Amid COVID and wildfire related closures, finding a sense of order and normalcy in my research process has been challenging. Therefore, I consider myself lucky that I am able to continue the lab-based aspects of my PhD research. Lab work is time consuming and can be tedious, required days to months of repetitive tasks, but I am grateful for the order and organization that my lab workflow brings me. In this blog post, I’d like to share what this workflow looks like, the kind of information I gain from lab analyses, and some of my expected results from my last six months of lab work.

The workflow

After collecting, identifying, and measuring the length of hundreds of juvenile fishes using SMURFs (see my May blog post), it is time to take these fishes back to the lab. My lab work flow looks something like this: I use forceps and a scalpel to peel back the dorsal (top) of the fish’s cranium from the nose to the beginning of the vertebra tools to very thin forceps – the tips are as wide as 0.7mm mechanical pencil lead – and begin to move the brain away from the lateral sides of the cranium. I work under a dissecting microscope. My eyes look through the eye piece while my hands manipulate the specimen. I prod, search, and finally find what I’m so carefully looking for. I remove small white object from either side of the brain. They are slightly smaller than a grain of short grain rice. I try not to let my hands shake as I deposit the object safely in a microcentrifuge tube for storage, and take a breath of relief. 400 dissections later, I relocate to a new microscope station – a compound and dissecting scope with cameras that allow me to see and capture the microscope images on my computer. I mount each of these samples to a microscope slide, use 2000 grit sandpaper to sand both sides of the sample, and place it under 400X magnification. I smile – now the fun begins.

So why all this fuss? What are these mysterious small, nearly microscopic white objects?

Most fishes (except sharks, rays, and lamprey) have ear stones called otoliths, which are the small, white structures found in the cranium. Otoliths are made of calcium carbonate, the same compound found in the shells of many invertebrates. These structures that aid orientation, balance, and hearing, similar to human ear bones. Otoliths are an important tool in fish biology and fisheries science because they serve as an annual record book, kept over a fish’s entire life. Otoliths have alternating translucent and opaque zones that correspond to alternating periods of fast and slow growth, respectively. Otoliths have a familiar terrestrial analog: tree rings. I remember my fourth-grade teacher leading our class through a guided exploration of a tree “cookie”. We counted the rings to age the tree, observed alternating light and dark bands of different sizes, and connected these observations with seasonality (light availability, precipitation) and growth rates in nature (see my January blog post on seasonality in the ocean). Otoliths are a similarly powerful tool for fish biology and management, as they allow us to understand how fish populations grow and age over time and in relation to a changing climate, pollution, and even management regulations. They are also a powerful ecological tool – allowing scientists to peer into the lives of the fishes and understand what kinds of environmental conditions result in faster or slower growth.

For many years, fish biologists have used otoliths from adult fishes to measure population vital rates and translate this information into management decisions. In 1971, a groundbreaking discovery credited to Yale geologist Giorgio Panella forever changed the fields of fish biology, fish ecology, and fisheries science: it was possible to read the information stored in larval and juvenile fish otoliths as well – only in these young fishes, the alternating light and dark rings represented a daily log book. Imagine the excitement of scientists when they discovered that they could now peer into the daily lives of young fishes! In marine fishes, upwards of 99% of fish eggs produced do not survive to adulthood. There is a mortality gauntlet through which all young fish must pass, and few survive, due to the challenges of finding food in a vast open ocean, of avoiding myriad predators, and of avoiding currents that would sweep them away from suitable habitat. Prior to the discovery of otolith daily increments, this mortality gauntlet was poorly understood, making it difficult to predict when and why adult fish populations undergo periods of boom and bust.

My research and expected results

Understanding this mortality gauntlet has been a central goal of my PhD research. Specifically, I study a socio-economically important nearshore groundfish found from Baja California, Mexico to Alaska, the cabezon (Scorpaenichthys marmoratus). Since COVID-19 made my 2020 field season impossible, I have instead been dissecting, polishing, and analyzing otolith data from juvenile cabezon with the goal of understanding what early life characteristics are important for growth and survival through the mortality gauntlet. Because the time series of samples for my project extend from 2013-2019, I am also able to investigate how these critical early life history characteristics change from year to year, and even from month to month.

