About James Kralj

My name is a James Kralj and I am a junior at the University of Wisconsin- Madison where I am majoring in microbiology. This summer I will be working with the EPA studying the biogeochemistry of salt marshes along the Oregon coast. This past fall I began research on Lake Michigan studying how invasive mussels impact its ecology and I am looking forward to continuing my studies this summer in Newport, OR.

Back to Wisconsin

Greetings from the heart of America’s dairy land, Madison, Wisconsin!  The past few days have been a whirlwind. I landed late in Milwaukee on Saturday night, and after a few days at work and a doctor and dentist appointment, I find myself back at the University of Wisconsin!

I am so glad to be back here in Madison, but I find myself already missing my friends and all the beautiful places from the west coast. It really was an experience that provided me with so much knowledge and lifelong friendships; two things that will serve me well in the future.


This semester promises to be a challenging one but I am looking forward to it. I will be taking physics, two microbiology classes, a biochemistry class, and will be continuing with my mentored research of Lake Michigan. Aside from what I’m sure will be a rigorous class load, I have 7 Wisconsin Badger football games at Camp Randall Stadium to break up my studies. I’ve been itching to get back to jumping around, and singing “Sweet Caroline” along with 85,000 other crazy badger fans.


There is still much to process from this summer. There are lots of notes to go through and I have many things to think about for grad school and my future. While there is much to do, I am so excited to see what my future holds and I know that this past summer was an amazing addition to that journey.

Again, I would like to thank everyone for all their support and guidance this summer. This is my last blog post as an Oregon Sea Grant Summer Scholar, but hopefully I will be able to post some more reflections in the future! See you soon, and On Wisconsin!

My Last Week in Oregon

Hello everyone! This is the final blog post I will be writing from Oregon! The past ten weeks have flown by in a way I could never have imagined. I’ve had the time of my life living on the Oregon Coast, and have learned an incredible amount of knowledge about estuaries and marine science during this brief time. I am incredibly grateful of everyone at the US EPA, Oregon Sea Grant, and the Hatfield Marine Science Center for all of the opportunities I have been presented with this summer.


Last week, all of the Oregon Sea Grant Summer Scholars presented our research at a symposium at the Hatfield Marine Science Center.  I found it to be very fun to present my work not only to those who helped me with it, but also to my friends and the whole of the Hatfield community.  It was a great feeling to summarize the huge amount of work I have done this summer and teach people about my research in the process. I also greatly enjoyed hearing about the research and work done by my fellow scholars, who are now my great friends.

The Oregon Sea Grant symposium was not the only presentation I gave. Earlier this week myself along with the other interns working at the EPA presented our work to all the EPA employees. After our presentation my mentor, Ted DeWitt, took us out to lunch and gave us a few awesome gifts to congratulate us on our hard work. It was a great way to wrap up my time at the EPA and say goodbye to the new friends I have made from working there.


Aside from presentations, I have been working on my final portfolio for Oregon Sea Grant. Writing our reflection essay and putting together all the work I have done over the past 10 weeks really made me realize just how much I did this summer! It is both sad to see my work finish, but also impressive to look at it as a whole and to reflect on my whole summer experience.

Last weekend was a quiet one spent here in Newport. I went surfing on both Saturday and Sunday and had an amazing time both days. On Saturday we went out surfing in the late afternoon and as we finished up, we were able to watch the most beautiful sunset of the summer while sitting in the waves on our surfboards. That was definitely a moment I will cherish forever!

Tonight is my final night here in Newport and all of the interns will be going out to dinner and celebrating our accomplishments.  The the interns, faculty, and staff here at Hatfield have become a family to me and it certainly will be incredibly sad to leave them. I know that we will all keep in touch and I cannot wait to see where life takes all of the incredible friends I have made during my time here.


I’ve had the time of my life here in Oregon! To any potential Summer Scholars reading this post and wondering if they should apply to the program, DO IT! You will not be sorry! I would like to thank everyone involved in my summer here and I am so grateful for everything!

