Week 4: Reptiles and amphibians and mollusks! Oh my!

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Despite being a short week for 4th of July weekend this week was full of activity.

Morning at the Cascade Head marine reserve

Tuesday, I helped with a fellow intern with his sea star survey. We went out to the tide pools at Cascade Head and measured all of the sea stars we could find and checked them for signs of wasting. Wasting disease has decimated sea star populations all along the pacific coast. Scientists are curious to see if populations are recovering this year and how the juvenile recruits are faring. We searched on hands and knees in every nook and crevasse and found some juveniles on the scale of millimeters as well as many larger adults.

Sea stars were not the only thing we found. The tide pools at Cascade Head are some of the best I have ever seen. We found a tiny octopus, a school of rockfish and my personal favorite, opalescent nudibranchs!

Opalescent Nudibranch

Opalescent Nudibranch

The word nudibranch translates to naked-gill. This describes the tentacle-like structures, or cerata, found all over their bodies that are used for breathing, digestion and defense. Nudibranchs prey on many stinging organisms including the venomous Portuguese-Man-O-War. They can take the toxins from their prey and incorporate them into their cerata to use for their own defense.

The rest of the week was spent reading papers, CBRAT project meetings and attending an interesting seminar given by Dr. Burke Hales about the effects of ocean acidification on oyster larvae in Willapa Bay, WA.

The weekend came with unpredictable coastal weather. Saturday we managed to find a rain free window in the afternoon for some browsing at the weekly Newport farmer’s market and hiking at Beaver Creek state park. A benefit of the rainy weekend was all of the wildlife we found out on the trail.

Garter snake at Beaver Creek state park

Garter snake at Beaver Creek state park

We caught a garter snake lounging on a blackberry vine, a newt making his way through a pile of soggy leaves and a few quarter-sized frogs. The clouds may have obscured most of the viewpoints but we made up for that with many berry stops to sample the thimbleberry and not-quite-ripe blackberries lining the trail. We were clearly not the only ones enjoying the berries, every few yards we came tracks and scat from bear, deer and elk. Unfortunately, all of the mammals managed to hide from us, we didn’t end up spotting any bears. Maybe next time!

 

 

Week 3: Science for a changing world

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Whoops a little overdue for an update. Week three was spent mostly reading, I’m still working through the literature related to decapods and pH. I had my most intern-like task of all this week which involved reorganizing my mentor’s bookshelves. Now I’m just waiting for the coffee orders to start coming in. Ha-ha.

Through all of my reading the thing that stands out the most is how far science has come in the past century. During our first days at HMSC it was remarked that now is a great time to be a scientist. This brings to mind the quote or curse (depends on who you ask) “may you live in interesting times.” Human caused global climate change has altered and will continue to alter our world in ways that are difficult to predict and understand. Many of the advances in science, especially ocean and atmospheric science in this century stem from pressing necessity rather than simple curiosity.

Waiting at the HMSC bus stop

The studies I look at focus on pH and its effect on marine invertebrates. Studies done after the year 2000 all include standardized methods of bubbling CO2 through ambient seawater pumped in from an area near to where organisms were collected. Multiple components of pH are measured and all other conditions are monitored constantly. Organisms are exposed to pH conditions predicted for the year 2100 determined by complex ocean/atmosphere computer models. In other words, good accurate science is being conducted.

In contrast, a study from 1975 looking at pH tolerance of crayfish simply put some crayfish in a jar of acid, a jar of NaOH and measured how long it took for them to die. Turns out crayfish will die within 24 hours if put in a beaker of HCl (Newcombe, 1975). They say there is no such thing as a bad question but there is definitely such a thing as poor scientific design and I am sure at least the crayfish involved would wonder if the question of how long an organism can live in pure acid is something we really need to answer.

Friday I caught a bus out of Newport and headed home for a long relaxing 4th of July weekend. It was nice to have a break from the bunkhouse and see family and friends. 

Mud, Ultimate, and Bacteria

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How is it already the end of week 4…? Crazy. Time is starting to really fly by. Not a whole lot of new stuff has happened at work this week. The samples from our Tillamook field work are still being processed slowly but surely. A few fairly cool things did happen this week though.

