A deeper understanding of viruses

With their existence made possible only by living off and infecting other creatures, not to mention their insidious role in human illness, viruses generally get bad press.

Still, this least appreciated of all life forms is exceptionally important to life on Earth, and there is growing interest in the subject among members of the scientific community. Now, some UD scientists have received a $1.2 million National Science Foundation grant to investigate viruses, and they are going to great depths to obtain their research samples.

K. Eric Wommack, UD associate professor of plant and soil sciences at the Delaware Biotechnology Institute, leads the team studying viruses that live at deep-sea hydrothermal vents found thousands of metersbeneath the ocean’s surface. Co-investigators on the project are Craig Cary, professor of marine and Earth studies at the University, and Shannon Williamson of the J. Craig Venter Institute. The team also includes UD postdoctoral researcher Rebekah Helton and doctoral student Danielle Winget.

Wommack says that hydrothermal vents, which are characterized by caustic chemistry, extreme heat and high pressure, are oases of life in the deep sea. The vents provide an ecosystem for ancient and unusual microbes that are capable of extracting energy from volcanic rather than solar sources.

Two decades ago, direct examination of water samples revealed that viruses were extraordinarily abundant within the global ocean, Wommack says, and subsequent research now indicates that viruses are the most abundant life form on Earth. He notes that within the past year, it has been discovered that DNA viruses comprise the largest pool of uncharacterized genetic diversity in the biosphere.

The central objective of Wommack’s research is to explore the abundant, but largely unknown, assemblages of viruses within the hostile environments of the hydrothermal vents. Because viruses can significantly alter the biological characteristics of their microbial hosts—in some cases changing benign bacteria into pathogens—it is possible that viruses at the vents are intimately involved in assisting microbial life cope with the challenging conditions of the deep-sea ecosystem.

The team will collect samples of bacteria and viruses from vents at a dive site near Guaymas, Mexico, and another known as Nine North in the Pacific Ocean that is a two-day ship voyage from Manzanillo, Mexico. After gathering samples, they will use high-throughput DNA sequencing technology and high-powered computing to analyze DNA sequences.

Data from the research will expand ongoing efforts to describe the full extent of genetic diversity on the planet, Wommack says, adding it will likely reveal thousands of new genes and protein groups and possibly entirely new viral clades, or families, existing at the vents.

Wommack says he has a long interest in viruses and has been studying those that are found at deep-sea hydrothermal vents since 2001, when his project co-investigator, Cary, offered him time aboard a research vessel. Cary also has an interest in life at the extremes and has been active in research at deep-sea hydrothermal vents as well as in the Antarctic.
Even collecting samples in the deep-sea environment is a difficult task.

“Working in the deep sea is extremely challenging,” Wommack says. “Several thousand meters down, it is cold, it is dark and the pressures are very high. That is something we have to take into account when designing devices to bring samples back.”

In addition to the problems associated with working at extreme depths, Wommack is sampling in parts of the ocean where there is geothermal and volcanic activity. In fact, it is such activity that provides an environment in which viruses can thrive.

Wommack explains the workings of deep-sea vent ecosystems, noting that cold seawater seeps down through the ocean floor where it interacts with volcanic activity, is heated to very high temperatures and is sent back out of the Earth, much like the geysers and boiling springs at Yellowstone National Park except deep under water.

While in the Earth, he says, the water picks up dissolved minerals, primarily sulfur and iron. The water is superheated, to several hundred degrees Celsius above boiling, and when it hits the cold seawater, the minerals fall out, forming chimneys of deposits. The impressive formations can reach tens of meters tall, and streams of black water pour out through them.

The chimneys are a porous type of rock and are hollow in the middle, with thick rims in which microorganisms can grow.
Winget says the environment is a geothermal system that is “not carbon energy-rich but is electron energy-rich.” There is no photosynthesis in this portion of the world that is so far removed from light, and it is volcanic activity that imparts energy to the system.

The ecosystem is interesting in the way it replicates environments in which early life began on Earth and also might provide a glimpse into what could be found in space, she says.
Researchers say they are just beginning to understand the magnitude of the emerging field. “Microorganisms provide extremely important ecosystem services to the planet,” Wommack says, “and we have no idea what a lot of them are.”

—Neil Thomas, AS ’76