Winding Down

Wow, I cannot believe 8 weeks have come and gone already! Our final presentations are just two days away and as I work on putting everything together I am amazed by how much I have done this summer working with the EPA. This past week was a scramble to obtain as much data and results as possible and involved many days in the field.


After going through all of our pictures, we found some interesting results! With our manipulative plots, the boxes we had put into the sediment were not showing many signs of sediment oxidation, so to see if anything was going on in the sediment we placed IRIS tubes into the center of each plot. We found that in the plots with the most algae, there was a large amount of sulfides in the sediment signaling anoxic conditions. Additionally, the plots that were placed in shrimp beds showed a lot of variance in how much sulfides the sediment there had. We found that the shrimp burrows act like highways for oxygenated water to travel down into the sediment, but we also found some differences between the two species of shrimp (ghost and mud).

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In the ghost shrimp area the IRIS tube showed sulfides in sediment that were deeper than in the mud shrimp areas. One hypothesis for this is the fact that ghost shrimp burrows are not as stable as mud shrimp burrows. Mud shrimp create a glue like substance that holds their burrows together, thus they are not constantly having to re-make them and water is able to travel through their burrows longer. Mud shrimp on the other hand are constantly burrowing as they do not produce any substance that helps stabilize their burrows. This might cause them to collapse more easily and thus limit the amount of oxygenated water that can travel through them.

In the lab we have also been finding some telling results. After completely covering the glass cylinders last week, I noticed that some of the algae is beginning to rot. No large changes have been observed from the sides of the chambers, so we have placed IRIS tubes into each cylinder and we hope they will show us sulfide concentrations under the varying conditions of the cylinders.


After a busy week at work, a group of interns from Hatfield trekked down to California for a weekend of camping and hiking in Redwood National Park. It was absolutely incredible to see such massive living things. The whole park seemed like it was in a different world and a far cry from reality. Standing next to a Redwood really puts your life into perspective!


The goal for the weekend was to find the Grove of the Titans, a secret grove of redwoods that contains some of the world’s tallest. The location is kept secret and they are not located near any trails, so the group of us blazed our own trail through the magnificent giants with a list of clues we found online. I’m sorry to report that their location still remains a secret, as we were unable to find them. However no disappointment was felt among the group as we saw some others that I’m sure must rival the Titans in size!


It wouldn’t be a trip to California without a little surfing! On Saturday and Sunday I was able to further practice my “skills” with some friends on the waves in Crescent City. I finally learned how to stand up and ride a wave all the way to shore! Plus the water was about 60 degrees which was much more pleasant than the 45 degree water off the coast of Oregon!


My time on the west coast is winding down and I wish there was a big “pause” button I could push and just stay here in Oregon forever.  I’ve been having the best summer of my life and cannot wait to share with others on Friday about my research and exciting adventures I’ve been having in the Beaver State!

Riding the Waves

Another week has come and gone. Things are beginning to wrap up for my internship and I am already dreading leaving the beauty of the Oregon Coast, but there is still work to be done! I am still working on my fieldwork and laboratory experiments and this week we will be going to our plots to photograph the sediment cross sections and see whether the oxidation line has become apparent in our natural observation plots and our plots where we controlled the amounts of algae.


Our laboratory experiments are showing some interesting results. We believed that the tubes with high amounts of macro algae would show minimal oxidized sediment, like what happens naturally in the estuary. However, we have seen that the tubes with the high amounts of macro algae are showing the highest amount of oxidized sediment. One hypothesis is that the large amounts of algae are producing oxygen as a result of photosynthesis, which is adding oxygen to the sediment. We have now completely covered the tubes with aluminum foil and we hope that it will prevent any further photosynthesis and hopefully it will help the algae rot. When the algae rots, it begins to produce sulfides in the sediment and the amount of anoxic sediment increases greatly.


