Unveiling the Viral Ecology of Earth

 

Viral infections modify and transform the functioning of individual cells.  They do this just not for humans, animals, and plants, but also for the microbes that drive Earth's carbon cycle.  Could this tiniest form of life impact the balance of nature on a global scale?


Joshua Weitz, Georgia Tech

Steven Wilhelm, University of Arizona and

Matthew Sullivan, University of Tennessee, Knoxville

Photo credit: Jennifer Brum, Sullivan Lab, The Ohio State University.


Ebola, HIV, influenza—even the common cold. Each of these maladies reinforces the commonly-held belief that viruses are harmful parasites that are potentially deadly to their host. The virus’ ability to disrupt human health belies its relatively simple form—it’s no more than a microscopic package of genes wrapped in a molecular shell. But when a virus infects a living cell, it can commandeer the genetic machinery of the host to replicate itself. What is not widely understood, however, is that not all viruses are bad for their host, or for the world around them.

Viruses infect all types of living cells, including those of animals, plants, and microbes. Indeed, the targets of most viruses are microbes—including the ubiquitous bacteria living in soil, lakes, and throughout the oceans. Viruses play a critical role in altering the fate of individual organisms, and potentially that of the Earth’s ecosystems. In effect, viruses modulate the function and evolution of all living things, but to what extent remains a mystery.

This uncertainty has many causes. For one, viruses are tiny, which makes them more difficult to isolate, study, and understand.  A virus is usually one- to ten- thousand times smaller in volume than a typical bacterium, and therefore, like bacteria, are invisible to the naked eye. Viruses seem simple, usually including just a handful of genes. But actually they are wildly diverse and not easy to identify and characterize. There is not a single gene common to all viruses, nor is there consensus about classes of viral genes. And this diversity is itself evolving. Some viruses multiply rapidly, creating a new generation as often as every 20 minutes. Other viruses need only a handful of genes (and a host) to make new copies of themselves, while still others carry hundreds of genes, blurring the lines of delineation from living cells.

The scope of our uncertainty of how viruses shape the planet is compounded by the fact that virus-host interactions operate on a huge scale. A liter of water in the Earth’s surface oceans typically contains hundreds of millions of cyanobacteria . These bacteria and other oceanic microbes take in carbon dioxide and convert it to organic matter (i.e., new cells and cellular life), and in the process “fix” as much carbon in a day as all of the land plants on Earth. The cyanobacteria, in turn, become the bottom of the marine food chain—food for zooplankton, which feed the krill, which feed the fish and whales. But viruses also infect, transform, and destroy uncounted billions of cyanobacteria every day—they are part of the ecosystem too.

When a virus infects a living cell there are several potential outcomes: it can kill the cell, it can go dormant until activated later, or it can co-exist with that cell for generations. Further, as mentioned above, not all viral infections are bad. They can create immunity to other infections, mediate the interaction of human gut bacteria and the immune system, or preferentially increase the food supply for some types of microbes by killing other microbes, releasing cell debris that is valuable feed material. Thus viruses shape ecosystem-level microbial diversity and metabolic processes. These same features make viruses increasingly attractive to biotechnology researchers who find them useful to deliver drugs and genetic therapies into living cells.

Viruses play potentially critical roles in ecosystems. However, a more detailed quantitative picture is needed to predictively model their impact. Of special note is the urgent need to understand the ecological role of viruses in the Earth’s carbon cycle—how viruses modulate the microbial processes that dominate the fixation and respiration of carbon that in turn modulates Earth’s climate. Microbial populations are now routinely mapped in soils, lakes, oceans, and even within humans, but the corresponding viral communities remain relatively unexplored. In the past, technological barriers impeded our ability to observe these nanoscale partners and investigate their actions. But emerging instrumentation and processing techniques, along with new methods we are proposing, now enable a quantitative understanding and the resulting predictive models for how viruses impact a changing Earth system.

We propose here a systematic study of environmental viruses, especially those that infect microbes, with the overall goal of linking virus-host biology to ecosystems ecology. An in-depth knowledge of viral ecology would lead to insights on the structure and function of living systems on a variety of scales, ranging from genes to ecosystems to the global carbon cycle.