First, I learned how to run particle size analysis (PSA) on sediment samples. While it may seem pretty useless to know what the sizes of your sediment grains are, this is actually very important information. By determining the particle sizes, you can infer lots of other info about the hydrology of the habitat. For instance, in marsh sediment samples PSA can help model how fast the marsh will drain as the tide goes out or how fast it will fill. I’m sure reading Jess’ blogs will give you more info about this since her research revolves around this kind of analysis. PSA also lets you infer what the microhabitat of the environment is like. The term “meiofauna” refers to organisms that spend their lives living in between sediment particles such as grains of sand on a beach. This is a very dynamic habitat and there is huge diversity in the taxa that call this environment home. The project I’m working on is mainly interested in how fecal indicator bacteria can colonize the top layer of sediment and potentially become resuspended by wave action and storm winds. For some reason I can’t caption the picture below but it’s a few of the representative meiofaunal taxa.

Meio

Second, Amy and I went on a road trip up Yaquina Bay Rd. to try and find some eelgrass sampling sites for my side project. All in all, we were pretty successful! We found three sites that were fairly accessible and easy to relocate so we can definitely resample them later in July. The mud was easier to deal with this time but I don’t think I’ll ever really enjoy standing on a surface that isn’t solid haha; my brother keeps making fun of me that I’m fine with freediving and skydiving but I hate walking on some soft mud. Something about solid ground giving way just isn’t natural haha. The mud was actually so bad in one site that Amy and I decided to butt-scooch down two fallen trees to get to the waterline. I’m sure anyone who saw us had a good laugh.

Third and finally, the results of the IDEXX tests targeting Fecal Coliform and Enterococci are continually returning high hits for eelgrass leaves! The loosely-attached biomass on eelgrass leaves is full of indicator bacteria and this result suggests that gentle agitation by rain, storm action, waves, and wake could release the bacteria into the water column. This is an important early result because it suggests that storm-based water sampling for indicator bacteria could be very inaccurate in Oregon and might be resulting in extended closures of shellfish harvesting areas.

On a non-work note I found out about an ultimate Frisbee league this week that happens every Monday and Thursday night in Newport. “League” might be a bit of an overstatement but it’s certainly a whole lot of fun! One of the researchers at the EPA and Jess’s boss, Jody Stecher, and his wife, Linda, are very into ultimate and always show up. Jess, another intern, Amy, and myself are actually going to their house tonight to make pasta. Not a bad way to round out week 4!

 

Image references:

http://www.marbef.org/wiki/Meiofauna_of_Sandy_Beaches

 

An Upward Trajectory: Setting Goals and Finding Peace

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I think I’m settled in on the Oregon South Coast – finally had time to unpack my bags and live that relaxing way of life that this region is known for!

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Throughout this relaxation, I’ve been able to focus on my goals of the summer. One of my favorite aspects about Oregon Sea Grant is that they’re interested in our development, not just professionally, but personally as well. One way that they have encouraged us to make the most of our time and experiences here is by setting S.M.A.R.T. goals, standing for Specific, Measurable, Achievable, Realistic, and Time-bound.

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I love goals. I make a goals/to-do list just about every day, but I had never heard of SMART goals before. I think they’re a great way to reach your end goal by focusing on bite-sized, manageable tasks every day. I also think that the best way to reach your goals is by shouting them to the world, and telling anyone who will listen. Even if they’re not too interested, talking about them is an easy way to keep you accountable to yourself. And so, here is my favorite personal goal that I made, and here is me shouting it to the world: “Determine how to focus my mind and energy to be my most peaceful, healthy, and productive self.” This is basically my way of saying “determine what makes me happy (including what attempts to take away my happiness) and brings me peace”.

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One way that I’m doing this is by taking an hour a day to do something that I enjoy, be it drinking coffee and listening to music, sitting outside, walking on the beach, running, yoga, or playing golf. I’ve been finding the activities that I enjoy the most, and when it comes time for researching for my senior project or studying for the GRE, I’ve noticed that I’m more relaxed and that those activities are more enjoyable as well. I’ve also been finding happiness in unexpected places, like the fresh morning air on my bike rides to work, or having all of my laundry done and my bed made. Maybe this is what growing up feels like?

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Never thought that my internship experience would include finding myself giddy over clean dishes, but I’m really glad that I’ve been able to take the time for personal growth and reflection. I think that these realizations will be extremely beneficial for my senior year, graduate school, career, and personal life moving forward. I definitely see an upward trajectory, and I’m grateful for the South Coast for giving me this peace of mind.

