Over the Ocean and Under the Bridges: STEM Cruise on the R/V Oceanus

By Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

From September 22nd through 30th, the GEMM Lab participated in a STEM research cruise aboard the R/V Oceanus, Oregon State University’s (OSU) largest research vessel, which served as a fully-functioning, floating, research laboratory and field station. The STEM cruise focused on integrating science, technology, engineering and mathematics (STEM) into hands-on teaching experiences alongside professionals in the marine sciences. The official science crew consisted of high school teachers and students, community college students, and Oregon State University graduate students and professors. As with a usual research cruise, there was ample set-up, data collection, data entry, experimentation, successes, and failures. And because everyone in the science party actively participated in the research process, everyone also experienced these successes, failures, and moments of inspiration.

The science party enjoying the sunset from the aft deck with the Astoria-Megler bridge in the background. (Image source: Alexa Kownacki)

Dr. Leigh Torres, Dr. Rachael Orben, and I were all primarily stationed on flybridge—one deck above the bridge—fully exposed to the elements, at the highest possible location on the ship for best viewing. We scanned the seas in hopes of spotting a blow, a splash, or any sign of a marine mammal or seabird. Beside us, students and teachers donned binoculars and positioned themselves around the mast, with Leigh and I taking a 90-degree swath from the mast—either to starboard or to port. For those who had not been part of marine mammal observations previously, it was a crash course into the peaks and troughs—of both the waves and of the sightings. We emphasized the importance of absence data: knowledge of what is not “there” is equally as important as what is. Fortunately, Leigh chose a course that proved to have surprisingly excellent environmental conditions and amazing sightings. Therefore, we collected a large amount of presence data: data collected when marine mammals or seabirds are present.

High school student, Chris Quashnick Holloway, records a seabird sighting for observer, Dr. Rachael Orben. (Image source: Alexa Kownacki).

When someone sighted a whale that surfaced regularly, we assessed the conditions: the sea state, the animal’s behavior, the wind conditions, etc. If we deemed them as “good to fly”, our licensed drone pilot and Orange Coast Community College student, Jason, prepared his Phantom 4 drone. While he and Leigh set up drone operations, I and the other science team members maintained a visual on the whale and stayed in constant communication with the bridge via radio. When the drone was ready, and the bridge gave the “all clear”, Jason launched his drone from the aft deck. Then, someone tossed an unassuming, meter-long, wood plank overboard—keeping it attached to the ship with a line. This wood board serves as a calibration tool; the drone flies over it at varying heights as determined by its built-in altimeter. Later, we analyze how many pixels one meter occupied at different heights and can thereby determine the body length of the whale from still images by converting pixel length to a metric unit.

High school student, Alishia Keller, uses binoculars to observe a whale, while PhD student, Alexa Kownacki, radios updates on the whale’s location to the bridge and the aft deck. (Image source: Tracy Crews)

Finally, when the drone is calibrated, I radio the most recent location of our animal. For example, “Blow at 9 o’clock, 250 meters away”. Then, the bridge and I constantly adjust the ship’s speed and location. If the whale “flukes” (dives and exposes the ventral side of its tail), and later resurfaced 500 meters away at our 10 o’clock, I might radio to the bridge to, “turn 60 degrees to port and increase speed to 5 knots”. (See the Hidden Math Lesson below). Jason then positions the drone over the whale, adjusting the camera angle as necessary, and recording high-quality video footage for later analysis. The aerial viewpoint provides major advantages. Whales usually expose about 10 percent of their body above the water’s surface. However, with an aerial vantage point, we can see more of the whale and its surroundings. From here, we can observe behaviors that are otherwise obscured (Torres et al. 2018), and record footage that to help quantify body condition (i.e. lengths and girths). Prior to the batteries running low, Jason returns the drone back to the aft deck, the vessel comes to an idle, and Leigh catches the drone. Throughout these operations, those of us on the flybridge photograph flukes for identification and document any behaviors we observe. Later, we match the whale we sighted to the whale that the drone flew over, and then to prior sightings of this same individual—adding information like body condition or the presence of a calf. I like to think of it as whale detective work. Moreover, it is a team effort; everyone has a critical role in the mission. When it’s all said and done, this noninvasive approach provides life history context to the health and behaviors of the animal.

