Marine Ecology

The Seagrass Microbiome Project: Bacteria, the Unseen Heroes?

By Jane Park, Undergraduate Intern



Though bacteria often get a bad reputation, many organisms depend on them. Humans, for example, have gut bacteria that aid with digestion. Similarly, marine plants, like seagrass, host a collection of microorganisms potentially vital to their health. At UC Davis, researchers have created the Seagrass Microbiome Project to learn about these microbial inhabitants. Through the project, they are looking to see whether certain bacteria are fundamental to the plant’s survival.

The Seagrass Microbiome Project started as a collaboration between Jay Stachowicz, a marine biologist, and Jonathan Eisen, a microbiologist. Their objective is to survey the microbiome of seagrass and to analyze its relationship with the plant. “It’s well known that all plants have microbes—bacteria and fungi—associated with them,” says Stachowicz. “Especially in terrestrial systems, people think about crop plants and legumes, or the mycorrhizal fungi associated with plant roots, being really important for those plants. But we haven’t looked at what goes on in marine systems on marine plants until recently.” The project aims to fill that gap of information by using seagrass as a model organism.

Seagrasses are important foundation species in coastal ecosystems. They provide structure in environments with loose sediment, which creates habitat for a diverse array of organisms like fish and invertebrates. The grasses also power the food chain by housing algae and bacteria, which are grazed upon by small invertebrates, which are then consumed by other animals. “Everything else literally rests on them,” Stachowicz says. “They provide both a source of food and a source of physical structure on which the entire ecosystem depends.”

Stachowicz’s lab studies the common eelgrass (Zostera marina), a species of seagrass found in the Atlantic and Pacific Ocean. “When we started, we didn’t know what microbes were there,” says Stachowicz. “And so, we had to start with the very basics of describing what was found on different parts of the plant, and whether that varied from place to place.”

Recently, Stachowicz and his team have managed to find a consistent pattern: the presence of sulfide-oxidizing bacteria that are more abundant on the seagrass roots than in the surrounding sediments. One challenge for rooted plants living in marine habitats is low oxygen. As accumulated organic matter in the sediment decomposes, oxygen is depleted, and toxic sulfides are produced as well. “There are bacteria on the roots that are capable of oxidizing those sulfides, rendering them harmless” explains Stachowicz. “We think this may be a way that the microbes play a role in the success of the plants, though this remains to be directly tested.”

Although researchers have surveyed the general outline of what bacteria are present, the picture isn’t complete yet. “We’re getting a good map of what’s there,” says Stachowicz. “Now we need to know: What do these bacteria do? Are they just responding to the plant? Do they influence the plant in some way? Or is it just the environment that drives them?” In order to investigate these relationships, more research is needed.

Currently, Stachowicz’s lab is conducting research on how the microbes affect the plant’s response to stressors like temperature and disease. He emphasizes the value of learning about the plant’s microbiome. “If we think seagrasses are important—which we do—and we want to restore or protect them, knowing the role of these microbes is something that we’re going to have to account for looking forward,” Stachowicz tells me.

Though invisible to the human eye, bacteria occupy every nook and cranny, even seagrasses, as the Seagrass Microbiome Project tells us. What do the bacteria do for these plants, and how important are they? Well, that’s a question that still needs to be answered.



“CSI” for the Marine Ecologist 

powdered seagrass
Powdered seagrass tissue suspended in a detergent solution during the early stages of DNA extraction.

By Nicole Kollars

A patch of a seagrass meadow in Bodega Harbor, CA.  A patch this size may contain many different genetic clones, but you won’t be able to distinguish which clone is which just by looking at the plants.

The popular television show CSI: Crime Scene investigation follows the day-to-day drama of a team of investigators whose job it is to determine whodunit.  While watching the show, it is common to see forensic scientists in lab coats using a variety of oddly-shaped tools and instruments to extract DNA (i.e., deoxyribonucleic acid - the building blocks of life) from hair or saliva samples collected at the scene of the crime. After extracting and visualizing the DNA, the scientists can then compare their results to samples collected from suspected persons and oftentimes, solve the mystery. 

Fictional television aside, the advent of DNA technologies has changed numerous aspects of modern life.  For example, scientists study genetics for the purposes of solving crimes, advancing human medicine, conserving endangered species, and managing food production (i.e., agriculture and fisheries).  As a marine ecologist, I use these same DNA technologies to identify clones of seagrass, a flowering plant that lives in shallow coastal bays and harbors.

Seagrass populations reproduce through seeds and by producing genetic clones of the plants already present in a seagrass meadow.  Nearly two decades of research has shown that the genetic identity of a seagrass plant matters.  Some clones grow faster than others, while other clones are more resilient to stresses in the environment (e.g., high temperatures or a hungry goose eating the plant’s leaves).  Furthermore, seagrass meadows that have a higher number of clones in the population are overall healthier than seagrass meadows made up of only one or two clones. Healthy seagrass meadows translate to benefits for human communities such as healthy populations of commercially important fishes, reduced water pollution, and increased protection from coastal storms.     

