Study Elucidates Biology of Ancient Nanobacteria

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Scientists have found bacteria in environments across the Earth, and many are responsible for essential processes like mineralization, nitrification, and nitrogen fixation. Despite technological improvements that have increased our knowledge of these microorganisms, there are many unculturable bacteria and as a result, they remain poorly understood.

The phylum Omnitrophota is one such group that has never been isolated, and only two of the species have been microscopically observed. These nano-sized bacteria were first discovered 25 years ago and have since been identified in a range of locations, including springs, freshwater lakes, wastewater, groundwater, and geothermal environments.

A team of international researchers that recently published their work in the journal Nature Microbiology set out to learn more about these elusive microorganisms. After analyzing more than 400 Omnitrophota genomes, the team discovered new details about this ancient group of bacteria.

“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 Brian Hedlund, UNLV microbiologist and the corresponding author of the study. “There is a finite number of major lineages of life on our planet, and it’s exciting to learn more about organisms that pre-date plants and animals and have been essentially hidden under our noses.”

To understand more about their biology, the researchers used data from 72 newly sequenced and 349 existing Omnitrophota samples to build single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). The samples were collected from different environments around the world, including some publicly available work from the Earth Microbiome Project.

After a thorough analysis, the results showed the Omnitrophota genomes in six classes are reduced, but they still maintain major biosynthetic and energy conservation pathways, such as acetogenesis and diverse respirations. In addition, many of the Omnitrophota have genetic markers typical of bacterial symbionts, suggesting that they are potential predators or parasites of other microorganisms.

Measurements of Omnitrophota metabolic activity showed they also have a hyperactive metabolism, another common characteristic of bacterial predators. Further investigations using fluorescence-activated cell sorting and differential size filtration showed that most Omnitrophota are ultra-small (~0.2 μm) cells, making them some of the smallest known organisms.

“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 the study’s lead author Cale Seymour. “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.”

To learn more, read the full study, “Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota.”