Wednesday, August 21, 2019

Iceland Ecosystems and Fieldwork

Whale Bones, Transects, and Ecosystems--Oh My!

 I have spent the past week with a group of amazing UC San Diego students exploring the beautiful country of Iceland on an Alternative Breaks trip focused on sustainability and science communication. The following post outlines what we have been up to, from learning ecology field techniques to visiting each of Iceland's unique ecosystems and talking about how they could be protected from actions we take at home.

Lava Rocks and Freshwater
Grabrok Crater
Our first stop brought us to Grabrok crater, where rocks made from lava provide the perfect environment for a unique moss to grow. Later in our trip we learned that this was the crater one of our Icelandic professors used to sneak to with other female university students for "secret feminist meetings" in the middle of the night when she was in college. Most of Iceland's geography has been sculpted by the volcanic activity in the area, and is exposed to rather extreme winds. With that said, most of the plant species there appear to be shorter with a strong hold to the ground, as displayed in the crater ecosystem of Grabrok. 
The icy and clear waters of Icelandic waterfalls tempted us with their beauty throughout our trip. These types of ecosystems contained fresh water fish and were usually accompanied by swarms of midges--small harmless flies. One waterfall seemed to contain a fish ladder to assist what we assumed to be salmon as they made their homeward voyage up the river. Plants were usually a bit taller here, as seen in the image above, and different species of moss were dominant in comparison to the lava rock moss.

The Forest and The Bog

Holar Forest
The thickness of the pine trees.
Upon our arrival at Holar University, we encountered an entirely different ecosystem, this one man-made. Here, planted pine trees formed an artificial forest, home to many species of birds, wandering sheep from the local farmers, and wild blueberries and crowberries. The most interesting aspect of the forest ecosystem at Holar was how it abruptly changed depending on the trees present. The two pictures above demonstrate this change, as they were all taken within 30 minutes of each other while hiking through the forest. 
The thickness of the pine trees provided less sun for ground-dwelling plants to grow, and the fallen pine needles prevented any shorter plants from growing. Therefore, the forest was primarily composed of taller pines and lichens that grew on them.
The accumulation of rainwater left behind a bog in the forest.
On the other hand, the center of the forest resembled a freshwater bog ecosystem. No trees existed here, I presume because of the water that accumulated from recent rains. The absence of trees allowed grasses and bushes to thrive here. 

Sorting through Arctic Fox scat.
In addition to visually experiencing the forest ecosystem, we got to learn some field techniques as well. While transecting one area of the forest, Dr. Carolyn Kurle taught us how to identify animals via dissection of their feces. Based on the seeds, hairs, or bones present in the scat, we were able to determine where Arctic foxes, sheep, and dogs had been.

 Interestingly, almost all of the species on Iceland are invasive. Glaciers dominated the island about 12,000 years ago, wiping out all life. Only with the assistance of migrating birds dropping seeds while passing over helped re-vegetate the land many years after the glaciers receded. One can see the bowl-shaped mountains carved by the glacier pictured below. From "The Ridge", we could see the grassland, bog, and forest of Holar. Legend has it that this lookout was the sacred place of one of Iceland's first bishops, who used to hike it barefoot everyday to pray. Ten minutes of silence after a prayer read in Icelandic allowed us to appreciate the area and its history.
"The Ridge" at Holar University.
To get a better idea of how the land looked 12,000 years ago, we visited a real glacier, parallel to the first glacier to melt in Iceland (called "OK Glacier"). Langjökull Glacier, the second largest glacier in Iceland, is predicted to melt by the year 2165. The runoff water from the many glaciers of Iceland provide fresh, clean, and inexpensive drinking water for Icelanders. Even though the water dripping from the ceiling was said to be the purest in the world, scientists have discovered one extremophilic bacteria with a 50-year dividing time that lives in the ice of another glacier. I collected a sample of glacier water to test for DNA when I get back to lab at Scripps. 

The Intertidal
Brightly colored eggs found under seaweed in the intertidal zone.
 Our search for more diverse ecosystems to transect lead us to the intertidal zone. Here the tide was low, but not as low as it could be. Nevertheless, we scoured the area in search of snails, algae, arthropods, and other sea critters. Transecting the area would allow us to statistically estimate the species populations via imaging and analysis without having to count every animal individually. It is a common technique in ecological field research. Upon walking farther down the beach, we were lucky enough to see a decomposed small whale skeleton. Laid in line, the vertebrates gave us a good indication of how large the whale was, and a piece of blubber displayed the layers that kept the whale warm--a rare, in-person sight.
Students transect the intertidal zone.

Whale bones and blubber found on the beach.

