Microbial diversity

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 different organisms."

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.