Cover Story

Are Viruses Another Branch of Life?

How Marine Microbes Support Ecosystems and Our Survival

IAS Senior Visiting Fellow Prof Curtis Suttle was among the first researchers to investigate viruses as components of ecosystems.

When we think of viruses, we may well think of sickness and disease. But viruses are much more than a cause of human illness. They are lifeforms that are essential to most living creatures, including all of us. Without viruses, no people on Earth would be able to survive. Many would be astonished that humans’ knowledge of viruses and their importance to maintaining life is rather recent. A few decades ago, even bacteria in the sea, let alone marine viruses, were hardly contemplated by scientists.

Prof Curtis Suttle, IAS Senior Visiting Fellow, was one of the first researchers to focus on marine virology, i.e. the study of viruses in marine environments.


The Ocean: Simple yet Diverse

Part of Suttle’s passion for the ocean may be due to his background. He spent a significant portion of his youth on the ocean, as his family was the first from Canada to sail around the world. Suttle traveled from the age of 9 through 14 and was inspired by a large variety of living organisms in the sea.

“My core interest has been why organisms live; what they are doing to our surrounding environment and their ecology. Virology has been around for many years and so have diseases. But when I started looking at viruses, few people thought much about viruses as part of the ecosystem as a whole,” Suttle recalls. “For the first 3 billion years after life emerged on Earth, all life on the planet was microbial. Microbial relationships have been around for billions of years, when there were no plants or animals. It was only relatively recently that other forms of life started to exist.”

“To me, the ocean is fascinating in so many ways. My childhood experiences opened my eyes to the amazing diversity of life that the oceans hold. But little did I realize that what I could see was only a small snippet of what was actually living there. The ocean is where life arose, and although we often think of the ocean as being an extreme environment, it is quite benign compared to the land. Temperatures are relatively stable, and there is always lots of water! It is here, billions of years ago, that life first appeared, and along with it, viruses.”


Viruses: More Our Friends than Our Enemies

Viruses are ubiquitous. In one study, Suttle and his collaborators found that even at the tops of mountains, 3,000 meters above sea level, the air was full of viruses. “The result was striking: in every square meter about 10 million viruses fall from the atmosphere every day. In the ocean, there are so many viruses that when we go swimming, we easily swallow 200–300 million viruses from water taken into our mouths. Interestingly, they do not make us sick. Despite the fact that we are surrounded by viruses all the time, they mostly float around and do nothing to our health.” Even though viruses must infect an organism to reproduce, each virus is very specific in terms of what it can infect, and the millions of viruses that we swallow when we go swimming cannot infect humans.

"Quite counter-intuitively, we rely on these microbial to survive. If viruses did not exist, neither would we. In order to have life, we must have death to recycle the nutrients that allow for processes such as photosynthesis in the ocean to occur. Viruses are probably more our friends than our enemies."

\\ If viruses did not exist, neither would we. In order to have life, we must have death to recycle the nutrients that allow for processes such as photosynthesis in the ocean to occur. \\

An image taken with an electron microscope of a “giant virus” from the ocean. Although a giant among viruses, if it was enlarged to the size of a pinhead, and a human at the same scale would be 10 kilometers tall.
Photo credits: Chuan Xiao, Matthias G. Fischer, Duer M. Bolotaulo, Nancy Ulloa-Rondeau, Gustavo A. Avila & Curtis A. Suttle,  (2017) “Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests novel assembly pathway for giant viruses”, Nature Scientific Report 7

Viruses Tell the History of Evolution

Through extensive categorizing and cataloguing of viruses and their genetic information, scientists are able to reconstruct a larger part of evolutionary history of viruses. Experiments that isolate certain viruses can reveal how these invisible organisms function.

“There has been a large debate over whether viruses constitute life. One of the reasons is that viruses possess a lot of the properties of living organisms but not all of them. They carry a lot of genetic nformation and evolve over time, but viruses cannot reproduce on their own and must infect a host cell in order to reproduce and be active. Otherwise, they are merely inert particles.” 

In a very recent study, Suttle’s team discovered a giant virus. “Viruses are usually thought of as small and simple, but this virus is very large in terms of the amount of the genetic information it contains, usually measured in ‘base pairs’. Humans have giga-bases of DNA, while bacteria have 1 million to a few million base pairs. The smallest viruses may have 2,000 base pairs, but the giant virus we found has 1.4 million, even more than many bacteria.”

What is Life and What is Not?

An emerging view is that cellular life and viruses represent two branches of life. Giant viruses are changing scientists’ views, because such complex coding machinery was thought to exist only in cellular organisms. Findings such as the discovery of this new giant virus are blurring the line between what is living and what is not.

Although the team has sequenced the genome—the coding information—of this virus, scientists do not know the purpose of more than 50% of the putative genes. “What is known, however, is that the virus is klepto-genomic. ‘Klepto’ is a Greek-rooted word for ‘steal’. This virus steals genetic information from other organisms and co-opts it into its own genetic repertoire. This virus infects a very small zooplankton—a microzooplankton—and likely acquired these other genes from organisms that were being digested by the microzooplankton. The types of genes found in this virus are typically found in much higher organisms. The fact that this virus has qualities of cellular life is totally fascinating!” 


Genetic information is contained in the “genome”, which is made up of the “base pairs” A, G, C, and T that encode the genetic information. The size of the genome is measured by the number of base pairs, which in turn make up genes that can be seen as colored blocks in this map of a giant virus genome. Image courtesy of Matthias G Fischer (Max Planck Institute for Medical Research) and Chuan Xiao (University of Texas at El Paso).

