Studying Biology’s Dark Matter

Microbiologist Brian Hedlund was recently selected to lead a team of scientists studying microbial habitats in the Great Basin hot springs. Image Credit: UNLV

Astrobiologists have long been interested in microorganisms that can survive in the harshest environments that Earth has to offer, from deep sea vents to geothermal hot springs. Unfortunately, these studies are hindered by a phenomenon known as ‘biological dark matter.’

Biological dark matter is a term that refers to the numerous microorganisms that live in natural environments on Earth that cannot be cultivated in a laboratory. In order to study how microorganisms function, and the role they play in terrestrial ecosystems, scientists have traditionally relied on their ability to grow and observe them in the lab. These laboratory studies have provided a wealth of information about Earth’s smallest living organisms. However, scientists estimate that as many as 75% of the major groups of microorganisms (i.e. phyla and classes) fall under the category of ‘biological dark matter.’ This means that our view of microbial habitats is limited to the remaining 25% we can actually study.

Scientists are now employing new technologies and techniques to solve this problem. With support from the National Science Foundation (NSF), Brian Hedlund of the University of Nevada, Las Vegas and colleagues recently began a five-year study of the Rehai hot springs in China’s Yunnan province. Based on DNA samples obtained from Rehai, scientists know that hundreds of unknown (and yet-uncultivated) organisms call the hot springs home.

Polydimethylsiloxane (PDMS) microchip used by the team to sort "dark matter" cells for single-cell genomics. The microchip is mounted on an inverted microscope stage. Credit: Paul Blainey and Steve Quake (Stanford)

To identify the ‘biological dark matter’ of Rehai, the team is employing methods like single-cell genomics, where DNA can be sequenced from isolated cells. These advanced techniques will allow them to study the organisms without the need to culture them in the lab.

Hedlund’s new project, “Exploration of ‘Biological Dark Matter’ in Geothermal Springs,” is funded by the NASA Exobiology and Evolutionary Biology Program, and will broaden his investigations to hot springs located in the Great Basin of the United States. Environments like the geothermal springs in the Great Basin and Rehai are helping astrobiologists determine how life is able to survive in Earth’s harshest environments. This information is essential to understanding how living organisms could gain a foothold on celestial bodies like Mars or Europa where environmental conditions are less hospitable than Earth. The organisms that live in environments like Rehai also produce unique types of lipids and enzymes that may have value to biotechnology and medicine.