12 December 2013

The viruses lurk below

Posted by pweiss

The Viruses Lurk Below

From hydrothermal vents to the soft mud of riverbeds, geophysical hideouts where viruses thrive are windows into how life evolved, and could be crucial to protecting human health. Here are two examples from Tuesday’s American Geophysical Union’s Fall Meeting in San Francisco:

A Geothermal Arms Race

For single-celled organisms like bacteria and archaea, hydrothermal vents offer an underwater life spring. As the magma splits the oceanic crust, heat-loving bacteria feast on an unusual diet of hydrogen, carbon dioxide, metals, and sulfides produced by hot rock reacting with water.

But they are not alone.

Hydrothermal vents are one of the underwater hangouts for viruses, according to reports from the AGU conference. Credit: NOAA Photo Library

Hydrothermal vents are one of the underwater hangouts for viruses, according to reports from the AGU conference. Credit: NOAA Photo Library

The ocean harbors enough virus particles to stretch across the Milky Way 100 times, and Rika Anderson and her colleagues at the University of Washington found that these viruses love hydrothermal vents and may drive microbial evolution.

Anderson’s research shows that viruses prey on this ecological niche, which benefits and harms the bacteria and archaea they infect.

“We could be seeing evidence of a viral-host arms race going on,” Anderson explained during her oral presentation Tuesday

While earning her doctoral degree in oceanography and astrobiology at UW, Anderson examined metagenomes or large collections of genetic material derived from deep biosphere oceanic samples. This allowed her to explore the give-and-take relationship in these communities.

When a virus infects a cell, it has two options. It can hijack the cell’s machinery, quickly reproduce, and burst from its host in search of a new home. Or the virus can lie low and integrate its DNA into the genome of its host. This option—called lysogeny—allows the virus to wait until conditions are optimal for spreading.

This clandestine activity is extremely abundant near hydrothermal environments along mid-ocean ridges, according to Anderson’s research. These regions harbor more vents and a higher degree of fluid flux—or movement—that is ideal for creating food for the bacteria and archaea. The viruses appear to capitalize on the rich microbial ecosystems established when the deep ocean is churned and brewed by hydrothermal vents.

The viruses may also drive the evolution of their hosts.  Certain genes in the Trojan viruses—called fitness factors—promote the survival of their hosts, making it easier for the bacteria and archaea to metabolize food or produce it through photosynthesis.

The viruses also carry advantageous genes from host to host, a process known as horizontal gene transfer.

But not all viruses are helpers, and the archaea and bacteria have developed a way to remember dangerous foes. Bacteria and archaea can save copies the invader’s genes, known as “spacers”, in their genomes.

If the same virus infects an archaea or bacteria again, the cells recall this spacer, recognize the invader and mount an immune response. The genes and enzymes that regulate this immune response are called the CRISPR system.

“It’s a lot like our own immune systems,” said Anderson, who continued that up to 40 percent of bacteria and 90 percent of archaea have these spacers. “They are essentially libraries of previous viral infections.”

So in these thermal vents, it’s CRISPR versus fitness factors as bacteria battle viruses trying to use them as hostels.

“What we’re starting to learn is these viruses could have substantial impacts on both ecological and evolutionary trajectories of their microbial hosts,” Anderson concluded.

Clay, Flu, and Duck Poo

Bird flu, also known as avian influenza, remains a constant threat to human health as new variants emerge across the globe.

Water fowl, like ducks and geese, are major carriers of these diseases, but unlike humans, the virus doesn’t infect their lungs. The germs reside in birds’ intestinal tracts and on any given day an infected bird deposits more than 1,000 virus particles into its aquatic home.

But once the virus enters the waterway, can it survive?

Duck standing by a boat pond in Central Park, New York City. Credit: NikBoiv.

Duck standing by a boat pond in Central Park, New York City. Credit: NikBoiv.

That’s the main question being answered by Adrianna Trusiak and her colleagues at the City College of New York in Manhattan. Trusiak is an undergraduate student studying geology with Karin Block, an earth and atmospheric scientist based at CCNY.

Prior work had shown that influenza can persist in lake sediments, but the reason why remains murky.

Trusiak conducted a simple experiment where she mixed flu particles with montmorillonite—a clay mineral found in most freshwater sediments. After waiting an hour, she collected the clay and scanned it with an electron microscope.

Rather than disintegrating instantly, the influenza particles set up shop between the montmorillonite platelets. The viruses kept their normal structure, which resembles a spike-covered peanut, while in the clay.

“Montmorillonite has an expandable interlayer that can absorb cations. This may produce stronger interactions with the virus envelope than non-expandable clay,” Trusiak said. “The ultimate goal is to reverse engineer an artificial lake sediment with clays, iron oxides, humic acids, then add virus and see what happens.”

This could provide a guide for tracking the optimal sediment habitats for viruses, and spot aquatic environments where virus loads might be higher, she said.

The next step is to see if viruses can still infect cells after spending time in clay. When mixed with red blood cells in a tube, known as a hemagglutination assay, the clay-extracted viruses caused clumps to form to the same degree as a regular virus. This suggests the viruses were still active, but the researchers need to confirm this with living cells.

In addition, they are collecting water and sediment samples from ponds in Central Park, the Hudson River, and other aquatic habitats with ducks and geese to check for the presence of influenza viruses.

“We plan to extract DNA and RNA from the samples and do some gene sequencing to see if we can actually isolate flu from natural environments,” Trusiak said.

Nsikan Akpan is a science communication graduate student at UC Santa Cruz