This week we will be starting to use a tool called IRIS tubes. IRIS tubes are pieces of PVC pipe coated in ferrous oxide. When the ferrous oxide, which is normally orange, reacts with sulfides in the sediment, the tube turns black. This allows us to see how much sulfides are in the sediment and also where they are found. Sulfides are important because they signal anoxic sediment. We are deploying the tubes in our algae plots to see if the amount of algae can be related to the amount of sulfides and we also will be putting them into our containers in the laboratory.  Hopefully we will see some great results!


I have also began to work on my final presentation and have really enjoyed putting together the story of my project. I have always enjoyed public speaking and I am greatly looking forward to teaching others about my work and estuary ecology. I also attended a presentation about how to put together an effective PowerPoint and I learned a lot of tips and tricks that I can’t wait to use when I present!

Aside from work, this past week has definitely been a great one. On Saturday, myself along with two other interns hiked Drift Creek Falls near Lincoln City.  It was beautiful to be walking through the forest and the waterfall at the end of the hike was incredible. That evening we made a delicious group dinner, and on Sunday I went surfing for the first time ever! I had no idea what to expect but I left the beach completely hooked.  I was able to stand up fully about 3 times, although I found myself falling over shortly there after! It was one of the most incredible feelings to be riding on the waves.  I was pretty surprised by how soon I was able to get up on my knees and I cannot wait to get back out there!


This week and next will be dedicated to preparing my presentation and finishing up my field work. This coming weekend a group of interns from Hatfield will be taking a camping trip to Redwoods National Park in Northern California and I cannot wait to see them. Stay tuned!

Another Muddy Week!

Yet another week has come and gone on the Oregon Coast; and it was a fantastic one at that!  Things started out at the EPA where I began transitioning from field studies to a laboratory experiment. In the field, we were observing the estuary sediment as it is naturally found and then with some added controls that we implemented last week.


We are now further expanding our control in the lab by setting up 9 estuary like environments in clear tubes to provide more insight into sediment oxidation under varying conditions. Three of the tubes have sandy sediment, with no algae cover in one tube, low algae cover in the other tube, and high algae cover in the final tube. The remaining 6 tubes are filled with muddy sediment. Three of the mud tubes are set up exactly like the sand tubes, and the remaining three are the same except they have mud shrimp added into them.


The tubes are tall, clear, glass cylinders that provide us with a large viewing area to see any sediment oxidation that may occur. The tubes are all connected to flowing seawater in order to replicate conditions in the estuary. The algae is held in place using netting, and the whole tube is covered in aluminum foil to prevent light from penetrating the sediment.


Collecting the sediment was quite the treat! It involved a fellow intern and myself trudging across the mudflats with carts and sleds to move 6 very heavy buckets of fresh Yaquina Bay mud and sand. I can only imagine the joy onlookers might have had upon seeing myself slowly sink into the mud, while pulling a sled full of it behind me. Aside from the humorous struggle of the day I was presented with an opportunity for science outreach. After I came up from the mudflats, I spoke with two people about my project. I was able to share with them my knowledge about wetland sediments and told them about my research. It is always exciting to share science with others, and after da Vinci Days, I learned how to talk to people about science in an effective manner.


Last weekend I began volunteering at the Hatfield Marine Science Center in the fish husbandry program.  I helped to clean tanks, and even got to play with the giant pacific octopus at the end. If you’ve never had an octopus wrap its tentacles around your fingers, I highly recommend it.  After volunteering, some fellow interns and myself made our way to Portland for the weekend. We spent our time exploring the city and all it has to offer.  We went to Powell’s Books, Voodoo Donuts, and I even was able to play a piano in Pioneer Square.


I also started taking a class about the computer program, R.  R is a statistics program that allows scientists to view and work with their data in an efficient way. However, R requires some knowledge about the “language” it uses, and the class will be covering how to understand and use the program. Luckily for me it is similar to Matlab, which I have used this past year at school to make ecological models of Lake Michigan. Hopefully it won’t be too difficult to understand!