Drone pilot, Jason Miranda, flying his drone using his handheld ground station on the aft deck. (Photo source: Tracy Crews)

Hidden Math Lesson: The location of 10 o’clock and 60 degrees to port refer to the exact same direction. The bow of the ship is our 12 o’clock with the stern at our 6 o’clock; you always orient yourself in this manner when giving directions. The same goes for a compass measurement in degrees when relating the direction to the boat: the bow is 360/0. An angle measure between two consecutive numbers on a clock is: 360 degrees divided by 12-“hour” markers = 30 degrees. Therefore, 10 o’clock was 0 degrees – (2 “hours”)= 0 degrees- (2*30 degrees)= -60 degrees. A negative degree less than 180 refers to the port side (left).

Killer whale traveling northbound.

Our trip was chalked full of science and graced with cooperative weather conditions. There were more highlights than I could list in a single sitting. We towed zooplankton nets under the night sky while eating ice cream bars; we sang together at sunset and watched the atmospheric phenomena: the green flash; we witnessed a humpback lunge-feeding beside the ship’s bow; and we saw a sperm whale traveling across calm seas.

Sperm whale surfacing before a long dive.

On this cruise, our lab focused on the marine mammal observations—which proved excellent during the cruise. In only four days of surveying, we had 43 marine mammal sightings containing 362 individuals representing 9 species (See figure 1). As you can see from figure 2, we traveled over shallow, coastal and deep waters, in both Washington and Oregon before inland to Portland, OR. Because we ventured to areas with different bathymetric and oceanographic conditions, we increased our likelihood of seeing a higher diversity of species than we would if we stayed in a single depth or area.

Humpback whale lunge feeding off the bow.
Number of sightings Total number of individuals
Humpback whale 22 40
Pacific white-sided dolphin 3 249
Northern right whale dolphin 1 9
Killer whale 1 3
Dall’s porpoise 5 49
Sperm whale 1 1
Gray whale 1 1
Harbor seal 1 1
California sea lion 8 9
Total 43 362

Figure 1. Summary table of all species sightings during cruise while the science team observed from the flybridge.

Pacific white-sided dolphins swimming towards the vessel.

Figure 2. Map with inset displaying study area and sightings observed by species during the cruise, made in ArcMap. (Image source: Alexa Kownacki).

Even after two days of STEM outreach events in Portland, we were excited to incorporate more science. For the transit from Portland, OR to Newport, OR, the entire science team consisted two people: me and Jason. But even with poor weather conditions, we still used science to answer questions and help us along our journey—only with different goals than on our main leg. With the help of the marine technician, we set up a camera on the bow of the ship, facing aft to watch the vessel maneuver through the famous Portland bridges.

Video 1. Time-lapse footage of the R/V Oceanus maneuvering the Portland Bridges from a GoPro. Compiled by Alexa Kownacki, assisted by Jason Miranda and Kristin Beem.

Prior to the crossing the Columbia River bar and re-entering the Pacific Ocean, the R/V Oceanus maneuvered up the picturesque Columbia River. We used our geospatial skills to locate our fellow science team member and high school student, Chris, who was located on land. We tracked each other using GPS technology in our cell phones, until the ship got close enough to use natural landmarks as reference points, and finally we could use our binoculars to see Chris shining a light from shore. As the ship powered forward and passed under the famous Astoria-Megler bridge that connects Oregon to Washington, Chris drove over it; he directed us “100 degrees to port”. And, thanks to clear directions, bright visual aids, and spatiotemporal analysis, we managed to find our team member waving from shore. This is only one of many examples that show how in a few days at sea, students utilized new skills, such as marine mammal observational techniques, and honed them for additional applications.

On the bow, Alexa and Jason use binoculars to find Chris–over 4 miles–on the Washington side of the Columbia River. (Image source: Kristin Beem)

Great science is the result of teamwork, passion, and ingenuity. Working alongside students, teachers, and other, more-experienced scientists, provided everyone with opportunities to learn from each other. We created great science because we asked questions, we passed on our knowledge to the next person, and we did so with enthusiasm.

High school students, Jason and Chris, alongside Dr. Leigh Torres, all try to get a glimpse at the zooplankton under Dr. Kim Bernard’s microscope. (Image source: Tracy Crews).

Check out other blog posts written by the science team about the trip here.

Are bacteria important? What do we get by analyzing microbiomes?

By Leila Lemos, PhD candidate, Fisheries and Wildlife Department, OSU

As previously mentioned in one of Florence’s blog posts, the GEMM Lab holds monthly lab meetings, where we share updates about our research and discuss articles and advances in our field, among other activities.