Geothermal Zones

Hot steam rises from the earth near volcanic activity.
 The last main ecosystem, and one most central to Icelandic energy production, was the hot springs. Here, the smell of rotten eggs overwhelms the air, a smell produced by sulfur emissions from deep inside the earth. This is another ecosystem full of extremophiles, namely archaea that love sulfur. Temperatures can reach thousands of degrees. Icelanders utilize this natural heat source for geothermal energy, which naturally powers most of the country and provides free hot water for its residents. Other than potential microorganisms, this ecosystem was devoid of other plant life or animals, most likely because the environment is not particularly ideal for supporting life.

The Best Ecosystem of All
 With so many diverse ecosystems, some naturally had to be omitted from this blog. However, I would have to say my favorite was the potato chip field, found deep within the Holar mountain ranges.
Potato Chips in their natural environment.

Stay tuned for my third and final blog regarding this fantastic trip!

With Love, 

Monday, August 12, 2019

Welcome Home, Welcome to Iceland

Welcome Home
Welcome to Iceland

After 21 hours of travel, the Alternative Breaks Sustainability group from UC San Diego made it safely to Iceland! This blog is to focus on our first day in this beautiful country, with special attention given to the food and cultural tour we took upon arrival and some striking and interesting differences of Iceland in comparison to our home countries.

One of the first differences I noticed was in the Keflavik airport. With no McDonald's or chain fast-food in sight, another chain, "Joe & the Juice" appeared on almost every floor. I counted three in total on our route from the gate to the parking lot. With the popularity of this joint, I tried it out myself (and man, was it delicious!). The menu highlighted a protein shakes, nutritious sandwiches, and freshly squeezed juices. I chose to try a strawberry-banana shake, leading me to wish America would replace all of its Starbucks stores with the better, healthier Joe.

View of Reykjavik from a path across from the University of Iceland.
Our first stop brought us to the University of Iceland, where we would stay for the night. Not only were the people kind and accommodating, but another striking discovery was made while there: silence. Iceland as a whole seems to be a very quiet place. We did not hear any sirens, nor did we hear any people talking loudly in the airport, Costco, or hostel. Even Iceland's largest city was completely silent. Everyone appeared to be whispering--a very joyful change from the hustle-and-bustle of most American cities. It gave me a chance to relax and enjoy the natural wonders of the country, as well as the ability to think in peace.
A restaurant famous for their lamb soup, served similarly to the clam chowder bread bowls of San Francisco.
 After a brief 20-minute nap, the group embarked on a food tour of Reykjavik, which was generously gifted to us from a donor. This opportunity allowed us to learn about and appreciate the culture and customs of Iceland. For example, I did not realize the importance of soup in Icelandic culture, and once attempted to eat my meal before receiving my soup (a faux pas). 

Traditional Lamb Meat Soup Bread Bowl
We began our food tour with lamb soup served in freshly baked bread bowls, a historical meal used by settlers to survive their first winters. Later we were presented with plates full of mussels, which tasted extremely fresh and did not have the grainy taste I have found mussels to have in the past. Many of us tried different pastries and hot cocoa for dessert. My pastry was a slice of white mousse cake that was perfectly rich with flavors of passion fruit and mango. We visited a famous hot dog stand and each tried an Icelandic hot dog with a special sauce on top that was delicious. Finally we entered a flea market, where fish was sold, and were given the opportunity to try a bite-sized bit of Greenland Shark. That's where our reactions got interesting...
Passion fruit and mango cake
with macaroon and whipped cream. 
Famous hot dog stand downtown.

Shark meat is very popular in Iceland, but may be an acquired taste for many people. Interestingly, sharks do not urinate, which helps balance internal salts with the external salts in sea water. This means that urea (not urine) is stored in their bodies their entire lives. 
Students at the fish market trying
Greenland Shark samples.
That being said, shark meat has to be processed to be safe to eat, which can lead to a very chemical-like after taste. I found that it actually hurt a little to swallow a tiny chunk, but noticed that the chemical flavor added a unique "spice" to otherwise regular meat. 

I personally found it to be a valuable experience to be present in a location and sample its traditional cuisines, an experience I've never had before. My group also had time to ask our guide questions about Iceland, such as what their most popular sport is ("golf") and if Iceland has a military ("hopefully never"). In addition, our guide gave us time to explore the famous Reykjavik cathedral, the tallest building in the city. Inside was a simple, yet beautiful, architectural design. A young woman played an organ with pipes that extended from the front wall. Later we walked by the Parliament building, and explored the area in search of art. 
Reykjavik's famous Lutheran cathedral with statue of Leif Erikson (founder of Iceland and North America) at the front.
Inside the cathedral.
Another exciting difference between the US and Iceland is their pride of Pride. I learned that the people of Iceland are very progressive, as they were the first country to legalize gay marriage (along with many other policies, such as being the first to have 99% of their energy produced by renewable resources). Even our guide made a truthful stab at American politics, saying that Icelanders recognize that they have no business or care to control other people's personal lives. I clapped in response to that statement.
Icelandic Parliament building.

Pride Parade preparations.
Interesting art placed around the city.

