2020 was a big year. We saw a global pandemic, protests in support of the Black Lives Matter movement, and wildfires raging across the state. Despite all of this, we had nine students pull through to defend their thesis research in 2020! Please join me in congratulating the following students:
Lindsay Cooper, Phycology Lab
Kenji Soto, Geological Oceanography Lab
Amber Reichert, Pacific Shark Research Center
Mason Cole, Vertebrate Ecology Lab
June Shrestha, Ichthyology Lab
Dan Gossard, Phycology Lab
Jacoby Baker, Ichthyology Lab
Emily Pierce, Invertebrate Zoology Lab
Miya Pavlock-McAuliffe, Physical Oceanography Lab
Please read below to learn a little more about each student's research. As always, please also check out the posts highlighting student research from previous years as well at the following links: 2019, 2018, and 2017.
Special author note: As I am one of the students that defended and graduated this year, this will be my last post for The Drop-In. From writing about classes to conferences and student research, it's been a pleasure writing for this blog. Hopefully someone else will carry the torch forward in the new year to highlight and celebrate the research of graduating students!
My time as a student at Moss Landing have been some of the most enjoyable years of my life. I have had the opportunity to learn from some wonderful professors, improve on my skills as a scientist, and do field work in places like Baja California and aboard the R/V Atlantis. While I appreciate the many academic experiences being an MLML student has given me, I am most grateful for the chance to meet you all. The MLML community is one of the most positive places I have been. Seriously, if I have talked to you before, I would really like to give you a hug and thank you for making MLML such a positive and supportive place. I have too many stories to mention here.
However, despite all of the good Moss has given me, there have been low moments too. None more so then the last few months.
To wrap up our coverage of the Habitat Mapping class projects, this week's post walks us through an investigation of the ways in which wildfires can impact both the physical condition of streams as well as the associated invertebrate community. Small invertebrates which live in the riverbed are closely linked to the sand itself. The size, shape, and composition of the sand --and therefore any changes to those conditions-- can directly affect the collection of animals found in a given stream.
Their class project explored changes in streambed characteristics resulting from one wildfire of interest: the 2016 Soberanes Wildfire. Burning throughout Monterey County, it was the most costly wildfire in U.S. history at the time, and it destroyed dozens of homes. Garrapata Creek, Soberanes Creek, Rocky Creek, and Big Sur Creek flow through the affected area, making them important streams for post-fire analysis.
We are back to covering class projects from Habitat Mapping this week. Julia Karo and Monica Appiano ("The Ladies") will walk us through their study of marshland growth in Elkhorn Slough. Recently designated a Wetland of International Importance, the Slough supports the most extensive salt marshes in California south of San Francisco Bay. Currently, a $6.5 million, 61-acre tidal wetland project is restoring drowning marshes to elevations that will better withstand changes in sea level in the coming century.
As a part of our Habitat Mapping Class this semester we undertook the mission of learning the ins and outs of seafloor mapping theory and practice to make our new Kongsberg M3 Multibeam system work. The M3 is a seafloor mapping system that has excited a lot of folks at MLML with its potential to collect geological, physical, and even biological data beneath the surface of the water. It depends upon many sensors as well as software, and right off the bat we would like to thank QPS for donating us a license to QINSY for data acquisition and Qimera for data processing! Another part of this project involved entering a National Geographic competition...which we’ll revisit later in this post.
First, we must discuss the scientific questions we hope to address. We are a part of the Geological Oceanography lab and are interested in the mysterious submarine landslides that occur, starting at the head of the Monterey Canyon. A lot of research by the Monterey Bay Aquarium Research Institute (MBARI) and California State University’s Seafloor Mapping Lab (SFML) have used deep water mapping technology and other high-tech equipment to study the canyon in the deep.
From these studies, we know that massive underwater landslides occur periodically at the edges of the canyon, and have been shown to move sand, mud, and rocks miles down. We aren’t sure why they happen and they don’t seem to match up with earthquakes or storms. Our hypotheses have to do with how sediment builds up at the head of the canyon and if it is connected to the longshore sediment transport system around the Monterey Bay. Does a submarine landslide occur following a large loss of sand on the beach? Are we losing beach sand to the belly of the canyon, forever? Can we correlate submarine landslide events with any other phenomena? In order to test our hypotheses we must map the head of the canyon more frequently than ever before and the M3 is a perfect instrument to allow us to do so.