In a past lab meeting we were asked to bring an article to discuss that had inspired us in the past to conduct research in the marine field or in our current position. I brought to the meeting a literature review regarding methodologies to overcome the challenges of studying conservation physiology in large whales [1]. This article discusses different non-invasive or minimally invasive matrices (e.g., feces, blow, skin/blubber) that can be gathered from whales, and what types of analyses could be carried out, as well as their pros and cons.

One of the possible analyses that can be performed with fecal samples that was discussed in the article is the gut microflora (i.e., bacterial gut community) via genetic analysis. Since my PhD project analyzes fecal samples to determine/quantify stress responses in gray whales, we have since discussed the possibility of integrating this extra parameter to our analysis.

But… what is the importance of analyzing the gut microflora of a whale? What is the relationship between microflora and stress responses? Should we really use our limited sample size, time and money to work on this extra analysis? In order to be able to answer all of these questions, I began reading some articles of the field to better understand its importance and what kind of research questions this analysis can answer.

The gut of a mammal comprises a natural habitat for a large and dynamic community of bacteria [2] that is first developed in early life. Colonization of facultative bacteria (i.e., aerobic bacteria) begins at birth [3], and later, anaerobic bacteria also colonizes the gut. In humans, at the age of 1 year old, the microbiome should have a stable adult-like signature (Fig. 1).

Figure 01: Development of the microbiome in early life.
Source: [3]

The gut bacterial community is important for the physiology and pathology of its host and plays an important role in mammal digestion and health [2], responsible for many metabolic activities, including:

  • fermentation of non-digestible dietary residue and endogenous mucus [2];
  • recovery of energy [2];
  • recovery of absorbable nutrients [2];
  • cellulose digestion [4];
  • vitamin K synthesis [4];
  • important trophic effects on intestinal epithelia (cell proliferation and differentiation) [2];
  • angiogenesis promotion [4];
  • enteric nerve function [4];
  • immune structure [2];
  • immune function [2];
  • protection of the colonized host against invasion by alien microbes (barrier effect) [2];

Despite all the benefits, the bacterial community might also be potentially harmful when changes in the community composition (i.e., dysbiosis) occur due to the use of antibiotics, illness, stress, aging, lifestyle, bad dietary habits [4], and prolonged food and water deprivation [5]. Thus, potential pathological disorders might emerge when the microbiome community changes, such as allergy, obesity, diabetes, autism, multisystem organ failure, gastrointestinal and prostate cancers, inflammatory bowel diseases (IBD), and cardiovascular diseases [2, 4].

Changes in gut bacterial composition may also alter the brain-gut axis and the central nervous system (CNS) signaling [3]. More specifically, the core pathway affected is the hypothalamic-pituitary-adrenal (HPA) axis, which is activated by physical/psychological stressors. According to a previous study [6], the microbial community in the gut is critical for the development of an appropriate stress response. In addition, the microbial colonization in early life should occur within a certain time window, otherwise an abnormal development of the HPA axis might happen.

However, the gut microbiome can not only affect the HPA axis, but the opposite can also occur [3]. Signaling molecules released by the axis can alter the gastrointestinal (GIT) environment (i.e., motility, secretion, and permeability) [7]. Stress responses, as well as diseases, may also alter the gut permeability, causing the bacteria to cross the epithelial barrier (reducing the overall numbers of bacteria in the gut), activating immune responses that also alter the composition of the bacterial community in the gut [8, 9].

Figure 02: Communication between the brain, gut and microbiome in a healthily and in a stressed or diseased (mucosal inflammation) mammal.
Source: [3]

Thus, when thinking about whales, monitoring of the gut microflora might allow us to detect changes caused by factors such as aging, illness, prolonged food deprivation, and stressful events [2, 5]. However, since these are two-way factors, it is important to find an association between bacterial composition alterations and stressful events, such as the presence of predators (e.g., killer whales), illness (e.g., bad body condition), prolonged food deprivation (e.g., low prey availability and high competition), noise (e.g., noisy vessel traffic, fisheries opening and seismic surveys), and stressful reproductive status (e.g., pregnancy and lactating period). Examination of possible shifts in the gut microflora may be able to detect and be linked to many of these events, and also forecast possible chronic events within the population. In addition, the bacterial community monitoring study could aid in validating the hormone data (i.e., cortisol) we have been working with.