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Week 3: Somehow July is Happening

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Hello, friends. Not much new on the work end of things. The survey data keeps trickling in, which is good, and I’ve been sifting through some papers on derelict gear and ghost fishing. There is a small collection of papers on derelict gear in trap fisheries; researchers have only been publishing on the subject since the late seventies. For the most part, people seem to agree that it is an issue. As to how big of one, for whom (commercial or recreational fishermen), and if there is an overarching economic benefit to cleaning up lost gear? The jury’s still out. The answers to these questions seem to be pretty dependent on the situation, so what works for the Dungeness crab fishery in Oregon may not work for Alaska, or for California, or for the blue crab fishery in Chesapeake Bay.

Work-wise, the highlight of the week was probably deploying “the world’s most expensive crab trap” (sound bite credits to Justin) last Friday. This crab pot is equipped with a battery, a flash, and a GoPro camera. It takes a picture once a minute, and it will be deployed for a week. A picture a minute for seven days à tons of data. After arriving at work a little earlier than usual, we loaded the gear into the truck and left for the marina. By 7:30 or so, we were out on the water. It was my first time being on the ocean since arriving (actually, now that I think about it, it may have been my first time ever on a boat in the Pacific), and it was a gorgeous day for it. On our way back into the marina, we spotted a few gray whales hanging around near the South Jetty. So, the weekend was off to pretty good start.

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Crab trap deployment

The rest of the weekend was pretty relaxed. We drove around and saw a few sites (Devil’s Punchbowl, Otter Crest Loop) on Saturday, and Sunday was a much-needed lazy day. On Saturday and Sunday night, we took advantage of the grills at the dorms to make some chicken kabobs and Korean BBQ. In my head, BBQ=summer, and it has the added perk of being more affordable than a night eating out. Wins all around.

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One of the many stunning views from Otter Crest Loop

The Fourth was filled with volleyball, cooking, and…eating! I slept later than I’ve probably ever slept in my life before joining in a lazy game of sand volleyball (i.e. there were scarce amounts of volleying, and a lot of time was spent lying in the sand). Monday evening, we somehow got ourselves invited to a Fourth of July potluck at a gorgeous apartment overlooking the bay. The food was amazing, and there were lots of people there that were close to our age but already doing a fantastic job of living very much like adults. Oh well, someday.

Also, please notice I just used the words “relaxed” and “lazy” three times to describe the weekend…I think that says it all.

Until next time. How is it already July??

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Sunset is a great time to go on a run to the South Jetty

Crashes, Cooking, and Climate Change

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Happy July!

This week was one of the most eventful, yet most uneventful weeks of my summer so far. Last Monday, I got into a bit of a bike accident that ended in a trip to the emergency room. With a sprained ankle and stitches, I spent a majority of the week confined to the couch. I am endlessly grateful to be hobbling around at this point and am hoping to make a speedy recovery so I’ll still have time to enjoy the rest of Oregon. Huge shout out to my roommates and fellow Summer Scholars, my mentors, Kaety and Kelsey, and the random strangers who have been SO helpful and understanding.

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Sorry if you’re eating

Seafood can be a tricky thing to deal with. Once you’ve got it, what do you do with it? We’re trying to fix this with an eating guide for Shop at the Dock participants. It will list common species to buy off the dock, its favor/texture, how sustainable it is, and a common and delicious way to cook it. 

This week, I also came across a poignant article about how the commercial fishing industry is declining due to warming waters. 

“The cod isn’t just a fish to David Goethel. It’s his identity, his ticket to middle-class life, his link to a historic industry.

“I paid for my education, my wife’s education, my house, my kids’ education; my slice of America was paid for on cod,” said Goethel, a 30-year veteran of these waters that once teemed with New England’s signature fish.

But on this chilly, windy Saturday in April, after 12 hours out in the Gulf of Maine, he has caught exactly two cod, and he feels far removed from the 1990s, when he could catch 2,000 pounds in a day.”

Even having studied it, climate change is definitely one of the more intangible, abstract topics for me. And while the science is crucial, hearing the more humanistic side of climate change really brings the issue home. The article is set on the East Coast, but presents some staggering statistics about declines in catches and also really interesting opinions from fishermen about climate change.

I’m determined to get back on my bike by the end of the summer, so I’ll finish this post with a little motivational tune. Thanks for reading and have a wonderful week!

Week 3

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Week 3 has come and gone! I already find myself planning trips for every weekend we have coming up and it’s scary to see that we really don’t have many left.