Using a tool called a pipette to add a known amount of alcohol to each extraction sample.

However, a scientist cannot know the clonal identity of a seagrass plant by just looking at it.  Here is where DNA technologies become incredibly useful tools for the marine ecologist.

The first step is to extract the DNA from a ~ 1cm2 clipping of the seagrass leaf.  Extraction involves grinding the leaf piece up into a powder, adding a detergent-based solution to get the DNA out of the cells, and using various types of alcohols (i.e., isopropanol and ethanol) to get rid of any non-DNA material that hitched a ride out of the cell alongside the DNA. After extraction, we use a technique called the polymerase chain reaction (or PCR for short) to make many, many, many copies of the DNA.  Having many copies of the DNA makes it easier for an instrument to determine the unique DNA code for that individual sample, similar to how it is easier to tell the type of tea your drinking by taking a long sip versus a tiny taste. We repeat this process for any sample we are interested in, knowing that clones will have the same genetic code.  By using these techniques, we know that a 1m2 patch of seagrass can have anywhere from 1 to 15 clones!

CSI ("clonal seagrass identification") for the marine ecologist may not solve crime, but like our scientific counterparts in the forensics department, we can use DNA technologies to solve mysteries of identity.



Into the Deep End

Helen Killeen on RVMP night cruise

By Helen Killeen

The rest of the crew and I have various nicknames for the gear we use to collect fish plankton from the depths, and none of them are particularly complimentary. Two months ago I found myself securing our nets for another deployment one last time. It was around 2am and I was thrilled that I would not have to scramble over nets and lines and hitch up the four heavy nets for another round of fishing. This was the last deployment of the last station of the last cruise for the year. Even with the rocking of the boat and the choppy seas, it only took me about five minutes to get things squared away. What a relief.

RVMPOnce I stepped away from the rig, ready to deploy the nets one more time 25 miles from shore, it flashed through my mind that doing this used to be much more difficult. On the very first cruise, a year before, it took three of us upwards of twenty minutes to get the stupid nets to hang correctly. To make things worse I was so seasick I could hardly keep myself upright for more than a few minutes at a time, let alone manage a crew much more seasoned than myself to conduct a complicated scientific sampling protocol. When we docked at the end of those first few trips, I felt sure that I was not the right person for the job and was sorely aware of my inadequacies as a scientist and leader.

What helped me through those first few trips was recalling moments when I’d felt similarly unprepared and inadequate. After college, I took a position as a high school teacher. The first few months were similar to what many first-year teachers experience: a total mess. I couldn’t manage the class, I struggled to craft lessons, and stay afloat in a sea of paperwork. However, as the months wore on, I stopped making the same small (and sometimes big) mistakes over and over again. Prior failures turned into valuable experience that gave me the confidence to make and carry out my decisions. I desperately hoped that the same would happen if I could stick it out through just a few more night cruises.

catchThe only way I was going to make it though was if I stopped sweating every little mistake. If I stopped feeling like a failure every time I didn’t set the computer up right, or didn’t hit the right target depth for a sample, or made the wrong call on the weather. So I decided that I would need to make a conscious, painful effort to let the mistakes go. I would focus on lessons learned, and take time to reflect on what I was doing right.

There are many elements to success in graduate school: a network of peers, strong mentors, and an inclusive academic community. But I am learning that no one escapes without a healthy dose of failure. And it is in part how we choose to respond to these failures that determines whether we are able to overcome obstacles and become better scientists. While I’m glad I won't have to clamber around a boat in the middle of the tumultuous nighttime sea for a while, I’m grateful for the opportunities to fail that doing so over the last two years has given me.



Remembering Susan Williams

Susan Williams

At the Bodega Marine Laboratory and CMSI, we couldn’t be more honored and humbled to have Dr. Susan Williams a part of our community for so long. On the 26th of October, over 180 people from around the world gathered to celebrate the life of Dr. Williams.  

“I wanted to be an oceanographer since second grade, without understanding what that meant other than being fascinated by "things" that washed up on the beach during seaside family vacations.” - Dr. Susan Williams in her CMSI Spotlight.

“Scientific discoveries help people understand our world and galaxies beyond, predict the future, fuel economic growth and reconnect all of us back to our childlike wonder.” - Dr. Williams for The Conservation on science advocacy.

CAMEOS Fellows J Bean and R Fontana

As program director of CAMEOS, Coastal, Atmospheric, and Marine Environmental Observation Studies, from 2010 to 2016, Williams helped build on national ocean and science literacy initiatives and broadens participation of underrepresented graduate and K-12 students in inquiry-based STEM education.






Dr. Susan Williams helped protect countless coral in Indonesia. Learn about the development of a new “spider” conservation technique. 

Another study revealed that a quarter of fish sold in markets contain man-made debris.


marine debris workshop

Above, Katie Dubois and Dr. Susan Williams in Indonesia from Dubois’s blog post, Encountering the Marine Debris Crisis in Indonesia.

Dr. Williams’ team also illustrated that restoration efforts could be improved by using diverse array of seagrass transplants rather than a single founder species.