Therefore, the main research questions that arise in this context that can aid in elucidating the stress physiology in gray whales are:

  1. What is the microflora community content in guts of gray whales along the Oregon coast?
  2. Is it possible to detect shifts in the gut microflora from our gray fecal samples over time?
  3. How do gut microflora and cortisol levels correlate?
  4. Am I able to correlate shifts in gut microflora with any of the stressful events listed above?

We can answer so many other questions by analyzing the microbiome of baleen whales. Microbiomes are mainly correlated with host diet [10], so the composition of a microbiome can be associated with specific diets and functional gut capacity, and consequently, be linked to other animal populations, which helps to decode evolutionary questions. Results of a previous study on baleen whale microbiomes [10] point out that whales harbor unique gut microbiomes that are actually similar to those of terrestrial herbivores. Baleen whales and terrestrial herbivores have a shared physical structure of the GIT tract itself (i.e., multichambered foregut) and a shared hole for fermentative metabolisms. The multichambered foregut of baleen whales fosters the maintenance of the gut microbiome that is capable of extracting relatively unavailable nutrients from zooplankton (i.e., chitin, “sea cellulose”).

Figure 03: The similarities between whale and other terrestrial herbivore gut microbiomes: sea and land ruminants.
Source: [11]

Thus, the importance of studying the gut microbiome of a baleen whale is clear. Monitoring of the bacterial community and possible shifts can help us elucidate many questions regarding diet, overall health, stress physiology and evolution. Thinking about my PhD project, it may also help in validating our cortisol level results. I am confident that a microbiome analysis would significantly enhance my studies on the health and ecology of gray whales.



  1. Hunt, K.E., et al., Overcoming the challenges of studying conservation physiology in large whales: a review of available methods.Conservation Physiology, 2013. 1: p. 1-24.
  2. Guarner, F. and J.-R. Malagelada, Gut flora in health and disease.The Lancet, 2003. 360: p. 512–519.
  3. Grenham, S., et al., Brain–gut–microbe communication in health and disease.Frontiers in Physiology, 2011. 2: p. 1-15.
  4. Zhang, Y., et al., Impacts of Gut Bacteria on Human Health and Diseases.International Journal of Molecular Sciences, 2015. 16: p. 7493-7519.
  5. Bailey, M.T., et al., Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium.Infection and Immunity, 2010. 78: p. 1509–1519.
  6. Sudo, N., et al., Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice.The Journal of Physiology, 2004. 558: p. 263–275.
  7. Rhee, S.H., C. Pothoulakis, and E.A. Mayer, Principles and clinical implications of the brain–gut–enteric microbiota axis Nature Reviews Gastroenterology & Hepatology, 2009. 6: p. 306–314.
  8. Kiliaan, A.J., et al., Stress stimulates transepithelial macromolecular uptake in rat jejunum.American Journal of Physiology, 1998. 275: p. G1037–G1044.
  9. Dinan, T.G. and J.F. Cryan, Regulation of the stress response by the gut microbiota: Implications for psychoneuroendocrinology.Psychoneuroendocrinology 2012. 37: p. 1369—1378.
  10. Sanders, J.G., et al., Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores.Nature Communications, 2015. 6(8285): p. 1-8.
  11. El Gamal, A. Of whales and cows: the baleen whale microbiome revealed. Oceanbites 2016[cited 2018 07/31/2018]; Available from: https://oceanbites.org/of-whales-and-cows-the-baleen-whale-microbiome-revealed/.


What REALLY is a Wildlife Biologist?

By Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

The first lecture slide. Source: Lecture1_Population Dynamics_Lou Botsford

This was the very first lecture slide in my population dynamics course at UC Davis. Population dynamics was infamous in our department for being an ultimate rite of passage due to its notoriously challenging curriculum. So, when Professor Lou Botsford pointed to his slide, all 120 of us Wildlife, Fish, and Conservation Biology majors, didn’t know how to react. Finally, he announced, “This [pointing to the slide] is all of you”. The class laughed. Lou smirked. Lou knew.

Lou knew that there is more truth to this meme than words could express. I can’t tell you how many times friends and acquaintances have asked me if I was going to be a park ranger. Incredibly, not all—or even most—wildlife biologists are park rangers. I’m sure that at one point, my parents had hoped I’d be holding a tiger cub as part of a conservation project—that has never happened. Society may think that all wildlife biologists want to walk in the footsteps of the famous Steven Irwin and say thinks like “Crikey!”—but I can’t remember the last time I uttered that exclamation with the exception of doing a Steve Irwin impression. Hollywood may think we hug trees—and, don’t get me wrong, I love a good tie-dyed shirt—but most of us believe in the principles of conservation and wise-use A.K.A. we know that some trees must be cut down to support our needs. Helicoptering into a remote location to dart and take samples from wild bear populations…HA. Good one. I tell myself this is what I do sometimes, and then the chopper crashes and I wake up from my dream. But, actually, a scientist staring at a computer with stacks of papers spread across every surface, is me and almost every wildlife biologist that I know.