\\ The discovery of this new giant virus is blurring the line between what is living and what is not. \\

A Neglected Part of the Ecosystem 

The ocean is microbial. By weight, about 95% of living biomass in the ocean is microscopic, and about half of the oxygen production on this planet is a result of the activities of these microbes. It turns out that in addition to marine microbes being food for predators, every day, viruses kill about 20% of these organisms by weight, most of which are bacteria.

The mortality imposed by viruses on marine life has consequent effects on the recycling of nutrients. In the near-surface waters of the ocean, where there is lots of light, single-celled plants called phytoplankton are abundant. They are crucial to our ecosystem because they convert carbon dioxide into organic carbon by photosynthesis, producing oxygen as a byproduct. They enjoy rich supplies of light and carbon dioxide but may lack other minerals that are available on land such as nitrogen, phosphorus, iron, and other nutrients. When viruses kill their microbial hosts, they release nitrogen and other nutrients into the ocean, thereby supplying food to microbes, including phytoplankton that can continue to photosynthesize. In this way, viruses are essential to keeping the system running.

“The ecosystem is so interconnected; each piece isn’t hard to explain, but there are so many connections and feedback loops that it is very hard to predict the effect of global warming on viruses and the processes they mediate.”


Advancement of Knowledge in Marine Microbiology 

Prior to the 1970s

The dogma among scientists was that bacteria and viruses played a relatively minor role in the ocean, and that foodwebs, where “big ate small”, represented the main flow of nutrients in the marine ecosystem. 

1970s

Larry Pomeroy, Farooq Azam and other scientists argued that bacteria were very important players in the sea, even though most could not be grown in culture. New methods to count bacteria and measure their activity were developed. 

1980s

Researchers capitalized on new methods to count bacteria and measure their activity, and the central importance of bacteria in marine ecosystems became widely accepted.

1990

Within a year of each other, three research groups, including one led by Curtis Suttle, published papers showing that viruses were abundant and acted as mortality agents in the sea, leading to a new perspective on their importance.

1990s-2000s 

Marine viruses were shown to harbor vast diversity and have major effects on the mortality and composition of marine ecosystems. Research interest and the number of research groups on this subject expanded rapidly. 

Recent developments

The paradigm is shifting, with viruses being incorporated into marine ecosystem models and included in textbooks. Viruses are beginning to be viewed as essential and beneficial components of marine ecosystems.


A Paradigm Shift in the 1990s – Viruses as Part of Nature 

When Suttle first submitted a grant proposal to study viruses in the ocean in 1990, he took his reviewers by surprise. At the time, the funding agencies could find no appropriate reviewers with a suitable background to evaluate the proposal. The proposal was sent to oceanographers and molecular biologists for review, neither of which appreciated the questions that he was trying to address. Little did he realize back then how this line of research would lead to a paradigm shift.

Prior to the 1970s, it was a common belief among scientists and the public that the ocean was full of plants and animals, big and small. Our knowledge about the marine world was typically a classic model of the food chain. Predators prey on creatures on the lower tiers of the hierarchy, while smaller animals and microbes feed off the remains of dead plants and animals.

Although the existence of bacteria in the sea was recognized, their significance, and later that of viruses, was vastly underappreciated. This began to change in the early 1970s when Larry Pomeroy, Farooq Azam and other emerging marine microbiologists argued that the role of bacteria in the sea was much more significant than had previously been thought. This new perspective was not only correct, but it also laid the foundation for the recognition of the significance of viruses in the sea.

In 1987, when Suttle was a postdoctoral fellow with Jed Fuhrman at Stony Brook University in New York, he was exposed to the work of Lita Proctor, a PhD student in his lab, who was finding that viruses were vast and abundant in seawater. Their observations, along with anecdotal observations of collapses of phytoplankton blooms and virus-infected cells and work done in the 1970s by PhD student Jolie Meyer and F.J.R. “Max” Taylor, inspired Suttle to explore whether viruses might be important pathogens of phytoplankton in the sea. This was the beginning of Suttle’s investigation into viruses in the ocean.

Suttle recalls that initially there were three research groups in the world, including his own, that were dedicating their efforts to studying viruses in the ocean. In recent years, interest has grown rapidly, and there are now dozens of labs investigating viruses in the ocean. An internet search of “ocean” and “viruses” reveals more than 64,000 publications on the topic. “Our knowledge has grown enormously in the past 20 to 30 years, but there is still much to be learned. We are continuously discovering new types of viruses and isolating new virus–host systems. As well, interest has expanded to understanding the role of viruses in regulating fish and shellfish populations and how this might tie in to global warming and ocean acidification.”

Although Suttle’s research is based at the University of British Columbia, he makes regular visits to HKUST and other parts of the world to collect samples and interact with others in the field. He was visibly excited about co-chairing the Gordon Research Conference with Prof Stanley Lau from HKUST Division of Life Science. “Our conference focuses on an approach but not exactly on a discipline. You see people talking about a lot of different ways research can be done. After all, working on the ocean is a multidisciplinary effort. You cannot understand it without using many different approaches and understanding many different aspects.”

\\ When I started looking at viruses, few people thought much about viruses as part of the ecosystem as a whole. \\

Life scientists add fluorescence to specimens so that they are visible under microscopes. Once the lights are off, a tiny piece of empty glass becomes a lively world overwhelmed by bacteria and viruses.