener@embl.de |
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