Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Whale bones and farm soil: Sequencing biodiversity

22.04.2005


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 – 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.

Trista Dawson | alfa
Further information:
http://www.embl.de

More articles from Earth Sciences:

nachricht Ice cave in Transylvania yields window into region's past
28.04.2017 | National Science Foundation

nachricht Citizen science campaign to aid disaster response
28.04.2017 | International Institute for Applied Systems Analysis (IIASA)

All articles from Earth Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Making lightweight construction suitable for series production

More and more automobile companies are focusing on body parts made of carbon fiber reinforced plastics (CFRP). However, manufacturing and repair costs must be further reduced in order to make CFRP more economical in use. Together with the Volkswagen AG and five other partners in the project HolQueSt 3D, the Laser Zentrum Hannover e.V. (LZH) has developed laser processes for the automatic trimming, drilling and repair of three-dimensional components.

Automated manufacturing processes are the basis for ultimately establishing the series production of CFRP components. In the project HolQueSt 3D, the LZH has...

Im Focus: Wonder material? Novel nanotube structure strengthens thin films for flexible electronics

Reflecting the structure of composites found in nature and the ancient world, researchers at the University of Illinois at Urbana-Champaign have synthesized thin carbon nanotube (CNT) textiles that exhibit both high electrical conductivity and a level of toughness that is about fifty times higher than copper films, currently used in electronics.

"The structural robustness of thin metal films has significant importance for the reliable operation of smart skin and flexible electronics including...

Im Focus: Deep inside Galaxy M87

The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.

Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...

Im Focus: A Quantum Low Pass for Photons

Physicists in Garching observe novel quantum effect that limits the number of emitted photons.

The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...

Im Focus: Microprocessors based on a layer of just three atoms

Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.

Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Fighting drug resistant tuberculosis – InfectoGnostics meets MYCO-NET² partners in Peru

28.04.2017 | Event News

Expert meeting “Health Business Connect” will connect international medical technology companies

20.04.2017 | Event News

Wenn der Computer das Gehirn austrickst

18.04.2017 | Event News

 
Latest News

Wireless power can drive tiny electronic devices in the GI tract

28.04.2017 | Medical Engineering

Ice cave in Transylvania yields window into region's past

28.04.2017 | Earth Sciences

Nose2Brain – Better Therapy for Multiple Sclerosis

28.04.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>