Cabezon exhibit a somewhat unique recruitment strategy – that is, the timing and magnitude with which juveniles arrive to the nearshore to settle and grow into adulthood. Unlike many other nearshore groundfishes, cabezon recruit in multiple events, spanning the April – September months. This is a departure from the “single-pulse” strategy, where the juveniles (e.g. rockfishes) arrive over a short time window (e.g. two weeks in July). By the time the cabezon are collected in the SMURFs, they could be anywhere between 2 and 4 months old. That they arrive over a 6-month window means that they have experienced a vast range of ocean conditions (e.g. winter storms, changing currents, upwelling, downwelling, water temperature). I expect to find a “portfolio” of early life characteristics that enable the young fish to survive in different ocean conditions. For example, individuals that arrive to the SMURFs in May were likely hatched in January, experienced “winter” conditions, and could have a “winter” growing strategy (e.g. slow growth due to poor feeding conditions). In contrast, individuals that arrive to the SMURFs in July were likely hatched in April, experienced “spring” conditions, and could have a “spring” growing strategy (e.g. fast growth due to enhanced feeding conditions). Altogether, I am interested in understanding how this portfolio effect of early life strategies may enhance the resilience of the cabezon population to disturbances such as the 2014-2016 marine heat wave and other climate and fishing related changes.

To echo many of my fellow Sea Grant Scholars, much has changed since my last post. It feels like COVID-19 is changing the world every day. The pandemic has asked us all – nations, communities, and individuals – to make decisions under great uncertainty. Many of us try to stay informed about best practices, infection rates, and scientific breakthroughs related to COVID-19, but they seem to change before we can even make sense of them. Recently, I read an article in The Atlantic entitled “Why the Coronavirus is So Confusing” (Yong 2020). The article summarizes several major sources of confusion about COVID-19 and explores key miscommunications that have compounded the uncertainty we feel. This pandemic has highlighted the importance of science communication for scientists, our nation, and the world. As I reflect on the role of scientists during this time, I am motivated to a) expand my science communication skills and efforts, and b) identify pathways for scientists to support our local communities.

Like many other field researchers, COVID-19 has caused major disruptions to my sampling season, potentially shifting the focus of my dissertation. It is easy to feel discouraged that I’ve been pulled away from my research – especially this time of year. May marks the beginning of a long and exciting field season to collect juvenile nearshore fishes from offshore moorings and tide pools.

Instead, I’ve chosen to use this time to strengthen and expand my science communication skills by partnering with a local high school teacher, Mr. Andy Bedingfield, to build marine ecology coursework and facilitate project-based learning during the pandemic. I’ve found this partnership to be extremely timely, fulfilling and synergistic – not only do I have to opportunity to practice science communication and education during a time when quality science communication is so desperately needed, but I also feel that I am able to use my training as a scientist to help my community during a time of need. Andy and I are working together for the remainder of Lincoln City High School’s academic year, and we hope to publish an article in the National Science Teaching Association journal so that other teachers can benefit from the coursework we’ve developed and our lessons learned.

Our goals are in this partnership are threefold:

1. Develop a marine ecology curriculum for high school students that can be delivered virtually

Andy and I have been working together for the past two months build online curriculum to meet the Next Generation Science Standards (NGSS) relevant to his Ecology class. We developed learning outcomes from each Disciplinary Core Idea (e.g. “LS2.A: Ecosystem dynamics, functioning, and resilience”) and identified specific marine ecology concepts that illustrate the core ideas. With this as our roadmap, we then searched for or developed videos and online content to meet each learning outcome. Using open source software like EdPuzzle and ScreenCastify, Andy annotated and personalized the educational videos we found and embedded questions sets in the videos to check for understanding. Andy refers to this part of his course as “The Workout”, where students put in time and effort to build their knowledge base such that they will be capable of carrying out an independent project of their choosing.

2. Engage students in project-based choice learning

Working with Andy and the high school students has shown me that for them, choice = motivation. Andy’s teaching philosophy centers on the idea that children and students are curious scientists by nature, and that a teacher’s role is to provide guidance, structure, and direction to facilitate their scientific process. To this end, Andy asked me to brainstorm several marine ecology projects that both pertain to the Disciplinary Core Ideas and develop NGSS core competencies (e.g. “Use mathematical equations to explain energy transfer”). I generated a list of activities and materials for marine ecology lessons that I had accumulated throughout my undergraduate career, and Andy and I worked together to hone these projects into manageable, grade-appropriate activities for the students. Andy has taught me several key teaching strategies to make projects more manageable for students including “chunking” or only assigning parts of a project at a time (e.g. Week 1 Introduction, Week 2 Methods) and using student examples to show students the caliper of final project we are hoping for, rather than reading them a rubric. The students have several marine ecology projects to choose from: Investigating trade-offs in marine spatial management using SeaSketch, Modeling sustainable fishing in tuna populations, Energy transfer in plankton food webs (thanks to help from the OSU Plankton Ecology Lab), and investigating human impact and resilience in the rocky intertidal zone (thanks to help from the OSU PISCO Lab). Each of these projects can be delivered online, is relevant to local, coastal Oregon ecology, and is flexible to meet each student’s individual interests. Andy refers to this aspect of his course as “a PhD for high school”, and emphasizes the importance of engaging his students in real, tangible science projects instead of canned labs, where they experience the joy of innovation and discovery, and gain confidence in their science identify and ability.