The “dry lab” on the R/V Nathaniel B. Palmer en route to Antarctica. This room full of technology is where the majority of the science takes place. Drake Passage, International Waters in August 2015. Source: Alexa Kownacki

There is an illusion that wildlife biologists are constantly in the field doing all the cool, science-y, outdoors-y things while being followed by a National Geographic photojournalist. Well, let me break it to you, we’re not. Yes, we do have some incredible opportunities. For example, I happen to know that one lab member (eh-hem, Todd), has gotten up close and personal with wild polar bear cubs in the Arctic, and that all of us have taken part in some work that is worthy of a cover image on NatGeo. We love that stuff. For many of us, it’s those few, memorable moments when we are out in the field, wearing pants that we haven’t washed in days, and we finally see our study species AND gather the necessary data, that the stars align. Those are the shining lights in a dark sea of papers, grant-writing, teaching, data management, data analysis, and coding. I’m not saying that we don’t find our desk work enjoyable; we jump for joy when our R script finally runs and we do a little dance when our paper is accepted and we definitely shed a tear of relief when funding comes through (or maybe that’s just me).

A picturesque moment of being a wildlife biologist: Alexa and her coworker, Jim, surveying migrating gray whales. Piedras Blancas Light Station, San Simeon, CA in May 2017. Source: Alexa Kownacki.

What I’m trying to get at is that we accepted our fates as the “scientists in front of computers surrounded by papers” long ago and we embrace it. It’s been almost five years since I was a senior in undergrad and saw this meme for the first time. Five years ago, I wanted to be that scientist surrounded by papers, because I knew that’s where the difference is made. Most people have heard the quote by Mahatma Gandhi, “Be the change that you wish to see in the world.” In my mind, it is that scientist combing through relevant, peer-reviewed scientific papers while writing a compelling and well-researched article, that has the potential to make positive changes. For me, that scientist at the desk is being the change that he/she wish to see in the world.

Scientists aboard the R/V Nathaniel B. Palmer using the time in between net tows to draft papers and analyze data…note the facial expressions. Antarctic Peninsula in August 2015. Source: Alexa Kownacki.

One of my favorite people to colloquially reference in the wildlife biology field is Milton Love, a research biologist at the University of California Santa Barbara, because he tells it how it is. In his oh-so-true-it-hurts website, he has a page titled, “So You Want To Be A Marine Biologist?” that highlights what he refers to as, “Three really, really bad reasons to want to be a marine biologist” and “Two really, really good reasons to want to be a marine biologist”. I HIGHLY suggest you read them verbatim on his site, whether you think you want to be a marine biologist or not because they’re downright hilarious. However, I will paraphrase if you just can’t be bothered to open up a new tab and go down a laugh-filled wormhole.

Really, Really Bad Reasons to Want to be a Marine Biologist:

  1. To talk to dolphins. Hint: They don’t want to talk to you…and you probably like your face.
  2. You like Jacques Cousteau. Hint: I like cheese…doesn’t mean I want to be cheese.
  3. Hint: Lack thereof.

Really, Really Good Reasons to Want to be a Marine Biologist:

  1. Work attire/attitude. Hint: Dress for the job you want finally translates to board shorts and tank tops.
  2. You like it. *BINGO*
Alexa with colleagues showing the “cool” part of the job is working the zooplankton net tows. This DOES have required attire: steel-toed boots, hard hat, and float coat. R/V Nathaniel B. Palmer, Antarctic Peninsula in August 2015. Source: Alexa Kownacki.

In summary, as wildlife or marine biologists we’ve taken a vow of poverty, and in doing so, we’ve committed ourselves to fulfilling lives with incredible experiences and being the change we wish to see in the world. To those of you who want to pursue a career in wildlife or marine biology—even after reading this—then do it. And to those who don’t, hopefully you have a better understanding of why wearing jeans is our version of “business formal”.

A fieldwork version of a lab meeting with Leigh Torres, Tom Calvanese (Field Station Manager), Florence Sullivan, and Leila Lemos. Port Orford, OR in August 2017. Source: Alexa Kownacki.