A Tale of Two Experiments…

- Extracting DNA from the filters

Extracting DNA from the filters

Screen shot 2013-04-21 at 10.01.14 AM

Sampling may have ended, but the work of analyzing data has just begun. After cleaning the equipment loaned from Dr. Morris, I headed to Seattle to use the Guava flow cytometer to determine the bacterial abundance present in our mesocosms. This data was needed to guide me in selecting the days we needed to run TRFLP analysis on the DNA collected by filtering mesocosm seawater. The preliminary flow cytometry graphs reveal two very different experiments occurred. The period after removing the shower caps and lowering the mesh bags show trend lines unique from those prior to increasing the amount of light in the mesocosms. While Dr. Morris and I are still in the process of teasing out the factors which might have participated in these results – the decision was made to run the TRFLP on the first and last days of the experiment and the day when the abundance began to increase exponentially. I completed the steps preparing the DNA to be extracted from the filters yesterday and cannot wait for Monday. At that time I will complete a lengthy protocol to determine the community composition of bacterioplankton within the mesocosms and, hopefully, determine if there are any trends correlating to the change in our flow cytometry trends. While I cannot wait for the DNA to reveal just what was growing in our mesocosms, I still have much work to do researching. The weather provides an opportunity to spend time out-of-doors researching and writing and I am taking full advantage of the sunny days.


A trip to the city..


179542_3643780006105_2023477582_nKiely Shutt

After a month of early mornings and long days, life after sampling has been a joy. Yesterday we (Kelly, Daneil, Amy & Natsuko) woke up bright and early for a different reason – catching a ferry. We decided to come back to Seattle for a weekend visit. Being at Friday Harbor is almost entirely opposite of the hustle and bustle in the city. While it has been nice to sleep in a real bed, take a bath, and see my friends, I’m excited to get back to the labs to finish analyzing my data and make progress on my research paper. It’s a little hard to believe that we only have 4 short weeks until the end of the quarter! We’ll be back Monday, and I can only speak for myself when I say that I’m surprised at how much I’m missing FHL. Leaving in June is going to be much harder than I thought. Who would want to leave such a beautiful setting and awesome peers?


Goodbye for now, FHL


The vessel taking us to Anacortes, WA

Life After Sampling

Screen shot 2013-04-07 at 11.46.57 AMKelly Govenar

Wednesday was our first day without sampling. Finally, I was able to sleep in and skip 7:45 am breakfast. I have never felt so rested. I spent most of the day relaxing in the sunshine.  Our busy schedule during sampling prevented me from venturing too far from the laboratories. Now I am trying to see more of the island and appreciate the beauty it has to offer. Kiely, Andrew, and I went to explore Eagle Cove Beach before dinner yesterday. Eagle Cove is located on the southern side of the island near American Camp.  The sandy beach and calm waters is an ideal place to launch kayaks or have a picnic.  The next places I want to see are British Camp and American Camp.

The majority of our group will be driving down to Seattle this weekend. It will be a good chance to relax, see friends, and begin writing our research papers. I will be meeting with Evelyn while I am in Seattle to talk about my project. It will be really helpful to discuss the results of the dilution experiment and speculate why the grazing rates changed as they did. We have a long month of writing ahead of us but I am looking forward to having plenty of time to write while exploring the San Juan Islands.


the path to the beach


a panoramic photo Andrew took of Eagle Cove


Screen shot 2013-04-07 at 11.46.23 AMNatsuko Porcino

T21 has been that magic number for the OA students since we learned that it was going to be our last day a week ago. After three weeks, it seems like we’ve been doing this forever – waking up and being on the dock by 8:30, rain or shine. We’d laugh at the (sometimes ridiculous) LICOR readings, chat around the sampler, exclaim over the weather, look for sea creatures around the dock, and try to catch photos of our tech, Barbara, and her seriously awesome sunglasses.

In some ways, I’ll really miss that – the familiarity of it all, how we’ve bonded over this experience and each found a bit of a niche in the early-morning dock environment. But I won’t miss waking up at 7:30 every morning, regardless of the day of the week. I’m looking forward to having weekends again. I’m also excited to begin looking at the data we’ve been gathering for the last 22 days, where before I’ve been too busy processing samples to truly look at and analyze the data we’ve been collecting.

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In Search of Water

Screen shot 2013-04-07 at 11.47.16 AMDaneil Newcomb

Ever since Amy and I rowed to town and saw a small waterfall, we’ve wanted to find the source. We began our expedition with Natsuko and Collin after dinner. Walking toward the entrance to Friday Harbor Labs we searched for a path to lead us to our destination. After a bit of walking we found a path and began to explore.

Natsuko looking out over the Harbor

Natsuko looking out over the Harbor

Initially, we tried to head down toward the water, but the path was steep and we didn’t want to risk getting caught at the bottom when sunset arrived, so we took a path heading in the opposite direction. This path happened to be a pleasant surprise. We found a bunch of young Madrona and the majority of an animal skeleton before heading back.

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The pHinal Days

PhilGravinesePhilip Gravinese

Our experiment began 20 days ago with dry clothes and warm hands.  Our final sampling days are now upon us and we have learned to deal with numb limbs and wet clothes.  Most of us can hardly believe that only 20 days ago our knowledge of mesocosm studies was diminutive.  Now as the experiment draws to a close we find ourselves engaged in conversations planning additional mesocosm experiments, commenting on ways to improve our protocol, and saying farewell to our international colleagues.  The apprenticeship provided critical training in experimental design, best practices in ocean acidification research and interdisciplinary collaboration with experts in the ocean acidification field.

As we launch into May we were eager to start the analysis and piece together our story.  Most of our time will be spent getting caught up on processing samples, comparing our data for statistical differences, and composing the first draft of our manuscripts (coming soon to the new Ocean Acidification Journal!).  Throughout the experiment we were aware of the daily chemical trends (i.e., chlorophyll, pCO2, alkalinity, nutrients) taking place within each treatment.  However, after spending the past 3 weeks hidden away in a dark room illuminated only by a small night light I am excited to see if any changes have taken place among the biological communities.  Soon I will be able to determine if high CO2 has an effect on the abundance and biomass of the microzooplankton.  Continue reading

The Perfect Ciliate

meAmy Stephens

The end is near! It has been a long few weeks but I’m going to miss sampling once it’s over. I wont miss the cold or the rain but I will miss the gorgeous scenery and eccentric discussions with my OA team on the dock.

Phytoplankton counts have gone up since we removed the mesh caps. I’m especially happy because it has made counting phytoplankton under the microscope more exciting. With my spare time, I’ve decided to go back and count more volume to get a more accurate picture of the phytoplankton community. The near empty slides from T0 make me appreciate the diverse and abundant community we have now even more.

To continue my trend of sharing what I see under the microscope, I’m sharing the perfect ciliate that I found while counting T16 today.