Study sheds light on ancient microbial dark matter

Bacteria are found everywhere – in the oceans, in the soil, in extreme environments like hot springs, and even beside and inside other organisms including humans. They are almost invisible, yet they play a huge role in almost every aspect of life on Earth.

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

This includes an entire strain of nano-sized bacteria called Omnitrophota. First discovered based on short fragments of DNA just 25 years ago, these bacteria are common in many environments around the world but are not well understood. So far.

An international research team has produced the first large-scale analysis of more than 400 newly sequenced and existing Omnitrophota genomes, revealing new details about their biology and behaviour. The team’s findings are published in the March 16 issue of the journal Nature Microbiology.

“We now have the most comprehensive view to date of the biology of a whole group of microorganisms and the amazing role they play in Earth’s ecosystems,” said UNLV microbiologist Brian Hedlund, corresponding author of the study. “There are a limited number of major lineages of life on our planet, and it’s exciting to learn more about organisms that predate plants and animals and are basically hidden under our noses.”

The tricky thing with Omnitrophota is that it’s still largely considered a microbial dark matter, meaning it exists in nature but can’t be grown as a single species in lab studies. Only two species have been observed microscopically, and only recently.

To provide a comprehensive picture of their biology, the scientists compared 349 extant and 72 newly mapped genomes of Omnitrophota. 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 noted that in most cases, Omnitrophota measure less than 450 nanometers, which places them among the smallest known organisms. They also showed genetic signs compatible with symbiosis – perhaps as predators or parasites of other microorganisms, which suggests they would have high metabolic rates. Indeed, when isotopic uptake was measured as an indicator of metabolic activity, Omnitrophota were hyperactive.

“How little we collectively know about Omnitrophota, they have long been cited by microbial ecologists. Our goal was to finally bring this lineage out of the dark,” said Cal Seymour, a recent UNLV master’s graduate and lead author of the study. “The more we know about possible energy conservation pathways and lifestyles, the closer we get to our goal of growing them in the lab and shedding light on them.”

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