91探花 oceanographer studies viruses 鈥� but not the viruses that get people worried. He studies viruses that infect ocean microorganisms, which are some of the most abundant living things on the planet.

Morris, a 91探花associate professor of oceanography, previously found that the most common bacteria in the oceans, SAR11, hosts a virus in its DNA. That virus is dormant most of the time, but when and how it erupts could play important roles in ocean ecology and evolution.

Now Morris and a collaborator at the University of California, Los Angeles, are going out with students to collect more of these tiny bacterial hosts and their viral guests to understand how these relationships change depending on the place or the season. They leave Dec. 16 aboard 91探花School of Oceanography鈥檚 small research vessel, the .

91探花News asked Morris a few questions about the upcoming cruise, which includes four undergraduate students, as part of an occasional series, 鈥�In the Field,鈥� highlighting 91探花field efforts.

Where are you going, and when?聽

Robert Morris: Our research cruise will travel from the to the San Juan Islands. This track gives us access to important areas in Puget Sound as well as to the Strait of Juan de Fuca, where open ocean water enters the Puget Sound.

We leave on Monday, Dec. 16 and return Friday, Dec. 20.

Have you visited these waters in the past?

RM: This is our third cruise. The first cruise was in September 2023 and focused on the Puget Sound main basin and Hood Canal. The second cruise was this past July and focused on the main basin, the Strait of Juan de Fuca, and areas around the San Juan Islands. This third cruise will be a repeat of the summer cruise, but at a different time of year to investigate seasonal differences in the viruses that infect marine bacteria.

Who is going on the cruise?

RM: I am chief scientist on all three cruises, and , at the University of California, Los Angeles, is co-chief scientist. Each cruise has one additional mentor and four UCLA undergraduates.

For this cruise, the mentor is Jason Graff at Oregon State (past mentors have been 91探花graduate students Kunmanee Bubphamanee and Dylan Vecchione). For this cruise, the undergraduate students are Grace Donohue, Natalie Falta, Eleanor Gorham and Madeleine Swope.

What does your team hope to learn from this place?

RM: On the scientific side, we hope to identify spatial and temporal patterns in viruses that infect the oceans鈥� most abundant bacteria, which is SAR11. More specifically, we collect samples to identify the number and types of SAR11 bacterial cells that have viruses in their genomes and isolate new SAR11 species and the viruses that infect them throughout Puget Sound in summer and winter. We鈥檙e also curious how the number of viruses affects infection patterns across our sample sites and seasons.

From an outreach perspective, the field program was designed to allow students from 91探花and UCLA to collaborate and learn 鈥渉ands-on鈥� oceanography and to see how research ideas and experiments inform each other, especially when working in interdisciplinary teams and with active mentorship. We expect this field experience to expose more students to oceanographic fieldwork, which may inspire further studies in oceanography or other sciences.

If this is a repeat effort, will this year be different in any way?

RM: The upcoming cruise is the first one that will be conducted in the winter, with the goal of identifying viruses with different infection strategies. For instance, in the winter we expect to find fewer SAR11 cells, but more with viruses hiding out in their genomes.

Briefly, what鈥檚 a typical day in the field (if there鈥檚 such thing as a typical day)? And what鈥檚 something you enjoy about doing this field work?

RM: We start the day by collecting samples and setting up an incubation study, where we incubate and grow more bacterial cells. We do four incubation studies on each cruise. The study is designed to multiply bacterial viruses in a way that increases the number of cells that are infected. After the incubation experiment is set up, we visit other sites to collect background data that tells us about the environmental conditions in the surrounding area.

One of the most exciting parts of the day-to-day activities is that you don鈥檛 know what the day will bring. Much of the work is outside, so it can be sunny and calm, or rainy and rough. The work gets done either way!

Anything you鈥檇 like to add?

RM: We are working on a collaborative manuscript that will include data from the incubation studies and all student participants. 91探花graduate student , a doctoral student in Earth and space sciences, conducted research in my laboratory for her 91探花Astrobiology research rotation, and was able to gain field research experience during the second cruise. Two 91探花graduate students in my lab, and , will include bacterial culture and genetic sequencing data in future manuscripts.