3. Document the process of integrating scientists and researchers into high school education

Andy and I hope to document the lessons learned through this process to facilitate collaborations like ours for other scientists and educators. Thus far, we’ve found that the more interaction the students have with the scientists (me), the better. In oppose to a visiting scientist giving a single lecture, we hope that having the visiting scientist work with students (e.g. office hours) and engage with them about their ideas and interests over the course of several weeks will build the student’s confidence and motivation. Last week, we introduced the projects and this week, we will be working on a literature review and methods description. They will they carry out their projects for two weeks, and complete a final presentation afterward.

I am very excited to continue working with Andy and the students. They are constantly challenging me to communicate my science in relevant and innovative ways. I am grateful for this opportunity to connect to my local coastal community and to inspire, equip, and empower the next generation of marine scientists. Stay tuned for a project update in the coming weeks!

How are ocean and terrestrial seasons different?

Humans are land-loving creatures and we intuitively understand that seasons are times of change; these transitions are often signaled by cues like day length or temperature. Organisms use seasonal cues like these to time events in their life cycle that maximize survival, growth, and successful reproduction. The timing of life cycle events to coincide with seasonal environmental factors is called phenology. For example, many insects, birds, and small mammals reproduce in the spring to maximize the number of warm months to grow and accumulate resources before a harsh, cold winter. We also see several examples of insect species that have co-evolved with plant species, such that insect larvae are born in synchrony with plant prey species is present or blooming.

In the ocean, we see several similar phenological patterns though the seasonal cues can be different. Most marine organisms have complex life cycles, where nearshore, bottom-associated adults spawn very small, dispersive larvae that feed in the water column for days to months before returning to the nearshore to settle, grow, and reproduce. Many fish and invertebrate species time their reproductive events such that their larvae are feeding in prey-rich conditions. Marine larvae are small organisms, often less than 10mm in length, and so they feed on very small prey items, such as phytoplankton and zooplankton (microscopic drifting plant and animal organisms). Similar to plants on land, many phytoplankton species bloom in the springtime, when day length increases and sunlight penetrates deep into the ocean. Zooplankton populations grow when there is an abundance of the phytoplankton they feed on, and fish and invertebrate larvae populations boom in response. Sunlight and food web cues play a large role in determining the phenology of marine organisms.

It is also necessary to consider that marine organisms exist in a dynamic fluid environment. Wind, currents, tide, and coastline features are all important in determining patterns of water movement in any given area. Because marine larvae are very small, they often travel or disperse with the dominant pattern of regional water movement. Many fish species are thought to time their reproduction not only according to sun-related cues, but also to water movement-related cues such that their larvae are retained in areas with favorable habitat (e.g. a nearshore rocky reef or kelp bed). Additionally, ocean conditions change dramatically along the coastline. For example, prevailing wind patterns in northern California are drastically different from wind patterns in central and northern Oregon, resulting in an abrupt change in nutrient input, phytoplankton productivity, and water movement patterns – all cues that marine organisms are tuned in to! Understanding phenology in the ocean requires an understanding of seasonality in the food web, seasonality in water movement patterns, and how these patterns are variable in space.

My dissertation research focuses on phenology of marine fish life cycles.

A major part of my dissertation research focuses on better understanding the phenology of marine fish life cycles. I study the most vulnerable life stages of the fish life cycle (larvae and juveniles, which are known to experience very high mortality rates) to better understand how food web interactions and water circulation patterns are different along the Oregon coast and throughout the year. My ultimate goal is to use the information I gain from my research to improve predictions about the future status of fish populations, especially as ocean conditions are changing.  

As a student of the ocean, my schedule aligns with ocean seasons.

As I reflect on the importance of ocean seasons on the lives of marine fishes, my study organisms, I realize that as a student of marine science I also depend on ocean seasons. In Oregon, the April-September months are marked by a transition to nutrient and phytoplankton rich waters (known as upwelling) and many larval and juvenile fish species are present in the nearshore waters. After September, the ocean transitions in to a relatively nutrient and phytoplankton poor state (known as downwelling) that lasts until the following April. The winter months also have larger storms, night tides, and less sunlight, making field work and sampling more difficult. These seasons are reflected in my work student as well: from April-September, I spend most of my time collecting samples, going on oceanographic research cruises, and organizing a team of dedicated undergraduates to conduct field work. By the time October comes around, most of my activities are land and office-based. This is a welcome change of pace after a busy summer season. This fall quarter was a special time for me because I passed my oral exams! This marks the completion of most of my coursework and the last major checkpoint in my program before my dissertation defense. As we transition into the winter term, I’m very excited to present other parts of my dissertation work to the Oregon Department of Fish and Wildlife Marine Reserves Program, and at an international conference in Japan. I’m also looking forward to teaching an introductory biology lab course, expanding my outreach opportunities, and preparing for another summer of field work!