Mapping and DNA Sequencing the Genomes of Uncharted Microbial Organisms - Microbial Dark Matter

Great Boiling Spring in Nevada
Credit: Brian Hedlund, University of Nevada, Las Vegas

Scientists led by the U.S. Department of Energy Joint Genome Institute (DOE JGI) are mapping the genetic make up of previously uncharted branches in the bacterial and archaeal cells and organisms. These cells, referred to as "microbial dark matter" cannot be cultured in a laboratory and because they live in specific conditions and environments, are hard to reproduce.

Living organisms are divided into three kingdoms or domains, Eukaryota, Bacteria, and Archaea. They are classified based on their cellular organization, biochemistry, and molecular biology which each share on a fundamental basis with others in the domain regardless of the diversity.

Microbes are important to life. Bacteria, for example, comprises about 10% of a human body's weight and can be found in all organs and tissues. These organisms have great influence on a body's biological and even behavioral processes. The influence of microbial life is not restricted to the human body, it can also have influence over other areas such as the environment, global cycles, and also climate processes. A recent study points to microbes as the cause for rising methane levels in the ocean.

With this undertaking, scientists visited nine habitats around the world to collected uncultivated microbial cells from which they were able to reassemble and identify 201 distinct genomes. The data can be used to align with 28 major previously uncharted branches of the tree of life.

The nine habitats visited were Sakinaw Lake in British Columbia; the Etoliko Lagoon of western Greece; a sludge reactor in Mexico; the Gulf of Maine; off the north coast of Oahu, Hawaii, the Tropical Gyre in the south Atlantic; the East Pacific Rise; the Homestake Mine in South Dakota; and the Great Boiling Spring in Nevada.

Synchrotron Infrared Spectromicroscopy Probes Deep Into Microbial Relationship Between Archaea and Bacteria

Using a particle accelerator, scientists at Berkeley Lab probe deep into the relationship between bacteria and one celled organisms called archaea.

Living organisms are divided into three kingdoms or domains, Eukaryota, Bacteria, and Archaea. They are classified based on their cellular organization, biochemistry, and molecular biology which each share on a fundamental basis with others in the domain regardless of the diversity.

Eukaryotes is the domain that includes animals, plants, fungi, and protists (eukaryotic microorganisms). The kingdom Bacteria constitutes simple microorganisms some of which are associated with disease. The third kingdom was just recently added in the 1970s; Archaea.

Organisms under the kingdom Archaea used to be classified under the bacteria domain. Archaeans on the surface look and sometimes behave similar to bacteria but they are different on a biochemical and even genetic level. Dr. Carl Woese at the University of Illinois was the one who proposed a separate domain for them.

Most archaea are found in harsh and extreme environments such as thermal vents where temperatures may exceed 100 degrees Centigrade or hypersaline water. Although much associated with these kind of hostile habitats, there are archaeans found in the open sea especially in plankton.