New Type of Virus Found in the
Ocean
The unusual characteristics of these abundant, bacteria-killing
viruses could lead to evolutionary insights.
By David L. Chandler, MIT News Office
January 24, 2018 -- A type of virus that
dominates water samples taken from the world’s oceans has long escaped analysis
because it has characteristics that standard tests can’t detect. However,
researchers at MIT and the Albert Einstein College of Medicine have now managed
to isolate and study representatives of these elusive viruses, which provide a
key missing link in virus evolution and play an important role in regulating
bacterial populations, as a new study reports.
Viruses are the main predators of
bacteria, and the findings suggest that the current view of bacterial virus
diversity has a major blind spot. These conclusions have emerged through
detailed analysis of marine samples led by MIT postdoc Kathryn Kauffman,
professor of civil and environmental engineering Martin Polz, professor Libusha
Kelly of Albert Einstein College of Medicine, and nine others. The results are
being reported this week in the journal Nature.
The newly identified viruses lack
the “tail” found on most catalogued and sequenced bacterial viruses, and have
several other unusual properties that have led to their being missed by
previous studies. To honor that fact, the researchers named this new group the Autolykiviridae
— after a character from Greek mythology who was storied for being difficult to
catch. And, unlike typical viruses that prey on just one or two types of
bacteria, these tailless varieties can infect dozens of different types, often
of different species, underscoring their ecological relevance.
This research “opens new avenues
for furthering our understanding of the roles of viruses in the ocean,” says
Jed Fuhrman, the McCulloch-Crosby Chair of Marine Biology at the University of Southern California, who was not
involved in this work. “In a practical sense, it also shows how we need to
alter some commonly used methods in order to capture these kinds of viruses for
various studies,” he says. “I’d say it is an important advance in the field.”
Current environmental models of
virus-bacteria interactions are based on the well-studied tailed viruses,
Kauffman explains, so they may be missing important aspects of the interactions
taking place in nature.
“We already knew that viruses are
very important there,” Kauffman says, referring to the surface ocean, where the
researchers’ samples were drawn, and where about 10 million viruses are found
in every milliliter of water. Polz says that while “most of the viruses studied
in labs have tails, most of those in the ocean don’t.” So the team decided to
study one subset of tailless viruses, which infects a group of bacteria called Vibrio.
After extensive tests, they found “that some of these were infecting unusually
large numbers of hosts,” he says.
After sequencing representatives of
the Autolykiviridae, the researchers found “their genomes were quite
different from other viruses,” Polz says. For one thing, their genomes are very
short: about 10,000 bases, compared to the typical 40,000-50,000 for tailed
viruses. “When we found that, we were surprised,” he says.
With the new sequence information,
the researchers were able to comb through databases and found that such viruses
exist in many places. The research also showed that these viruses tend to be
underrepresented in databases because of the ways samples are typically handled
in labs. The methods the team developed to obtain these viruses from environmental
samples could help researchers avoid such losses of information in the future.
In addition, Kauffman says, typically the way researchers test for viral
activity is by infecting bacteria with the viral sample and then checking the
samples a day later to look for signs that patches of the bacteria have been
killed off. But these particular nontailed viruses often act more slowly, and
the killed-off regions don’t show up until several days have passed — so their
presence was never noticed in most studies.
The new group of viruses may
especially be widespread. “We don’t think it’s ocean-specific at all,” Polz
says. For example, the viruses may even be prevalent in the human biome, and
they may play roles in major biogeochemical cycles, he says, such as the
cycling of carbon.
Another important aspect of theses
findings is that the Autolykiviridae were shown to be members of
an ancient viral lineage that is defined by specific types of capsids, the
protein shell encasing the viral DNA. Though this lineage is known to be very
diverse in animals and protists — and includes viruses such as the adenoviruses
that infect humans, and the giant viruses that infect algae — very few viruses
of this kind have been found to infect bacteria.
“This work substantially changes
the existing ideas on the composition of the ocean virome by showing that the
content of small, tailless viruses … is comparable to that of the tailed
viruses … that are currently thought to dominate the virosphere,” says Eugene
V. Koonin, a senior investigator at the National Institutes of Health, who was
not involved in this research. “This work is important also for understanding
the evolution of the virus world because it shows that viruses related to the
most common viruses of eukaryotes (such as adenoviruses, poxviruses, and
others), at least in terms of the capsid structure, are much wider-spread in
prokaryotes than previously suspected.”
Koonin adds, “I further wonder
whether the viruses reported here might only represent the tip of the proverbial
iceberg, because capsid proteins can be highly diverged in sequence so that
many are missed even in sensitive database searches. The findings are also of
practical importance because the tailless viruses appear to play a major
ecological role in the ocean, being responsible for a substantial fraction of
bacteria-killing.”