Lastly, this has been an amazing experience and although many of the students from UCLA have not stayed in oceanography, most have applied to or have gone on to graduate school in science. It has been fantastic interacting with all of the students and seeing them grow into experienced oceanographers over the length of the cruises.

For more information, contact Morris at morrisrm@uw.edu.

The most common organism in the oceans, and possibly on the entire planet, is a family of single-celled marine bacteria called SAR11. These drifting organisms look like tiny jelly beans and have evolved to outcompete other bacteria for scarce resources in the oceans.

We now know that this group of organisms thrives despite 鈥� or perhaps because of 鈥� the ability to host viruses in their DNA. A published in May in Nature Microbiology could lead to new understanding of viral survival strategies.

91探花 oceanographers discovered that the bacteria that dominate seawater, known as Pelagibacter or SAR11, hosts a unique virus. The virus is of a type that spends most of its time dormant in the host鈥檚 DNA but occasionally erupts to infect other cells, potentially carrying some of its host鈥檚 genetic material along with it.

鈥淢any bacteria have viruses that exist in their genomes. But people had not found them in the ocean’s most abundant organisms,鈥� said co-lead author , a 91探花associate professor of oceanography. 鈥淲e suspect it’s probably common, or more common than we thought 鈥� we just had never seen it.鈥�

This virus鈥� two-pronged survival strategy differs from similar ones found in other organisms. The virus lurks in the host鈥檚 DNA and gets copied as cells divide, but for reasons still poorly understood, it also replicates and is released from other cells.

The new study shows that as many as 3% of the SAR11 cells can have the virus multiply and split, or lyse, the cell 鈥� a much higher percentage than for most viruses that inhabit a host鈥檚 genome. This produces a large number of free viruses and could be key to its survival.

鈥淭here are 10 times more viruses in the ocean than there are bacteria,鈥� Morris said. 鈥淯nderstanding how those large numbers are maintained is important. How does a virus survive? If you kill your host, how do you find another host before you degrade?鈥�

The study could prompt basic research that could help clarify host鈥搗irus interactions in other settings.

鈥淚f you study a system in bacteria, that is easier to manipulate, then you can sort out the basic mechanisms,鈥� Morris said. 鈥淚t鈥檚 not too much of a stretch to say it could eventually help in biomedical applications.鈥�

The 91探花oceanography group had published a previous paper in 2019 looking at how marine phytoplankton, including SAR11, use sulfur. That allowed the researchers to cultivate two new strains of the ocean-dwelling organism and analyze one strain, NP1, with the latest genetic techniques.

Co-lead author collected samples off the coast of Oregon during a research cruise. She diluted the seawater several times and then used a sulfur-containing substance to grow the samples in the lab 鈥� a difficult process, for organisms that prefer to exist in seawater.

The team then sequenced this strain鈥檚 DNA at the in Seattle.

鈥淚n the past we got a full genome, first try,鈥� Morris said. 鈥淭his one didn’t do that, and it was confusing because it’s a very small genome.鈥�

The researchers found that a virus was complicating the task of sequencing the genome. Then they discovered a virus wasn鈥檛 just in that single strain.

鈥淲hen we went to grow the NP2 control culture, lo and behold, there was another virus. It was surprising how you couldn鈥檛 get away from a virus,鈥� said Cain, who graduated in 2019 with a 91探花bachelor鈥檚 in oceanography and now works in a 91探花research lab.

Cain鈥檚 experiments showed that the virus鈥� switch to replicating and bursting cells is more active when the cells are deprived of nutrients, lysing up to 30% of the host cells. The authors believe that bacterial genes that hitch a ride with the viruses could help other SAR11 maintain their competitive advantage in nutrient-poor conditions.

鈥淲e want to understand how that has contributed to the evolution and ecology of life in the oceans,鈥� Morris said.

Co-authors are postdoctoral researcher and associate professor in the 91探花Department of Biochemistry. The study was funded by the National Science Foundation and the National Institutes of Health鈥檚 National Institute of Allergy and Infectious Disease.

For more information, contact Morris at morrisrm@uw.edu or 206-221-7228 and Cain at kcain97@uw.edu.