Williams shared her research in the short documentary, The Time is Now, the Future is Here.

CERF presidents



Dr. Williams served as President-Elect, President, and Past-President of the Coastal & Estuarine Research Federation.



Susan Williams"She is a great listener and peacemaker. She has integrity and compassion. But she's very forthright and candid. She's a leader. People respect her." - Rick Grosberg when Williams became BML director in 2000.

“Dr. Williams was recognized as one of the most renowned marine ecologists in the US and globally, and she was a cherished mentor who encouraged women to pursue careers in marine science.” - The Press Democrat on Williams life.

market sampling
Sampling fishes in market, Makassar, Indonesia.

“Her legacy is absolutely one of an incredibly hard-working, rigorous scientist who worked at the interface of some of the most interesting science, but also science that mattered to people and impacted people. She cared very deeply about making sure that people had access to that science, that any person — senators, members of the media, students — had access to it.” - Tessa Hill via The Aggie

“Her scientific excellence, outstanding teaching and caring mentoring will be missed.” - Mark Winey for The Scientist.

A fund has been established in honor of Dr. Susan Lynn Williams. Find more here.

Learn more about her life here.



Volunteer/Research Credit Opportunity Observing Krill Abundance and its Role in Fisheries Dynamics

The Morgan Lab is seeking volunteers and students needing undergraduate research credit to assist in a project to examine variation in krill abundance and its role in fisheries dynamics in the California Current System.

Read more



Where has all the bull kelp gone?

by Jordan Hollarsmith

Under the unseasonably warm June sun with the Seattle Space Needle as our reference point, Dr. Jamey Selleck and I don our thick wetsuits. The air may be warm, but the water is still frigid. Our small boat bobs in the water as our captain, Brian Allen, scans our surroundings.

“Nothing.” He remarks with resignation.

We sigh, finish connecting our hoses and checking our gauges, then plunge into the icy water.

urchin barren
A small urchin barren dominated by green urchins (Strongylocentrotus droebachiensis) which have grazed all of the kelp.

While others may visit the Puget Sound looking for orcas, I was here looking for bull kelp (Nereocystis leautkeana). Bull kelp is a large seaweed that attaches at the sea floor and floats on the surface, creating something akin to a forest underwater. And just like their terrestrial counterparts, kelp forests provide critical habitat for many species of marine animals. For millennia, the bull kelp forests of the Puget Sound provided bountiful food for people who lived in and traveled through these inland waters. But slowly and subtly, bull kelp beds started shrinking and disappearing. Now, the once-common sight of bull kelp bobbing on the waters’ surface is a rarity. The million-dollar question is, why?

I’m out on the boat with Jamey and Brian trying to answer that very question. Jamey is a scientist with the National Oceanic and Atmospheric Administration, a federal agency charged with managing our nation’s marine resources. Our boat captain, Brian, works with the Puget Sound Restoration Fund, a non-profit organization dedicated to protecting and preserving marine ecosystems in the Puget Sound. Also involved are experts in remote sensing, Kate Tiedeman and Aniruddha Ghosh from the University of California-Davis, resource managers with the Washington Department of Natural Resources, and the many tribal nations whose ancestral lands abut the sound. The potential consequences of kelp loss at such a huge scale make this is an all-hands-on-deck situation.

puget sound
Brian Allen (Puget Sound Restoration Fund) adjusting the anchor with a backdrop of the Seattle skyline.

As Jamey and I settle onto the bottom with 25 feet of green-tinged water above us, I begin to understand why the cause of kelp disappearance remains so elusive. We visit three sites, all of which used to have bull kelp, none of which do now. The first site is covered in green urchins (Strongylocentrotus droebachiensis), kelp-eating invertebrates infamous for their ability to turn kelp forests into barrens of rock. Maybe it’s all a giant urchin barren! The lightbulb alights in my head as I picture the millions of acres of urchin barren currently stretching across the Northern California coast. But the next site is covered in an invasive seaweed (Sargassum muticum) that dominates the canopy without an urchin in sight. Could bull kelp be outcompeted by the invasive? The lightbulb starts to flicker. The final site is a rich diversity of native algae with no urchins or invasive species, but none of these native algae grow to the surface and create the important underwater forest habitat. The light bulb flickers and dies. What is going on here?

Back on the boat, my eyes drift to the land surrounding the Puget Sound. It is scarred by clear-cut patches marking recent and decades-old logging sites. For over a century, people have denuded the steep hillsides in this rain-soaked region, leaving watersheds prone to landslides and rivers choked with mud. That mud combines with other land-based nutrients and pollutants and eventually travels to the sea where can reduce the light that bull kelp needs for energy and deposits those nutrients and pollutants, upsetting the careful natural balance which determines which species thrive and which suffer. Some of my colleagues and I think that this mud from clear-cut logging, combined with ever-warming temperatures from global warming, may be a major reason the kelp is disappearing. However, like anything in ecology, the full answer will be anything but straightforward. 

A forest of the invasive seaweed, Sargassum muticum.