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.
: Nature Biotechnology, August , 2008.
Photo Copyright © Dennis Kunkel Microscopy, Inc. (Color by Ekaterina Latypova)