Next week looks to be filled with more laboratory experiments and going out into the field to check on our plots.  We are anxious to see what they look like and are hoping for good results!

Living the Dream!

Life sure is good here on the West Coast, especially in Oregon. Week 5 marks the halfway point of my time here in the Beaver State, and things are still in full swing at the EPA. The past week has been full of fieldwork and the coming weeks look to be the same; and I couldn’t be more excited!


In the first few weeks of my internship we were studying sediment oxidation in the estuary under natural conditions. This means that we went out into the tide flats and observed the sediment as is. The next phase of our project is to try and add some control to things. This coming week we will be going out into the estuary and setting up different plots with varying amounts of algae covering the sediment surface. More clear, plastic food storage containers will be placed into the sediment like before, except this time, on either side of them, there will be one meter quadrants with netting, holding down a specified amount of algae. This will allow us to see how different amounts of algae can impact sediment oxidation in a more coordinated way.


Additionally, we are hoping to learn about how estuary organism can impact sediment oxidation, especially burrowing shrimp. To study this, we will be putting some plots in areas where there is a high amount of shrimp burrowing, which creates features that look like mini volcanoes from the surface. Two of our plots will be put in ghost shrimp areas, two in mud shrimp areas, and two more will be placed where the sediment is mostly free of burrowing shrimp.  We are hoping that these experiments will give us a really good picture of what is happening beneath the surface of the estuary here in Newport.


This past weekend was Oregon State University’s annual science and art festival called da Vinci Days.  Myself along with the other Sea Grant interns created posters about our research and presented our work to the people who attended the event. Before presenting, we learned a lot about how to effectively communicate science to the public in a way that makes sense and allows them to understand a topic which can often times be quite challenging to grasp. I though it was great practice, and I know that the things I learned will help me throughout my career as a scientist.


Da Vinci Days was opened by a talk from Dr. Jane Lubchenco, a professor at Oregon State University and the former director of the National Oceanic and Atmospheric Administration.  She served as NOAA’s director for 4 years and during her talk she shared many stories about her time in Washington D. C.  As someone who has always been interested in politics and policy in addition to marine science, I found it to be a very eye-opening experience.  I never through about combining my passions for the oceans and policy into one, but after hearing her stories and about her time with NOAA, I realized that it could be a very real prospect.  After her talk I was able to personally speak with Dr. Lubchenco and she offered me some advice for preparing for a career in marine science.  I was told to “keep getting my feet wet” and to get as much experience as I can; it looks like I am on the right track! It truly was a once in a lifetime experience that I will never forget!


I was also able to squeeze in a little volunteer work this week. I was able to help with a project being run by Cheryl Horton who is a graduate student studying murre colonies along the Oregon Coast. A murre is a seabird and Cheryl is studying the colonies and how they respond to disturbances from bald eagles and other predatory birds.  I was able to help by observing bald eagles on the colony and how they interrupted the birds.  I learned a lot about seabirds and it was a great experience to be a part of. Plus, Cheryl took another student volunteer and myself down to the tide pools for a break, which proved to be quite the experience. We were able to see all kinds of marine life and it sure made waking up at 5:15am worthwhile!


Week after week Oregon continues to impress me with everything it has to offer. Although it has been 5 weeks, I have learned so much about marine science in a way I could never have done otherwise. I cannot wait to see what adventures the second half of my internship holds… stay tuned!

Good Times All Around

I think I’m falling in love… with Oregon that is. With a four-day weekend last week thanks to the Fourth of July holiday, myself along with some fellow interns were able to get out and see more of what Oregon has to offer.

