Discovery Files

Study sheds light on ancient microbial dark matter

Scientists use genomes to reveal first in-depth look at Omnitrophota, one of the world's oldest and tiniest bacteria

Bacteria are literally everywhere — in oceans, in soils, in extreme environments like hot springs and even alongside and inside other organisms, including humans. They're nearly invisible, yet they play a big role in almost every facet of life.

Despite their abundance, surprisingly little is known about many microorganisms that have existed for billions of years.

This includes an entire lineage of nano-sized bacteria dubbed Omnitrophota. These bacteria, first discovered based on short fragments of DNA just 25 years ago, are common in many environments around the world but have been poorly understood. Until now.

A U.S. National Science Foundation-supported research team has produced the first large-scale analysis of more than 400 newly sequenced and existing Omnitrophota genomes, uncovering new details about their biology and behavior. The team's findings are reported in the journal Nature Microbiology.

"We now have the most comprehensive view to date of the biology of an entire phylum of microorganisms and the surprising role they play in the Earth's ecosystems," said University of Nevada, Las Vegas microbiologist Brian Hedlund, the study's corresponding author. "There is a finite number of major lineages of life on our planet, and it's exciting to learn more about organisms that predate plants and animals and have been essentially hidden under our noses."

The tricky thing with Omnitrophota is that they're still largely considered microbial dark matter, which means they exist in nature but can't yet be cultivated as single species in lab studies. Just two species have been microscopically observed, and only very recently.

"Inhabiting the cells of other organisms may partially explain why these ultra-small microbes have been difficult to cultivate and observe microscopically," said Matt Kane, a program director in NSF's Division of Environmental Biology.

To present a comprehensive picture of the microbes' biology, scientists compared 349 existing and 72 newly mapped Omnitrophota genomes. This included a review of publicly available data and new samples collected from geothermal environments, freshwater lakes, wastewater, groundwater and springs located around the world.

The team observed that, in most cases, Omnitrophota measure less than 450 nanometers, which places them among the smallest of all known organisms. They also displayed genetic markers consistent with symbiosis — possibly as predators or parasites of other microorganisms, which suggested they would have high metabolic rates.

"Despite how little we collectively knew about Omnitrophota, they've long been cited by microbial ecologists. Our goal was to finally drag this lineage out of the dark," said Cale Seymour, the study's lead author. "The more we learn about their energy conservation pathways and possible lifestyles, the closer we get to our goal of cultivating them in the lab and bringing them into the light."