Signs of a global catastrophe about 680 million years ago, known as Snowball Earth, have been found in the DNA of living bacteria in the oceans. Their genomes show that they nearly died out around this time, says Haiwei Luo at The Chinese University of Hong Kong.

“Their population size became hugely decreased,” says Luo.

Today, tiny photosynthetic bacteria called Prochlorococcus are incredibly abundant in the surface waters of oceans. A litre of seawater can contain more than 100 million of these cyanobacteria.

When Luo and his colleagues studied the genomes of these bacteria, the researchers found that at some point in the distant past, the most common types of Prochlorococcus had acquired many harmful mutations and lost hundreds of genes altogether.

This shows they went through what is called a population bottleneck. When a population shrinks to a low number, natural selection is much weaker and damaging mutations can accumulate.

The researchers published these findings in 2017, but were left puzzling over what caused this bottleneck. The ancestors of Prochlorococcus evolved around 2 billion years ago, and they have long been abundant and widespread. Only a global catastrophe could explain such a bottleneck.

Luo and his colleagues have now worked out that this bottleneck occurred approximately 680 million years ago . They did this with the help of a so-called molecular clock, which is based on the idea that, on average, genomes mutate at a constant rate. The team estimated that rate based partly on the ages of fossils found by other teams, whose appearance suggests they are the ancestors of cyanobacteria such as Prochlorococcus.

That means the bottleneck occurred during a period of super ice ages when the planet got so cold that even the seas around the equator mostly froze over, hence the term Snowball Earth. This would have been a disaster for Prochlorococcus. “This explains very well the genetic evidence,” says Luo.

While some other cyanobacteria thrive even in polar waters, modern Prochlorococcus prefer the tropics and usually don’t grow when the temperature is below 10°C, he says. “They love to live in warm water,” he says.

Yet during Snowball Earth events, a few might have managed to adapt to the cold and cling on in refuges such as in the briny water in sea ice.

Luo thinks some of the genetic changes that occurred at this time are related to cold adaptation. For instance, the proteins in the cell membrane that transport substances such as nitrogen compounds don’t work well in the cold, and several of the genes for these transporter proteins were lost.

Instead, the bacteria may have got the nitrogen they needed from ammonia, which can diffuse into cells without a transporter. The genes necessary for using ammonia as a nitrogen source were retained.

“I think these interpretations are reasonable,” says Gregory Fournier at the Massachusetts Institute of Technology, who studies how genomes change over geological timescales. But calibrating the molecular clock with fossil evidence involves a lot of assumptions, he says.

“The work done here was sound,” Fournier says. “But there are large inherent uncertainties.”

Paul Hoffman at Harvard University, the geologist who discovered key evidence supporting the Snowball Earth hypothesis, also points to the uncertainties in the dating. But Snowball Earth would have left a mark in the genomes of all the organisms that survived it, he says.

“All living taxa descended from Snowball survivors,” says Hoffman. “In general, I do believe that when all is said and done, the evidence for Snowball Earth events will be most pervasively observed in the genomes of living taxa.”

Reference:bioRxiv, DOI: 10.1101/2020.11.24.395392