These are , a diverse group of organisms that includes microalgae, viruses, bacteria and archaea. They serve as the base of the marine food chain and are responsible for controlling much of the ocean’s nutrient flow and health.

But given their prevalence, very little is known about how they interact and carry out fundamental processes in the ocean, particularly in deep, low-oxygen waters where the impacts of climate change are becoming significant. In these areas, up to half of all available nitrogen 鈥� a nutrient that is essential for all ocean life 鈥� is lost due to microbial processes on overdrive because of warmer ocean water and less circulation.

Now, a 91探花 team has on a common but poorly understood bacteria known to live in these areas. By culturing and sequencing the microbe’s entire genome, the oceanographers found that it significantly contributes to the removal of life-supporting nitrogen from the water in new and surprising ways.

“If we want to understand how the oceans are working and be able to model them in any sort of predictive way, we need to more accurately understand what the inputs and outputs are,” said senior author , a 91探花associate professor of oceanography. “This is an important organism that fixes carbon, is involved in nitrogen loss and is in parts of the ocean that are shifting due to climate change. We now have the first-ever culture in the laboratory and we can study its physiology.”

The were published聽July 19 in the , a Nature publication.

This organism, given the name Candidatus Thioglobus autotrophicus, is present in low-oxygen waters around the world and is one of the dominant organisms in these areas 鈥� between 40 and 60 percent of all cells in some regions.

Living things use oxygen for their metabolic activities, but in low-oxygen areas, bacteria and archaea have evolved to “breathe” other elements available in seawater. One of those is a chemical called nitrate which, when respired, produces gaseous nitrogen. That gas escapes to the atmosphere, effectively leaving the ocean and removing valuable nitrogen from the water.

The bacteria grown and sequenced by the 91探花oceanographers have been pegged as playing a big role in removing nitrogen from the ocean, but until now scientists didn’t have a complete picture of how it happened.

“We are filling in the gaps by providing a full genome,” said lead author , a 91探花doctoral student in oceanography. “Now we can talk about both what these organisms can and can’t do.”

The research team confirmed the bacteria are contributing to nitrogen loss, but in a different way than expected. More specifically, they are responsible for a key step 鈥� converting nitrate to a similar chemical called nitrite 鈥� which then goes on to fuel other nitrogen-removal processes. Earlier research had hypothesized that these microbes also produce ammonia, another nitrogen-containing chemical. Instead, the 91探花team found that the microbes consume ammonia, essentially competing with other organisms for this nitrogen compound that is also important for growth and development.

At a global scale, the areas of the ocean where these bacteria live are getting bigger as climate change creates conditions that produce low-oxygen zones, including warmer ocean temperatures and less water circulation.

“In the very big picture, we know that different types of oxygen minimum zones that house these organisms are getting bigger and more persistent,” Shah said. “So, whatever influence these bugs have on water chemistry and the atmosphere is going to get more and more important 鈥� basically, their habitat is expanding.”

Growing this organism in the lab was no easy task. The 91探花oceanographers combined several techniques to culture the bacteria in as close as possible to their native ocean environment. It took almost a year to stabilize them to the point where researchers could start doing physiological experiments.

Even the experiments, however, took more time than usual, because these organisms grow much slower than most cultures grown in the lab.

“Most experiments lasted 10 to 15 days because they were growing so slowly. But the advantage is they are actually behaving very similarly to how they do in the ocean environment,” Morris said.

Shah collected the organism from a low-oxygen fjord off the coast of British Columbia from the R/V Thomas G. Thompson during a . She then used these organisms to grow identical offspring in the lab.

The researchers will look next at the role this bacteria play in the ocean’s carbon and sulfur cycles. They also recently received National Science Foundation funding to study this organism and its relatives in other low-oxygen areas around the world, including off the coast of Mexico.

of the UW’s Joint Institute for the Study of the Atmosphere and Ocean is a co-author on this study. The work was funded by the National Science Foundation, the 91探花Royalty Research Fund and the .

###

For more information, contact Morris at morrisrm@uw.edu or 206-221-7228 and Shah at vs1@uw.edu or 206-685-4118.

Grant numbers: OCE-1232840, DGE-1068839