Along the way, the MLML “Shop Guys” built us a pole mount to attach the M3 to a MLML whaler, a boat that we can take out to the canyon and survey within an hour or two. Dr. Ivano Aiello brought the M3 to the lab and QPS supplied the software to be able to acquire and process data. Dr. Tom Connolly supplied a field laptop that is water resistant, has a bright enough screen to beat the sun, and has a fantastic battery life, and we brought student brains that figured the rest out. This meant lots of reading manuals, troubleshooting, and more troubleshooting. When we couldn’t troubleshoot alone anymore, Pat Iampietro from CSUMB helped us through a major sticking point with his expertise. The wonderful community and affiliates of Moss Landing Marine Labs were integral to our journey the past few months.
Though we’ve had many challenges throughout the semester, we’ve succeeded in conducting some promising preliminary surveys with the equipment we have available: the field laptop, a Trimble ProXH GPS, and our M3. We’ve collected preliminary data in the Moss Landing Harbor as well as the head of the Monterey Submarine Canyon. See a map of some preliminary depths below:
Still, we are in need of a few additional sensors to make any data collected with our system truly scientifically sound, including something called a Motion Reference Unit (MRU) and a gyro compass. Seafloor mapping draws from the fact that sound travels about five times faster in water than in air. The M3 is a transducer --or speaker-- that emits sound toward the seafloor, listens for the return, and calculates the two-way travel time to infer the depth of the seafloor below the boat.
Therefore, you must supply tide information (tide info found from NOAA tide gauges online), speed of sound information (which we do not yet have a way of measuring), information of the boat due to waves, as well as precise position information. An MRU would provide very precise information regarding the motion of the boat due to the motion of the ocean. Without athese measurements, we can’t be sure if the depths we are gathering are accurate. We can’t be sure because the motion of the boat would affect the angle at which the sound from the M3 is emitted which would affect the angle of return and therefore depth measurements. A gyro compass would give us accurate measurements of heading, which is critical to determining the direction the boat is moving with very high precision. We hope to get these sensors soon so that we can continue investigating the cause(s) of submarine landslides in the Monterey Canyon.
Having struggled with instrument troubleshooting, system setups, and constantly untangling cables, we gained a vast appreciation for marine technicians. Throughout this journey, we noticed that we couldn’t really find information about the inevitable struggles of setting up a new scientific system for the first time and decided to keep track of our trials and tribulations by way of a National Geographic Open Explorer Expedition. Read more here!
You can subscribe to our Open Explorer page to receive updates when we reach new milestones (or more likely encounter new challenges). The Open Explorer page was also a part of a National Geographic Competition to win an underwater drone (aka remotely operated vehicle (ROV)), which we found out that we won! We hope that the underwater drone will provide a method of validating our seafloor mapping data once we’ve gathered the rest of the equipment we need, as well as prove useful for the rest of the MLML community.
Finally, we’d like to thank MLML for their amazing support in following our Open Explorer Expedition. We grew from 2 to 76 followers in two days, and are overwhelmed with the amount of help from our small community.
Dunes are essential to protecting our low-lying coastal communities and agriculture fields here in Monterey from storms, waves, and erosion. The beautiful slopes of these beach dunes are naturally controlled by the wind and the waves. The dunes that we see here are blanketed by green and red ice plant. Ice plant (Carpobrotus edulis) was introduced in the early 1900s to stabilize the naturally shifting dunes, but scientists now think that it may actually increase erosion.
It grows very quickly, forming a thick, heavy mat which can collapse the soil or sand underneath. The ice plant then drops to the new elevation, instead of anchoring the sand. In addition, ice plant is an invasive species that hampers ecosystem diversity and the growth of native plants. The latter have longer root systems that serve to stabilize the dunes. They don’t drop in elevation but allow dune sand to shift around them and build back up when less intense winds drift sand their way. It may be important to eradicate ice plant and introduce native plants for the preservation of not only our dunes but also our communities as climate change increases the frequency of storm events.
