From soil to water and to the human gut, microbes are everywhere. In a sense, bacteria and other microorganisms are the basic underpinnings for all life on Earth. These microbes drive the planet’s nutrient and energy flow to ensure that every ecosystem is stocked with the components it needs to thrive.
Earth’s environments are also rife with predator-prey relationships that sustain a careful balance within these communities. Some of the fearsome predators that target bacteria are viruses – biological entities that rely on a host to multiply.
Researchers have characterized a fraction of the millions of viruses that likely exist in even a single drop of seawater. As they uncover new ones in ocean communities around the globe, scientists can harness novel methods to explore what hosts these viruses infect and kill. They can also learn how viruses affect ecosystems – which has implications for phenomena such as climate change.
“In every ecosystem we look at, microbes seem to do some pretty important stuff,” says Matthew Sullivan, a microbiologist at The Ohio State University and Moore Foundation grantee. “Then viruses manipulate that system in subtle and very direct ways.”
Probing the Ocean
Technological advancements have boosted studies that explore our planet’s viral diversity. Previously, researchers relied on methods where they raised bacteria in the lab and searched for evidence of viral infection. But scientists have not yet grown most oceanic microbes in a lab, which in turn limits the viruses they detect.
Now, DNA sequencing has revived the search for novel viruses by exploiting their genetic material to uncover elusive types.
In two studies – the first published in Nature in 2016 and the second in Cell in 2019 – an international team of scientists, along with Matthew Sullivan and members of a Tara Oceans expedition, described thousands of DNA viruses that circulate in seawater around the globe, including the Arctic Ocean. The most recent number stands at nearly 200,000 marine virus populations.
Sullivan’s group has developed multiple ways to both sequence the viral communities in an ecosystem and investigate their role within it. Blindly sequencing and analyzing all the viruses from seawater, for instance, can describe what types are there. But it doesn’t tell researchers what bacteria they infect – a key feature that would help determine how viruses impact an ecosystem.
“This remains a big holy grail in the field,” says Sullivan, whose experiments were funded by a Marine Microbiology Initiative grant. “We all chip away at different ways.”
For example, in a key study published in Nature in 2014, Sullivan and his team described a method he calls ‘viral tagging.’ They add a fluorescent dye to viruses collected from the field and mix them with a ‘bait host,’ such as a bacterium. Researchers can then separate infected and non-infected cells to link viruses to a specific host.
When the team screened a marine bacterium, they discovered that phages infecting it clustered into distinct populations, or ‘species’ – a controversial idea since viruses rapidly evolve and share genes. The results were the “first brick in the wall” for the idea that viruses are actually structured in nature, says Sullivan.
A 2016 study from Sullivan’s lab published in BMC Genomics again described how to separate viruses into populations. Through a variety of genetic analyses, their group observed a network of related viruses that seemed to belong to different so-called viral ‘species’ in seawater samples. These methods were also applied in their Cell 2019 study of Earth’s oceans.
Understanding these communities can help better predict how an ecosystem will respond to climate change and possibly ways to combat it, Sullivan says.
“If we assume that all microbes matter… then viruses become part of that equation,” he says. “And the first thing we had to understand with viruses was what to count.”
Sharing the Methods
Exploring a frontier such as marine virus research requires brute trial and error to develop new tools. Often scientists do this in their isolated laboratories and only share the technique when it is perfect. But often the nuances of a technique are lost in translation – meaning that when other groups try it out, trivial errors can lead to failure.
An online repository for scientific protocols aims to solve that problem. Sullivan and 293 other scientists are members of the Viral Ecology Research and Virtual Exchange network – called VERVE Net. VERVE Net is an online forum housed in the protocols.io platform, both of which are funded by the Moore Foundation’s Marine Microbiology Initiative.
The protocols.io platform was borne out of frustration, when CEO Lenny Teytelman spent a year and a half of his post-doctoral position troubleshooting a method. “I became obsessed with creating a sort of central repository,” Teytelman says. One “where it's easy to share details and share the corrections and innovation long after we publish.”
Researchers post their methods to VERVE Net through protocols.io and it becomes a “living document,” says Bonnie Hurwitz, a computational biologist at the University of Arizona, VERVE Net creator and Moore Foundation grantee. Others can comment or make suggestions to improve a protocol, with the goal that users won’t struggle with issues someone else has already solved.
Now, Sullivan is collaborating with Jody Deming, a marine microbiologist at the University of Washington and Moore Foundation grantee. Under a Moore Foundation grant, Deming is studying the dynamics of microorganisms that reside at sub-zero temperatures in sea ice.
As seawater freezes, some of the salt is held within the ice to form brines – a liquid with high salt concentration that has a freezing point much lower than normal seawater. Such pockets within sea ice or ancient permafrost (called cryopegs) provide an isolated haven for microbial life.
Though researchers have studied sea ice brines for years, the viruses in sea ice remain a mystery. Part of the reason, Deming says, is that people haven’t taken the time to look. “It takes some crazy person like myself to want to explore those extreme places,” she says.
In a study from 2016 published in FEMS Microbiology Ecology, Deming and her colleagues discovered that an ancient cryopeg harbored 1000 times more bacteria than the surrounding ice and had a high number of viruses. Since bacteria and viruses are notorious for exchanging genes with one another, Deming now wants to know if shared genes help them survive in these extreme environments.
Sullivan and his lab are utilizing a method to learn whether the viruses in liquid brines are actively multiplying – i.e. whether they are ‘alive.’ The technique, called BONCAT, was developed by Victoria Orphan, a geobiologist at the California Institute of Technology and Moore Foundation grantee.
The team is also tracking gene flow in the system. Together, Deming, Sullivan and their colleagues could learn how it’s possible for microbes to live in a frozen tundra of ice – which could in turn reveal how life might survive on other planets with similar environments. For example, Mars and moons Enceladus and Europa all have ice on their surfaces that could shelter microbial life forms.
“If we're going to spend millions of dollars of taxpayer money to explore the solar system for life, we better know as much as we can about how life exists in extreme environments on this planet,” Deming says.