Overall, the group had an amazing (and delicious) educational experience learning about the history and culture of Iceland. More to come on further educational research adventures!

UC San Diego's Alternative Breaks Sustainability group posing with food tour guide.

Saturday, July 27, 2019

FLIP the Ship!

Image result for the flip ship
"Why is that picture hanging sideways? Oh, wait a minute..."

On June 1st, I was invited to tour the RP FLIP, a famous ship part of the Scripps Institution of Oceanography fleet. The FLIP ship is an oceanographic research vessel with a long, weighted "tail" that is designed to keep the ship steady when rotated vertically by 90 degrees. By not succumbing to wave movements in the open ocean, the FLIP allows researchers to accurately measure wave height, along with other things like ocean conditions and acoustics.

The "tail" section of the FLIP is more than 90 meters long and stabilizes the research platform when rotated 90 degrees into the water.
The FLIP is a one-of-a-kind vertical research platform, but the inside is even more of anomaly. The bathroom has 2 sinks, 2 toilets, and two shower heads--each pair with one that appears to be normally placed and the other at a 90 degree angle next to it. This is so the bathroom can function normally once the vessel completes its 90 degree "flip" in the open ocean. The beds and shelves are able to rotate with the boat so that nothing falls during the flip, and other items, such as chairs are tied to the ceiling so they can be accessed once flipping is complete.

The condiment shelf is able to rotate with the FLIP's 90 degree upright rotation
Chairs are secured to the ceiling with a desk that is secured to the post-flip floor.
During the 20-minute vertical rotation, researchers and crew must hold on to a bar with one foot in position for when the flip completes. The flip is slow, and at the last second jerks upright, so it is a relatively safe process. 
Researchers and crew must hold on to this support with leg in-place during the 20-minute flipping process.
Once the flip is complete, the vessel stays in place until it is ready to flip back and be tugged somewhere else. During this time, however, the sun bakes the barnacles stuck to the hull and the smell of decaying sea critters floods the living quarters, making a difficult environment to work in.

Although extreme, the FLIP is an iconic vessel, and it was such a privilege to explore it. Thank you for a FLIPping great tour!!

A successful hike to the end of the FLIP ship's 90-meter "tail" with the body of the vessel in the background. Thank you for a FLIPping great tour!

Tuesday, July 16, 2019

Orange Bloom

Image result for bioluminescence la jolla
Bioluminescent algae light-up the waves at La Jolla Shores.
Image courtesy of John H. Moore at The San Diego Union-Tribune. 

"Bioluminescence tonight!" read the email sent over the Scripps list-serve. A group of scientists carefully monitoring the water off of the pier at the Scripps Institution of Oceanography in La Jolla had picked up signals of a bioluminescent bloom to occur later that week.

Bioluminescence is a sort of light given-off by certain organisms. In the ocean, and particularly that week at La Jolla Shores, red algae that glows when disturbed can cause grandiose displays of blue light when their population numbers are high. This is sometimes called a "Red Tide" and can be extremely toxic depending on the species of algae present. 

Beyond the blue, I saw this bloom as an opportunity to try to culture some cool bacterial species from the algae-infested waters. So, when my professor invited me on a bioluminescent night swim with the rest of the lab, I tucked a few Falcon tubes into my dive glove to take some water samples with while swimming through the brilliant blue bloom. 

Upon return to the lab, I spread the samples onto different types of agar plates. Agar has the texture of stiff jelly and is what scientists put in Petri dishes to grow bacteria on in the lab. It contains most of the nutrients certain bacterial species need depending on their preferences. 

After waiting a few days, I noticed a neat little orange spot on one of my plates. It was a sort of iridescent, peachy color, so I isolated it onto a new plate. After the isolate grew up and I saw that it was free of contaminants, I was able to extract the 16S rRNA from the bacterial cells and sequence it.

After making more copies of the 16S rRNA with a technique called PCR, making sure I had bacterial 16S rRNA (instead of fungal) by running a bit of the sample through an agarose gel, and sending the RNA to a sequencing lab (science, science, science), I was able to identify the species name of my mystery bacteria. 

Machine generated alternative text:
This is an agarose gel that I ran for one of my previous sequencing experiments. The column with many bands on the right is a "ladder". Each band in the ladder represents a different length of base pairs, with the shortest strand at the bottom. The thick bands on the left of the ladder indicate the presence of 16S rRNA from bacteria!
Flammeovirga arenaria--the orange bacterial species I isolated--doesn't seem to have been studied much in the past. From Wikipedia, I know that it was originally isolated from Mexican sands, which leads me to believe it was independent from the bioluminescent bloom. Nevertheless, I still think the mystery work of solving an unknown bacteria's species name is one of the most satisfying tasks in the world!

I always wonder what more there is to find and learn about these small but tenacious organisms. With so little studied on this particular species of bacteria, I wonder what brought it all the way to La Jolla, and what other mysteries its genome could reveal about its function. 

There's always more to discover!