For a class project in the Habitat Mapping class taught at MLML in Fall 2018, we worked with the Central Coast Wetlands Group (CCWG), which is an affiliate research group at Moss Landing Marine Lab (MLML) focused on the study, preservation and restoration of Central Coast Wetlands in the Monterey Bay Area. They are currently working on a restoration project along the Salinas River State Beach, removing ice plant and planting native plants. The area being restored is from just south of the Protrero Road entrance down to the mouth of the Salinas River. Thanks to the CCWG and the MLML’s Geological Oceanography Lab, we acquired drone surveys from 2015 and 2016 and a plethora of additional information of the same area we surveyed for our project.
Questions for our study and how we planned to go about it
In our study, we focused on some basic questions: how much and where sand erosion is occurring on dunes around Moss Landing, and, how does dune morphology respond to restoration over time, specifically from October 2015 to December 2018?
Our experience: what we did for our fieldwork and post processing; hardships
To answer these questions, we surveyed 2 sections of beach in front of MLML. Our first survey took place on the beach in front of the aquaculture center adjacent to the head of the Monterey Submarine Canyon and continued south to the Protrero Beach entrance. This was our ‘practice run’ - gathering data for MLML, but not in connection to the CCWG restoration project. Our second survey was from the Protrero Beach entrance, continuing south for approximately 300m. This section is part of the CCWG project and where we are able to show possible changes in dune morphology with restoration over time.
In order to survey an area, the protocol is to set up specific ground control points for geospatial accuracy. We did this by using a Terrestrial Laser Scanner (TLS), a GPS, and some spray paint. We spray painted marks on the beach where we plotted ground control points with the TLS, and then flew a drone to take pictures of the dunes and the marks on the beach.
Back at the lab, we identified the ground control points from the drone photos using Pix4D software. Pix4D evaluates the quality of our survey data, and if the quality report looked good, we could move on to verifying our accuracy in comparison to the data from 2015. We did this by finding the same geographical points on each survey and confirmed that the didn’t differ by more than a few meters.
Unfortunately, we had some trouble with the pre-processing of our drone surveys of survey Area 2 (Area 2) in Pix4D. We found out (after attempting to survey the same area multiple times) that the camera optimization parameter was off. Thankfully, this was an easy fix, and we could still salvage the survey data from that location.
We made some beautiful figures of our raster calculations comparing elevation changes from 2015-2016, 2015-2018, and 2016-2018 for both survey areas. For clarity and elucidation, we narrowed it down to the elevation changes from 2015-2018 in both locations.
Getting ready to fly the drone in survey Area 2, south of Protrero Beach entrance (Amelia Labbe)
Using ArcMap, our 2018 drone surveys, and the CCWG 2015 drone surveys, we could analyze how much the dunes have changed due to weather events, erosion, ice plant removal, etc.
Since survey Area 1 (Area 1) has not had dune restoration in more than 20 years, it served as a control area and an opportunity for us to learn about dune changes and familiarize ourselves with the Pix4D and ArcGIS software. Figure 1 shows changes in elevation from 2015 to 2018 in Area 1. For this comparison, we used a raster calculation in ArcMap. It is important to remember that dunes shift naturally, so if even the face of the dune shifts forward or backward by a couple of centimeters, it can appear as a drastic change in elevation.
On the face of the dunes in survey Area 2 (Figure 2), we can see more accretion than erosion. The CCWG implemented dune restoration in the polygons outlined in pink. The restoration aimed to decrease the rate of dune erosion on the face of the dunes. In Area 1 (Figure 1), we can see elevation loss at the face of the dune. High wave energy is associated with natural erosion dune faces. Area 1 is located adjacent to the head of the Monterey Bay Canyon where it is exposed to higher wave energy than areas further south, explaining the erosion in this location. The back of the dunes in Area 1 experienced very little change in elevation, while in Area 2 (Figure 2), we see a fair amount of accretion. This may be due to the offset of the processed file having a possible bias towards accretion in this zone.
In Figures 1 and 2, we took cross sections of the elevation changes at locations ‘Profile A’ and ‘Profile B’. We then made profile graphs of these changes in Arcmap (Figures 3 and 4).
