My name is Crystal Weaver, and I am a graduate student researcher at the Romberg Tiburon Center for Environmental Studies at San Francisco State University, where I am pursuing a master’s degree in Marine Science. Now, before you assume I want to be a dolphin trainer someday, let me assure you: I really just want to tromp around in the mud, restoring coastal habitats. At the interface of land and sea, the coastline is the last barrier before our man-made pollutants hit the ocean. Coastlines in top-notch shape, however, can filter out a lot of these pollutants, cleaning up a pretty big mess in a relatively small amount of space. Impressive, right? Yet, most of our coastlines are so impacted by excessive chemical input, choked rivers, extra sediment, and invasive species (to name a few issues), sometimes we need to help out these coastal zones through restoration.


My current research revolves around the restoration of one subtidal habitat in particular: eelgrass beds. Eelgrass is an underwater, flowering plant found along coasts around the northern hemisphere. It has long, slender blades that look vaguely eel-like, and forms lush meadows we refer to as “beds.” Eelgrass beds, like coral reefs and kelp forests, create a home for a large variety of fishes, crabs, shrimp, mollusks, and other marine life. In the San Francisco Bay, it provides a spawning ground for Pacific herring, an economically-important local fishery and an excellent food source for several species of coastal birds. Eelgrass is even a food source itself, particularly for migrating Brandt geese. Aside from creating this stunningly rich habitat, eelgrass has been shown worldwide to have several additional benefits, including improving water quality, reducing coastal erosion, and even combating climate change through carbon sequestration.


Eelgrass currently covers about 1% of the San Francisco Bay, living in the narrow subtidal range where it is shallow enough to photosynthesize but not so shallow that it would desiccate when the tide goes out. With how bay conditions have changed in the last century, including a drastic improvement to water clarity, there appears to be plenty of room for expansion of eelgrass. Thus, some major “restoration” events, through transplanting and seeding, are underway in order to enhance the eelgrass habitat in the San Francisco Bay. Restoration locations are very carefully selected, taking into account the available light, depth, wave action, and sediment grain size. However, our restoration efforts are only intermittently successful, often for unexplained reasons.


With how important soils and the microbes therein can be in terrestrial plant systems, our logical next step in understanding eelgrass beds systems is to look a bit closer at what’s happening in the sediments. Thus began this coastal ecologist’s first foray into molecular biology. Yes, you read that correctly. A complete novice to anything “genetics,” I decided to tackle a project in which I would characterize the microbiomes of natural and restored eelgrass beds. I would do this by collecting sediment cores from ten locations around the bay, then extracting and sequencing the DNA of the microbial communities within. In order to sequence these communities, I targeted the V3V4 region of the 16s rRNA genes. This region is incredibly comprehensive, including most bacteria species and many archaea, which allows me to look at an enormous diversity of microbial species present at each eelgrass site.  


Fortunately, some of the most daunting decisions to make while conducting this research have turned out to be surprisingly straightforward. For example, when it comes to extracting DNA from marine sediments, MO BIO’s PowerSoil®DNA Isolation Kit is clearly the gold standard. Not only did the kit yield an incredibly high amount of DNA, it worked consistently across a variety of sediment textures from 90% sand to 90% clay/silt. Furthermore, the process was made so straightforward and streamlined that, even as a beginner, I felt confident that I was completing each step correctly.


Jumping into this new field has been challenging, but so worthwhile for the potential of what we might be able to figure out. Our first bits of preliminary data are just in, and the results are looking very promising. With the guidance of my many mentors, and the continued use of MO BIO’s PowerSoil®DNA Isolation Kits, I am more confident than ever that we are on the right track to understanding the eelgrass sediment microbiome, and will soon unlock the secrets of more successful restoration.