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Viruses Leave Behind Fossils

Sarah C.P. Williams

A new finding by geologists suggests that the evolutionary history of viruses could be studied by analyzing ancient rocks. Read more...

On ocean bottoms, lake shores, and slick rocks, bacteria and single-celled organisms have been doing the same thing for millions of years: forming dense, thick “microbial mats” to help them thrive in large colonies. As the microbes form symbiotic layers, exchange chemical messages, and tighten their physical connections, they also produce mineral byproducts. Over time, the mat slowly mineralizes, preserving its structure in rock.

Researchers have now, for the first time, shown the vital role of viruses in both the life and mineralization of microbial mats (1). Their findings don’t just have implications for understanding the intricate biology of microbial mats, but could also mean that viral signatures from millions of years ago remain in fossils.

Mysterious Nanospheres

Virus-like particles distributed throughout microbial mats are shown in these transmission electron microscopy (TEM) images (1)

Microbial mats represent one of the more primitive ecosystems on earth. Fossilized microbial mats from the Archean eon (1.5 to 4 billion years ago) are among the earliest signs of life on the planet. To interpret how the structure and content of a microbial mat is reflected in these fossils—and to better understand what microbes were present on ancient Earth—researchers often turn to living microbial mats to recreate the mineralization process that preserves them.

In the 1990s, researchers using powerful electron microscopes first spotted tiny nanospheres within microbial mats. They dubbed the spheres “nanobacteria,” hailed them as a new type of primitive microbe, and defined them as any bacteria smaller than 200 nanometers across. But these nanospheres were never isolated or shown conclusively to be bacteria.

In the 2000s, geologist Muriel Pacton, at the Swiss Federal Institute of Technology in Zurich, began to look for nanospheres in her microbial mats. And in 2010, she found the miniscule structures and began preparing to present the observation at a conference. “But four days before my presentation,” she said, “I was taking one more look and realized the spheres had tails.” They weren’t bacteria, but viruses.

Rather than present a confirmation of nanobacteria at the meeting, Pacton presented a new theory: viruses thrive alongside bacteria and Archaea in microbial mats. She was met by many skeptics and doubters. “People just don’t think that viruses existed in microbial mats,” she said. “For geologists, this was a very new idea.”

Conducting a Genetic Survey

To back up her microscope-based hypothesis of viruses in microbial mats, Pacton spent the next four years teaming up with microbiologists to add to her pile of evidence. The first—and biggest—clue that viruses are present in microbial mats came when she and her collaborators extracted viral DNA and RNA from a microbial mat collected from lake Lagoa Vermelha in Brazil.

A metagenomic analysis of the nucleic acids revealed viruses related to 585 known viral strains. The vast majority were from double stranded DNA viruses, with less than 10% coming from single stranded DNA or RNA viruses. And most of the microbial mat viruses live in prokaryotes, including a high number of bacteriophages and a few archeoviruses.

In light of what is known outside the geology community about the importance of viruses, Pacton said the large number of viruses wasn’t too surprising. “Microbiologists realized quite some time ago that viruses play an important role in the food web in both marine and terrestrial environments.”

Microbial Mats from Scratch

In addition to looking at microbial mats collected from the natural environment, Pacton’s team also collected data on mats that were stored in dark, low-oxygen environments in the lab for a period of 6 months to 3 years. This time course let them study how the prevalence and morphology of viruses changed as sections of a mat mineralized. Over time, the researchers found that the abundance of viral particles increased. And not only that—some of the viral particles became mineralized themselves, morphing into spheres of magnesium carbonate or magnesium silicate.

Based on the results of their microbial mat studies, Pacton thinks that viruses—in addition to bacteria and Archaea—can act as scaffolds for the mineralization that takes place in microbial mats. If true, this means that viral particles could be preserved in microbial mat fossils.

As for the “nanobacteria,” Pacton doesn’t think they ever existed. Researchers were looking at viruses all along. “Not everyone is convinced,” she admitted. “But I’ve spent the past three years working to really support the viral theory.”

Fossilized Viruses?

As a geologist, Pacton is most excited by the consequences of her findings for understanding how fossils form in the first place and what role viruses have in the global geochemical cycle. But her discovery has implications that reach far beyond geology.

“Once a virus is mineralized, it can be preserved for millions and millions of years,” Pacton said. For virologists and those studying evolution, the potential to find virus fossils millions-of-years-old could revolutionize the study of how viruses evolved. But before that can happen, Pacton’s team must first find signs of viruses in ancient microbial mats. Their next step is to analyze lithified microbial mats—older mats that have turned to rock but are not yet fossilized. Then, she will team up with researchers drilling for ancient rock in South Africa to determine whether viral spheres are present in those samples. The integrity of the viral morphology preserved in these fossils—if Pacton can indeed pinpoint nanospheres within them—will be key to how useful they are.

“I’ve already gotten a lot of positive emails about my work,” Pacton said. “And I’m going to continue collecting evidence for viruses in the ancient sediment.”


Pacton, M., Wacey, D., Corinaldesi, C., et al (2014). Viruses as new agents of organomineralization in the geological record. Nature Communications 5:4298.

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