How do bacteria and viruses respond to climate change? What happens when we go from an ice age to a warm period and back again?
Microbiologists, climate scientists and others ask these questions fairly regularly, and while there’s a path toward answers, it’s not always the easiest. To answer these questions, research samples need to be old and well-preserved, rarely two attributes that go together—unless the sample is freezing.
In a new study, scientists from the Ohio State University have found 15,000-year-old viruses in ice samples extracted from glaciers on the Tibetan Plateau in Western China, an area not well-studied previously.
The cores, collected in 2015 at 22,000 feet above sea level, contain layers of accumulated ice that trapped whatever particles were in the surrounding atmosphere at the time—creating a physical epitome of the phrase “frozen in time.”
"These glaciers were formed gradually, and along with dust and gases, many, many viruses were also deposited in that ice," said Zhi-Ping Zhong, lead author of the study and a researcher at Ohio State University. “Our goal is to use this information to reflect past environments; and viruses are a part of those environments."
But, before the team could analyze the components trapped inside the ancient ice, they had to create a new, ultra-clean method of analyzing microbes and viruses without contamination. Other methods have been published, but none suited Zhong’s specific research purposes.
The microbiologist developed a three-step decontamination process to remove 1.5 cm of the core radius. First, the researchers scrapped away the top 0.5 cm of the ice core with a sterile band saw before rinsing it with 95% ethanol to remove another 0.5 cm of the surface. Lastly, a final 0.5 cm of the surface was washed away with sterile water. The ultra-clean method was executed on mock “contaminants” before being applied to the actual ice core samples from China.
“These results indicate that the decontamination procedure removed contaminants such as bacteria, viruses, and free DNA from the surface ice and left clean inner ice that was free of detectable contaminants for microbial and viral analysis,” the researchers write in their study, published in the journal Microbiome.
With clean ice to analyze, the research team found genetic codes for 33 viruses—28 of which are novel. Of the 11 most abundant genera, 6 were unclassified within the following families: Microbacteriaceae, Comamonadaceae, Sphingobacteriaceae, Sporichthyaceae, Actinomycetales and Rhizobiales. The analysis also revealed that the viruses likely originated with soil or plants—not with animals or humans—based on current databases of known viruses as well as the glacial environment.
This frozen environment not only played a role in the preservation of the viruses, but also in the types of viruses present. During analysis, the researchers determined that almost half of the 33 identified viruses are putative temperate. Compared with more moderate environments where microbes typically grow, glacier ice is an extreme habitat with low temperature, high UV and low nutrient concentration. However, it seems these temperate phages grew and survived not in spite of the glacial environment, but because of it.
"These viruses would have thrived in extreme environments. They have signatures of genes that help them infect cells in cold environments—just surreal genetic signatures for how a virus is able to survive in extreme conditions,” said Matthew Sullivan, co-author of the study and director of Ohio State's Center of Microbiome Science.
The researchers say their results suggest temperate phages likely dominate glacier ice, highlighting the importance of specifically targeting these viruses in future studies. Additionally, they say future work studying viruses in glaciers—which is a relatively new research area—will benefit from “emerging technologies that can detect microbial growth, better capture small, diverse viral operational taxonomic units and hypervariable regions (including ssDNA and RNA viruses) and high-throughput cultivation.”
“These are not easy signatures to pull out, and the method that [Zhong’s] developed to decontaminate the cores and to study microbes and viruses in ice could help us search for these genetic sequences in other extreme icy environments—Mars, for example, the moon, or closer to home in Earth's Atacama Desert,” concluded Sullivan.
Photo: Yao Tandong, left, and Lonnie Thompson, right, process an ice core drilled from the Guliya Ice Cap in the Tibetan Plateau in 2015. Credit: Lonnie Thompson, Ohio State University