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Generating Genomes

Scientists have found a way to sequence unidentified life through their study of lake sediment. The purple and orange microorganisms, seen above, are from a mud sample collected in Lake Washington. They are relatives of Methylotenera mobilis, whose complete DNA sequence has been determined.

"This work demonstrates that we can get a complete genome for a totally unknown organism,"said lead author Ludmila Chistoserdova, a chemical engineer at the University of Washington.

The researchers targeted a particular ecological function: eating single-carbon compounds such as methane. First they collected mud samples from the bottom of Lake Washington, a freshwater lake with average sediment levels of methane produced by decomposing organisms. Then they mixed the mud with five different samples of food labeled with carbon-13, a heavier isotope of carbon usage. Over the time, organisms that ate the lab food incorporated the heavy carbon into their cells and their DNA. For five different single-carbon food sources, the scientists then separated the DNA by weight, knowing that the heavier pieces must belong to organisms that ate the lab-catered food.

Chistoserdova estimates the original mud sample contained about 5,000 different microbes, but the five batches of enriched DNA each contained only a dozen or so organisms. Researchers then were able to piece together carbon-13.

DNA fragments to create one entire genome for Methylotenera mobilis, a microbe that eats methylamine, a form of ammonia. (This microbe was already known, though the team did not use that knowledge to create the sequence.) They also produced a partial genome for Methylobacter tundripaludum, a methane-eating microbe that so far resists cultivation in the laboratory.

SOURCE : Nature Biotechnology, August , 2008.

Photo Copyright © Dennis Kunkel Microscopy, Inc. (Color by Ekaterina Latypova)

ENVIS CENTRE Newsletter Vol.6,No 3 September 2008 Back 
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