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Germ warfare between bacteria and viruses is a standoff

USC marine biologists have found that the endless struggle between viruses and bacteria ends in a stalemate, scientific proof of the evolutionary principle known as the “Red Queen.”

ocean microbe testing bacteria and viruses
USC researchers test the offshore waters of Southern California to study how microbes adapt and evolve. (Photo/Jennifer Beatty)

In the waves offshore of Southern California, germ warfare occurs in a struggle as old as life itself.

It’s where USC marine biologists completed a comprehensive new study that shows the tactics bacteria and viruses employ to gain advantages against each other. What they found is that an unlikely standoff occurs, regardless of time, season or location — proof of the evolutionary principle of the “Red Queen” hypothesis.

“The Red Queen concept in biology means a species running fast in place just to keep even, and that’s what we found in these microbial communities,” said Jed Fuhrman, lead author of the study and marine biologist at the USC Dornsife College of Letters, Arts and Sciences. “This is one of the modern tenets of evolutionary biology, and our observations fit nicely within the framework.”

The research was published today in Nature Microbiology.

Why does bacteria versus viruses end in a stalemate?

The battleground for this clash of microscopic organisms is a sliver of the Pacific Ocean between Los Angeles and Catalina Island. Those waters are immediately adjacent to some of the most popular beaches in the United States.

Oceans are full of viruses and bacteria; they are the oldest and most diverse creatures on Earth. Though small, if taken together in one lump they comprise 90% of the weight of all living creatures in the ocean. They perform essential functions in the ecosystem, recycle nutrients and influence the planet’s climate. They’ve been in the ocean since the beginning of life, and they mostly don’t bother swimmers and bathers. But they are not nice to each other.

Viruses are constantly trying to infect algae and bacteria. At first glance, the fight appears lopsided, because viruses vastly outnumber other marine organisms. A cup of ocean water can hold 1 billion virus particles. Yet, bacteria rely on countermeasures to protect themselves.

The USC scientists sought to explain why the struggle is a stalemate.

“It has been a puzzle how marine viruses, which are astoundingly abundant at about 10 million per milliliter of seawater, persist at such high abundances despite the ability of their hosts — mostly bacteria — to defend themselves,” Fuhrman said.

Virus communities: Stable yet mutating

The researchers sampled surface seawater almost every month for five years between the summers of 2009 and 2014. They analyzed more than 1 billion genetic sequences to sort the different types of viruses. They compared those findings to weather and ocean conditions and to bacteria populations.

Two key findings emerged:

  • The virus communities remained stable. Some 95% of the same virus species were identified in nearly all the samples. The stability persisted over time and location. While similar findings have been reported previously, the new study is unique because no other study showed this extent of stability over such a long period.
  • Within each virus species, there was constant churning of mutants, each of which dominated the populations for only a few months. The scientists say this churn allowed the viruses to stay one step ahead of host defenses, which means they need to keep changing in order to survive.

The dynamic occurring among microbes in the ocean “strongly resembles Red Queen dynamics, which are rapid changes of genotypes within a population from ecological and evolutionary mechanisms,” the study says.

The Red Queen hypothesis proposes that organisms must constantly adapt to spread or else die in a changing environment of competitors. The USC study is one of but a few to show this evolutionary dynamic anywhere in nature.

The USC marine science program, largely based at the USC Dornsife College and the USC Wrigley Institute for Environmental Studies, has 22 scientists — about one-quarter of the university’s biology department — who are focused on marine and environmental biology.


The study authors are Fuhrman, J. Cesar Ignacio-Espinoza and Nathan Ahlgren at Clark University, formerly a postdoctoral researcher at USC. The work was supported by a National Science Foundation Grant (1737409), a National Institutes of Health grant (1R01GM120624-01A1), the Gordon and Betty Moore Foundation Marine Microbiology Initiative (3779), a Community Sequencing Project from DOE Joint Genome Institute, and the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (549943).

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Germ warfare between bacteria and viruses is a standoff

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