Similar to Week 2, this past week mainly consisted of soil processing in the lab. We did have one field day in Tillamook Bay which ended up being really nice. The trip was mainly to make sure our wells were still in place and hadn’t been tampered with. Unfortunately, one of our wells had the logger taken out of it and we found the logger lying next to the well. In the field we were able to download the data and it looked like the logger was pulled only two days into the sampling period. It was a huge bummer to realize we lost basically all of the data for that well and we most likely won’t be able to make great conclusions about that transect because of it. We are fairly certain that it was most likely a person that tampered with the well due to how we found the scene and the time that the logger was pulled. Since the logger was found right outside of the well, it was pretty clear that whoever pulled it wasn’t doing it to steal, they were probably just curious. I do understand that, but their curiosity cost us really valuable data. So, just as a disclaimer to the public, PLEASE do not touch field equipment that clearly isn’t yours. In the grand scheme of things we are actually trying to help you.

On a more positive note, we’ve lucked out so far that every day we have gone into the field the weather has been beautiful. This past field day we of course stopped for some ice cream and then we got lunch at the Blue Heron which was an awesome little cafe.

Hopefully this coming week we will be able to start doing particle size analysis (PSA) on our samples and analyzing some of the data we have gotten back.

On the personal side of things, we took some cool trips to Otter Rock, the Devil’s Punchbowl and Lincoln City. We have also been barbecuing a lot which has been delicious.

Yesterday was the 4th of July and it ended up being one of the warmest days we’ve had since being here. We went to a small party at one of the apartments across the bay from Hatfield which had a perfect view of the fireworks Newport put on. We met some extremely nice people who lived in the community and ate so much that we had to go to sleep as soon as we got home.

Hopefully in the upcoming weeks I’ll be able to talk about some interesting trends in the data we’ve been collecting and maybe some cool weekend trips inland (I really need to get warm for a little while).

Until next week!

Week 3 – The Curious Case of the Cabezon

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For those of us old enough to remember (or young enough, depending on your age), the word SMURF most likely evokes memories of little blue woodland figures brought to you by Saturday morning programming. But to members of the ODFW Oregon Marine Reserves team, SMURFs are something radically different: Standard Monitoring Units for the Recruitment of Fishes.

Which is fancy terminology for what basically amounts to a floating bunch of plastic encased by even more mesh plastic. However, to a juvenile fish, these artificial refuges offer a safe haven in the desert that is the open ocean.

A SMURF attached to its mooring. Photo courtesy of oregonmarinereserves.com.

Upon deployment in nearshore waters, SMURFs are left to soak for two weeks before being retrieved, during which time they are colonized by the young of a variety of fishes (in our case, mainly rockfish and cabezon). The SMURF is then enveloped in a large net, dragged onto the boat, and unceremoniously shaken against the deck to dislodge any creatures stuck within the inner crevices of plastic. Back in the lab, each fish is meticulously measured and dropped into individually labeled baggies destined for the freezer. On a good day of SMURFing, the total haul can tally in the hundreds.

Juvenile fish being measured with calipers in the lab.

Researchers with the marine reserves program and Hatfield Marine Science Center use these sample collections to piece together various aspects of the early life histories of fish. One process known as recruitment, which is defined by NOAA to be the “time when a young fish enters a fishery or enters a specific habitat such as a juvenile or adult habitat,” is of particular interest. Many larval fish species, rockfish and cabezon included, spend a portion of their time in a pelagic phase, in which they are subject to surface currents that carry them offshore. As they continue to grow, they make their way back to nearshore waters and become recruits of the more mature populations. SMURFs intercept these transients, providing valuable information on the understudied temporal and spatial links between larval and adult stages.

One of the more notable observations on our SMURFing expeditions this year has been the presence of an abnormally large size class of juvenile cabezon.

Top and middle: Juvenile cabezon. Bottom: Unidentified juvenile rockfish. The cabezon is the largest member of the sculpins, a group of highly camouflaged, demersal fishes. Their mottled coloration enables them to expertly blend in with their rocky surroundings.

A quick discussion with colleagues back in the office has led to a few conceivable conjectures, all regarding recent El Niño conditions (Earth is currently experiencing neutral conditions, but a La Niña event is scheduled to be in place later this year). The occurrence of an El Niño leads to weakened winds that would otherwise normally push surface waters westwards across the Pacific. This in turn causes depressed upwelling of nutrient-rich cold water along the western coast of the Americas; the opposite effect is seen during La Niña conditions. Past SMURF research has shown that the periods of surface current relaxation and reinforcement associated with these climatological events favors recruitment of certain rockfish species over others, which could indicate similar successful outcomes for other larval fish species.

