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Illuminating Microbial Dark Matter
Microbial dark matter is a term used to describe major lineages of microorganisms that have never been studied in the laboratory. It is pervasive and practically invisible, yet it can have profound influences on significant environmental processes. It contributes to plant growth and health, nutrient cycles in terrestrial and marine environments, the global carbon cycle, and climate processes.
Scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI) and their collaborators, including UNLV microbiologists Brian Hedlund and Jeremy Dodsworth, are bringing microbial dark matter to light. They're filling in uncharted branches in the tree of life by conducting DNA sequencing of genomes isolated from single cells, and recent findings of the group's exploration were published in the latest issue of the journal Nature.
"Microbes are the most abundant and diverse forms of life on Earth," said Tanja Woyke, DOE JGI Microbial Program Head and senior author on the Nature publication. "They occupy every conceivable environmental niche from the extreme depths of the oceans to the driest of deserts. However, our knowledge about their habits and potential benefits has been hindered by the fact that the vast majority of these have not yet been cultivated in the laboratory."
The microbial dark matter campaign targeted uncultivated microbial cells from nine diverse habitats that host an abundance of unknown microbes, including Great Boiling Spring in northern Nevada. Thousands of cells were isolated from these environments in a process that involved separation of each sample into many individual, tiny droplets. Those droplets containing single microbial cells were identified using lasers and subsequently separated from the rest of the sample by electrostatic forces, very similar to the way an ink-jet printer precisely directs individual droplets of ink to form a letter on a page. From the single cells that were obtained, modern DNA sequencing and analysis techniques enabled identification of over 200 individual genomes representing 28 major, previously unexplored branches in the tree of life.
"There are approximately 100 major lineages of microbes, and of those, 30 or 35 of them are 'light', meaning they can be grown in a lab and studied," said Hedlund. "The remaining microbes are considered 'dark', meaning they can't be grown in a lab. For the most part we don't know what they look like, what they eat, or what they breathe. We know they are there because we find genetic signatures, which can be mapped, almost like forensics work, to a tree of life. But putting a meaning to that genetic information has been a long and difficult challenge."
The results from this study not only offer a first glimpse of the metabolic potential of dozens of microbial dark matter lineages, but also help to clarify the relationship between these novel microbial groups and more familiar microorganisms.
"For people that care about the microbial world, this is a significant advance," Hedlund said. "These microbes have enzymes and genes that might be useful. Because some of them are high-temperature microbes, these could also be used for biomedical diagnostics and industrial processes."
In a separate paper in the online journal Nature Communications, Hedlund and his team focused on one dark matter lineage that they named phylum Atribacteria. This study shed the first light on a group of microbes that is present in hot springs as well as in more "close to home" environments such as wastewater treatment plants.
About the Study
The study, "Insights into the Phylogeny and Coding Potential of Microbial Dark Matter" was published online on July 14 in the journal Nature. Researchers on this project are from the DOE JGI; Bielefeld University, Germany; University of California, Davis; University of Technology Sydney; Bigelow Laboratory for Ocean Sciences; University of British Columbia; UNLV; University of Western Greece; Woods Hole Oceanographic Institution; University of Illinois at Urbana-Champaign; and the Australian Centre for Ecogenomics of the University of Queensland, Australia.
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