These cross sections show how much height was gained (positive numbers) or lost (negative numbers) between 2015 and 2018. In figure 3, Profile A shows erosion at the face of the dune (~30m cross-shore distance), which is typical at high wave energy zones. In both of the profiles in figure 3, we do not see a wide range in elevation changes until they cross the face of the dune. In figure 4, just a few meters from the shoreline, these profiles show that there is a relative trend toward accretion. In the same figure, we can also see that the accretion is higher in profile B at the face of the dune (~30m cross-shore distance), where there was no dune restoration. It is important to note that the removal of ice plant is not scientifically proven to decrease erosion rates or increase accretion rates.
What we can hope to accomplish in thefuture
In the future, we can continue to monitor dune morphology using drone surveys as the restoration progresses. We can see if the type of restoration has any influence on how much accretion appears on the dunes. We can also survey at a smaller scale to understand exactly how much erosion of the dunes is associated with ice plant.
Overall, this project helped us both learn about how to survey beaches and dunes using a TLS and a drone. We spent countless hours on ArcMap and Pix4D and have learned more about the programs than we thought we were capable of. We want to give a huge thank you to Ivano Aiello for helping us every step of the way and to the CCWG for giving us valuable information and continuing to preserve our land. Also, a huge thanks to Miya Pavlock-McAuliffe for helping us with ArcMap and thanks to David Carpenter for making some beautiful crosses on the beach.
On Wednesday, September 27th, Professor Ivano Aielloo and GA Tyler Barnes lead the students of Geological Oceanography on an exploration of the fascinating sedimentary record at Manresa State Beach. It was a beautiful day for a beach adventure, and a pod of dolphins blessed the budding geologists with aerial displays.
After bushwhacking their way through invasive pampas grass and ice plant, the students were rewarded with a remarkable record of California's coastal geologic history. The eager pupils got up-close and personal with the marine terraces in order to piece together the fascinating story of sea level rise and fall over the last 120 thousand years.
It’s 6pm on Thursday August 25th and somehow I find myself in a sharply dressed gathering of people on the second floor of Steuart Tower in the financial district of San Francisco, one block away from the Embarcadero. Making up the crowd are people from Autodesk, Google, 3D modelers, educators, artists, and scientists. There’s a bartender serving beer and wine, a snack table filled with a variety of mini meat and vegan kabobs paired with corresponding dipping sauces, an assortment of focaccia samplers, and toast with even more sauces. This is all too fancy for me, a humble jean wearing graduate student, and I feel a bit out of place even in my dressy-casual button up shirt that I luckily remembered to bring (I did however forget my jacket!).
I am at this swanky event to attend The Hydrous’ first ever happy hour. It took place in the Autodesk Gallery, which is filled with the many beautiful and innovative creations that an Autodesk program was used to create: a soccer ball with a battery inside that is charged by playing with it, an ultra-light, but super protective race car frame, a kayak that folds into a carriable box (see picture), and intricate golden artwork the size of your hand to name a few. From week to week the gallery features different projects from companies like Nike, Lego, and Ferrari. But today it’s the Hydrous’ turn to show off its work.
What is The Hydrous, you might ask? It is a non-profit comprised of scientists, engineers, and artists who love the ocean and whose goal is to provide the public with a meaningful connection to the ocean which they hope will inspire people to explore, understand, and protect the ocean. “Providing a meaningful connection” is a phrase that really spoke to me and is one reason why I find the work at The Hydrous especially inspiring. In her opening statement, Erica Woolsey, the CEO of The Hydrous, stated how during her PhD and PostDoc she published a number of papers about coral reefs, but none of it seemed to make any difference in protecting the reefs that she loved. And for the most part all of the things that she learned stayed within academia because “the facts don’t speak for themselves.” Due to these shortcomings of “traditional” science, she, Nora Hall (COO), and Sly Lee (Co-Founder) started The Hydrous as a better approach towards ocean advocacy, protection, conservation, and education.
A core belief at The Hydrous is that if you want people to care about something, they have to be able to see it and even better if they can touch it. In order to achieve this they are using different 3D modeling techniques to bring the ocean to everyone. On display today, are physical models of corals created with a 3D printer, a virtual reality (VR) exploration simulator of three different ocean experiences, a drone and plane camera rig used to create 3D maps of islands, an education and outreach desk, and information on how you can get involved with The Hydrous’ tropical reef photogrammetry (more on this in a bit) trips aboard a luxury ship for the price of $5000 (maybe one day).
