Mysterious 'Microbial Dark Matter' Dominates Our Planet

Nearly every environment on Earth is dominated by “microbial dark matter,” according to researchers from the University of Tennessee, Knoxville (UTK).

Scientists use this term to describe all of the microbes that have never been grown in a lab culture, either because of a lack of knowledge or an inability to produce the right conditions. Their existence poses a problem, because to learn about microbes and their role in the environment, you need to be able to culture them.

"Calling uncultured microbes "dark matter" borrows from astronomical dark matter, since both have been found to be ubiquitous, yet neither have been adequately characterized," Karen Lloyd of UTK’s Department of Microbiology told Newsweek. "Of course, we know quite a bit more about microbial dark matter, since we can guess at what they do from their genomes, but the word 'dark matter' is meant to emphasize the possibility that they have quite different physiologies from cultured microbes."

While researchers have long been aware of these undocumented organisms, determining their abundance on the planet is extremely challenging. Counting the microbes one by one would be impossible, and even estimating their numbers has proved to be a difficult task.

But now a team led by Lloyd has made the first estimate of the global uncultured microbe population. According to their paper, published in the journal mSystems, uncultured microbes are numerically dominant in all major environments on Earth, including seawater, freshwater, the soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, snow and non-human hosts.

More specifically, they found that uncultured “genera,” or groups of species, make up 81 percent of all microbial cells on Earth.

“Our key findings were that, with the exception of the microbes that live on the human body, most microbial cells on Earth are pretty much unknown to us,” Lloyd said. “Also, we found that most of them are alive, meaning that they are doing some sort of functions—we are just starting to guess what those could be, based on their genes—in various environments.”

The team came to its conclusions after collecting the DNA sequences of around 1.5 million uncultured microbes in public gene databases and comparing them to 26,000 DNA sequences of those that have already been cultured.

The latest findings could have important implications for various fields, according to the researchers.

GettyImages-939747876 A scientist shows bacteria cultivated at the University Hospital Institute Méditerranée Infection, in Marseille, France, on March 29. ANNE-CHRISTINE POUJOULAT/AFP/Getty Images
"They are exciting because it means that the natural microbial world has a lot of unknowns that might be interesting or useful to us," Lloyd said. "Some of these microbes might have genes that could be useful for pharmaceuticals, food and energy production, or mitigating the effects of climate change in agriculture."

"Microbiologists definitely have our work cut out for us—we need to get more of them into culture, and also use new methods to study those of them that continue to be resistant to our culturing efforts."

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