Bacteria are microscopic, single-cell organisms that are everywhere in the environment, including in the soil, air, in and on our bodies and in
extreme environments like hot springs. They can be good or bad: Some
make us sick, others help us digest food, still others are used for antibiotics. But researchers in Los Alamos National Laboratory's Bioscience
Division have discovered that they are not as simple as once believed, and
that there are more different types of them than anyone ever imagined.
After 150 years of studying bacteria colonies in petri dishes, scientists
have finally acquired an arsenal of molecular, DNA-based techniques
that allow them to observe the organisms in their natural environments.
"What can be cultured is only a very small fraction of what's out there,"
said Cheryl Kuske, a scientist working on the project. "Microbial organisms are much more diverse than we ever
imagined. We are just beginning to understand
how vast that diversity might be."
The Department of Energy has an interest in
identifying these previously unknown bacteria
for a number of reasons. Bacteria are critical for
decomposing and recycling nutrients at a
global scale. They also are a valuable resource
of novel metabolic abilities useful for pharmaceuticals and industrial processes. There also is
a need to survey the natural microorganisms in
the environment to be able to detect pathogens
for forensic applications.
"We need to know which bacteria are naturally
present in our environment to be able to specifically detect outsiders, "Kuske said. "It's kind of
like 'Where's Waldo?'— trying to detect
pathogens in a diverse environment where the
background may have traits that are similar to the detection target. We've been tasked to survey a number of different
environments, everything from natural soils to city air, and look at how
variable the background bacteria might be and how they fluctuate."
The procedure for identifying these "new" bacteria involves extracting
and sequencing one gene from all the bacteria in an environmental
sample. The bacterial genome is about a tenth the size of the human
genome. The 16S gene is the marker gene that all bacteria have, and
with the use of molecular biology techniques, scientists can sample all
representatives of that one gene and analyze them. In this way,
researchers have been able to assign relationships to bacteria, essentially
constructing family trees.
"A number of people have conducted studies of individual copies of
this gene, developing 16S gene libraries," Kuske said. "We analyzed
many of these libraries and together we've compiled an enormous
tree of the bacteria we've found. In all of our studies, we haven't seen
the same thing twice. We think there are probably millions of
Kuske and her team use different scientific methods to answer
questions about the bacteria, depending on what scale they are
studying. In a single cell, they want to understand how the bacterium's
DNA controls cell functions. In studying entire communities of
microbes, the questions include who are the community members and
what their functions are in the ecosystem.
Some of the other questions Kuske and her team would like to answer
include how complex are these communities and how are they
changing? Because of the difficulty in studying so many organisms, they
have developed community fingerprinting techniques, essentially
looking at the problem at a much lower resolution. This molecular
fingerprint analysis can be used to monitor bacterial complexity, the
relative abundance and dynamics of these microscopic communities at
a landscape level in the real world.