Investigating the Seagrass Microbiome

Sea turtles and other marine animals browse on seagrass meadows. NOAA photo
Sea turtles and other marine animals browse on seagrass meadows. NOAA photo

Seagrass carpets the seafloor creating a unique and vital ecosystem in shallow marine environments. Sea turtles graze on seagrass leaves while smaller organisms seek refuge in the green fields but, on the microscopic level, seagrass is also home to microbial communities. Such microbes compose the seagrass microbiome and potentially play a role in seagrass ecology.

UC Davis integrative genetics and genomics Ph.D. student Cassie Ettinger identifies and characterizes seagrass-associated microbial communities. A study published last year in the journal PeerJ suggests how understanding the role of these microbes could reveal new information about seagrass sulfur cycling and establish seagrass as a model organism.

“This paper serves as a foundational study for the field of seagrass microbiomes,” said Ettinger. “The study can be thought of as part natural history, part starting to tease apart environmental factors that might impact the composition of the seagrass microbiome.”

Who lives here? DNA as a footprint

With the rise of genome sequencing, researchers have been able to characterize the microbes associated with organisms and environments. Current technology allows scientists to identify microbes by extracting their DNA directly from their host organism or environment. Researchers at UC Davis performed DNA extractions on sediment, leaves, and roots collected from a single seagrass patch in Bodega Bay, Ca.

When it comes to bacteria, the 16S ribosomal RNA gene acts as a barcode for identification. Each bacterium contains enough differences and similarities in their 16S gene to distinguish who is who at some level of classification. ­­

Ettinger and colleagues amplified 16S genes from the extracted DNA and used computational methods to organize the data. She compared finalized sequences to an online database that contains sequences for thousands of bacteria and other organisms, allowing Ettinger to give a name to each of the bacteria present on the collected samples.

Predicting bacteria’s capabilities

Ettinger found that there were distinct communities located on the seagrass leaves, roots and sediment. Additionally, sediment without seagrass had different communities than sediment containing seagrass. These distinct communities point to how these microbes might have specific functional roles for seagrass ecology.

Her research revealed that the sediment and root-associated bacteria have metabolic processes that may play a role in seagrass biogeochemical cycling, such as sulfur cycling.

Sulfur cycling is a process where sulfur compounds are converted from one form to another. Sulfides are naturally occurring sulfur compounds that are present and toxic to seagrass at high levels.

Seagrass can release oxygen from its roots to help convert the sulfide into less harmful compounds, but the entire processes isn’t well understood. However, since many of the bacteria characterized in this study are known sulfur-reducers and sulfur-oxidizers, it is possible that these bacteria could play a role in the seagrass sulfur cycling.

Implications for seagrass ecosystems

Unfortunately, seagrasses are at risk due to climate change, pollution, and habitat destruction. Understanding the role of the seagrass microbiome in the environment can lead to a better understanding of seagrass ecology and, therefore, restoration processes.

In addition, there aren’t any model systems for marine plants, but seagrass is promising due to the research on it and its importance in ecosystems.

“We believe that seagrasses could be a model system for marine plant-microbe interactions, and this study provides key insights into the natural community associated with these plants,” said Ettinger.

Coauthors of this study include Sofie Voerman and Jenna Lang, who designed the experiment and collected samples, as well as UC Davis professors Jay Stachowiz and Jonathan Eisen, who reviewed drafts and contributed lab materials. The research was supported by a grant from the Gordon and Betty Moore Foundation.

More information

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge (PeerJ)

For Seagrass, Biodiversity Is Both a Goal and A Means For Restoration

Karley Marie Lujan is a fourth-year biological sciences major at UC Davis. This post was originally written for a University Writing Program class, “Writing for biological sciences.”

This story originally appeared on the UC Davis Egghead Blog.