One of our personal theories is that the slower currents induced by the El Niño equate to a longer time spent offshore, and thus an extended period of growth before being brought back nearshore. An interesting way to test this would be to observe the temporal abundance of recruits – later arrival times than normal could lend support for this theory. Another guess is that the warmer surface water increases the metabolism of the larvae and accelerates their growth prior to recruitment. Perhaps it’s a combination of the two, or possibly something entirely different.

A cursory online search of research literature yielded little insight, although I did find this lone paragraph on cabezon and El Niño conditions from a 2009 NOAA assessment:

“The recruitment patterns…suggest a possible link between environmental forcing and population dynamics. Specifically, strong ENSO conditions…may be a pre-cursor to significant recruitment events.”

Just to be clear, it certainly is possible that the data is simply coincidental. But based on our own observations and the one above, the potential correlation of increased cabezon size with El Niño is a plausible hypothesis to be sure, and one that requires further investigation to tease apart the true dynamics of the situation. For now, though, the phenomenon remains a mystery as cryptic as the fish itself.

Skyler’s Weekly Review – Week 3

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The Buzz: Clamboree, RTK, Mission Planner

Clamboree: Every year, Coos Bay hosts an event to celebrate their fondness for Empire clams (otherwise known as gapers, horse clam, horseneck clam, or Tresus capax) and more recently, glass art. This year was particularly important for ODFW to make their presence known due to upcoming estuarine studies being conducted in the bay. Despite being located by Clamboree staff in the most distant corner from the action (you would think being near the kids section, which also happened to be next to the beer/wine garden, would draw lots of people), we had ample amounts of wanderers playing in our touch tank full of clams, crabs, and other invertebrates. Loaded for bear with pamphlets, sport fishing regulations, identification charts and shadow boxes, crab gauges, visual displays of legal and non-legal crab, and plenty of things to poke and touch, SEACOR did their best to provide educational outreach for the event.

2016 Claboree Poster

Bay Clam Nutrition Facts

RTK: RTK, or real-time kinematic, is a rapid survey style that utilizes several GPS reference stations to calculate highly accurate “rover” or moving GPS positions on-the-fly. This style allows us to record locations with very low error and accuracies down to about 1 centimeter quickly (under 2 minutes per location), easily (push of a button), and without more additional computer processing. The purpose of RTK surveys for SEACOR projects remain primarily in the realm of conducting estuarine bathymetry surveys; combining echosound measurements with precise GPS locations. However, with some additional equipment, RTK provides a massive benefit to our UAV imagery we plan to collect. Precise GPS data makes our imagery able to be used for measuring distance on the ground from aerial photography; a game changer that allows us to measure and count clam shows that are roughly a centimeter in size over a much larger area and long after the tides have returned to obscure them. These clam shows also happen to be the most recreationally harvested bay clams: gapers, cockles, littlenecks, and butters. UAVs plus RTK ground-truthing might allow far more advanced and accurate calculation using much fewer resources than typical quadrat surveys of bay clam populations; a boon to clam resource management.

Example Mission Planner Grid

Mission Planner: Few software developers have pursued a complex suite of UAV applications as well as the open-source UAV community. A well-known platform, Mission Planner, can be used to control a variety of remote controlled autonomous vehicles including copters, planes, rovers, and to some extent even submersible vehicles. Recently, the community developing the software added in features to make UAV aerial photography and mapping even easier such as creating gridded flight plans that ensure a certain percentage of image overlap. SEACOR’s UAV flights will require 80% or higher image overlap; flying manually and achieving this is next to impossible. But Mission Planner and its compatibility with most common UAV flight controllers allow us to design an automated flight path to ensure we get the data we need from our on-board camera sensor.

Next week: UAVs, UAVs, and UAVs!

Little Green Aliens

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Invasive species are an especially hot topic among today’s scientific community. Non-native species have been shown to negatively impact the health of native ecosystems, especially in aquatic environments (e.g. Lionfish, Snakehead, Zebra Mussel, Nutria, and Asian Carp). It is important for coastal managers to detect invasive species soon after their arrival so that successful eradication and management plans can be implemented. Therefore, invasive species monitoring is conducted at most NERRs.

The South Slough NERR alone is home to over 50 non-native marine species. Of these species, few are as infamous as the European green crab. As I discussed in my last post, I recently started a project aimed to investigate the distribution and population of green crabs in South Slough. I collected samples continuously for 2 days at my first set of sites. While dungeness and hairy shore crabs were most abundant, I collected 15 green crabs at the mouth of the estuary. Specimens were measured, sexed, and weighed before being humanely disposed of. The data collected from this project will be used to manage the spread these little green aliens and potentially prevent future invasions along other coastlines.