I first talked to Elle Stapleton, a fabrication artist, about the physical 3D coral models on display. She explained how the process of photogrammetry stitches together multiple pictures to create a single image, in the case of one the corals on display, 250 pictures were taken to create a digital 3D model which was then printed out with using a 3D printer. A particularly cool coral on display was one made out of calcium carbonate. I had seen plenty of models created with a 3D printer using different types of plastics, but I had no idea that CaCO3 could be used as a printing material. The Hydrous partnered with architect Professor Ronald Rael (UC Berkeley) in order to make this cool powder based printing material. Unfortunately, this coral was too delicate to be handled. But, it was created in hopes to use in ocean acidification tests compare rates of CaCO3 decay in different ocean conditions. In addition to these physical models of 2” to 12” corals, The Hydrous wants to use photogrammetry to create 3D maps of entire reefs.
I then stopped by the next table to learn how drones and Cessnas were being used to map tropical islands and island chains, respectively. Both drones and planes were equipped with GoPros to take pictures along their flight paths, but the planes used a special camera rig with three GoPros on it. After this, I used their VR rig to explore a deep sea whale fall community and coral reef. It was my first time using VR and I got completely immersed in the experience. I am pretty sure that if I put on noise canceling headphones, I would have started holding my breath. After being kindly reminded that there were other people around waiting for their turn (sorry, I forgot!).
Lastly, I talked to Nora, who explained how The Hydrous is working with educators to create “kits” of lesson plans, activities, 3D models, and VR to be used by teachers in their classrooms. Additionally, they offer presentations and workshops to be used at company events, conferences, or museums. She hopes that this outreach will help them make those meaningful connections with the ocean and create a community that is inspired to “make positive differences for the ocean.”
And thus concluded my evening at The Hydrous’ Happy Hours, thank you Nora and Erika for such a fun evening. Maybe one day you can present at MLML. For more information on The Hydrous, you can go here: https://www.thehydro.us/ .
To say that I was not intrigued by science as a teenager would be an enormous understatement. I despised science. I often attribute uninspired teaching and an inadequate education system for this reaction, but in reality I was just a moody teenager preoccupied by other interests (for the record, I have enormous respect for the teachers and administrators that have influenced my education). My disregard for science at the time is somewhat surprising. My earliest memories included being unwillingly dragged away from the beach after hours of exploration, or learning to cast a fishing rod just right so as not to snag a tree branch. These experiences morphed into forecasting swells with my dad before surfing and competing in local junior lifeguard competitions. So why was I so uninterested in science?
Clearly, I have had a slight change of heart since then, largely due to my search for a major as an undergrad. In high school, science felt like an exercise in memorizing facts to pass a test. In college, I started making connections. I learned about how the tectonic history of continental margins influences ocean swells (and thus, my preferred surf breaks). I discovered the connection between watershed practices and water quality. Science became a system-based approach to explain natural phenomena that I cared about deeply, rather than a memorization drill.
Fast-forward a few years and I find myself part of the geological oceanography lab at MLML. So what do I do here? Basically, the same thing I did as a toddler—I explore the beach. To get technical, I assess small-scale beach variability using ground-based LiDAR. In 2009 the US Geological Survey completed a California-wide coastal change project, finding the highest long-term erosion rates in Monterey Bay, about -0.6 m/y over about 120 y (Hapke et al., 2009). This conclusion presents numerous local challenges as beaches and adjacent dunes function as the sole barriers between land and sea. In response to this finding, a terrestrial laser scanner, commonly known as ground-based LiDAR, is employed to create high-resolution 3-D maps. Change in terms of beach volume, mean seal-level contour, foredune position, etc. is assessed by surveying the same beach over time. My thesis research, as well as other research within our lab, strives to understand coastal change in Monterey Bay. This work is supported by various organizations through grants and scholarships, including the California State University Council on Ocean Affairs, Science, and Technology and the Monterey Bay National Marine Sanctuary.
I still have days when I despise science. I am a grad student after all. But those days are dwarfed by awe I experience when talking about the processes behind mountain building or the feeling of uncovering trends in my data for the first time. I do not think I will ever get tired of exploring the beach.
Hapke, C.J., Reid, D., Richmond, B, 2009. Rates and Trends of Coastal Change in California and the Regional Behavior of the Beach and Cliff System. Journal of Coastal Research, Vol. 25, No. 3 pp. 603-615.