But before we began our adventures, there was work to be done.  The project I am working on that uses clear buckets to study soil oxidation requires a good low tide so that the sample site is clear of water. This allows us to easily photograph the sediment layer without disturbing the surrounding area. To answer a question from my last post, the reason we removed and weighed the macroalgae was to see if there is any correlation between the depth of the oxidized soil and the amount of algae on top and to see how much algae is covering different parts of the estuary. The tides this past week weren’t low enough, so instead of being out in the field, I was helping out with another lab’s research project that had finished up earlier in the week. I helped to count Zostera japonica plants which are a type of sea grass.  The experiment was studying growth rates of the plants under varying conditions. It was a pretty quiet week at the EPA, but this week promises to be much busier with four days of field work.


On the Fourth of July, a group of us went to Olalla Lake where we spent the day swimming and jumping off of rope swings. We then made our way back to Newport for an all American cookout complete with a little slice of Wisconsin, grilled bratwursts. When we finished our feast, we watched the fireworks that were launched from Yaquina Bay, right next to the Hatfield Marine Science Center.

After the holiday, some of us went to Devil’s Punchbowl where, for the first time in my life, I saw a whale, which just so happens to be my favorite animal. It was pretty far away from us but nevertheless it was still amazing to see one in the wild.  We stopped at the Whale Watching Center in Depoe Bay to see if we were able to spot anymore but we had no such luck, however we did get to drive along a beautiful stretch of the coast which made up for it.


The next day we went to Corvallis where we spent the afternoon floating down the Willamette River. After driving to what seemed like every store in the city, we finally found tubes and began to drift down the river only to realize we had forgotten our car keys back at the start. Luckily some fellow floaters offered us a ride to the starting point, and we were able to laugh it off. We certainly learned our lesson!

Then on Sunday, which was my birthday, we went to the beach to celebrate. Nothing says “Happy Birthday” quite like a quick dip in the 50 degree Pacific Ocean! It sure was a weekend I will never forget. Oregon truly is a beautiful place to live!  This week I will be sampling in Yaquina Bay and traveling to Nestucca Marsh, Netarts Marsh, and the Bandon Marsh for four long days of field work, and I can’t wait!

Starting Fieldwork

It has been another great week here in Oregon!  I’ve done so much and cannot believe I have already been here for two weeks. These past few days were filled with fieldwork at the EPA. Myself along with two researchers started one of our experiments in the Yaquina Estuary here in Newport on Tuesday and Wednesday. Then on Thursday we traveled and hour north to Pacific City, Oregon to collect data on the Nestucca Estuary and on Friday we went three hours south to Bandon, Oregon to do the same data collection on the Bandon Marsh.


It was a week full of very long days, but it was great to be doing fieldwork. I had never done any fieldwork before and didn’t know what to expect, but I really enjoyed it. Plus, I got to ride in the EPA’s hovercraft which was pretty awesome! In the Yaquina Estuary we placed clear boxes in the sediment to see the different rates of soil oxidation, while in Nestucca and Bandon we measured how quickly sediments have been building up over the past few years.

In addition to that, I cleaned and measured the macro-algae that was covering the sites where our clear boxes were placed in the Yaquina Estuary. We are interested in seeing how much macro-algae is on the estuary and if that correlates to the oxidation layer in the sediment.  After collecting the algae from our plots in the estuary I had to wash off the sediment and weigh it to see how much we had collected. During this process I realized how great it is to be working at the Hatfield Marine Science Center. While I was cleaning off my algae another researcher came into the lab to do her work. She turned out to be a professor from Oregon State University and an expert on algae who, just last week, gave a presentation at Hatfield about the algae that comes to the Oregon Coast on the debris from the Japanese tsunami. She has been responsible for collecting and identifying the foreign species. We were able to share the same workspace and we talked for about two hours all about marine science. It was a great experience and made me realize how lucky I am to be working at such a unique and intellectual place.


This week wasn’t all about the work, however. Yesterday, I traveled south of Newport to Waldport where, along with some fellow residents, I collected fresh clams and mussels straight from the water! We also went to Cape Perpetua and Devil’s Churn, both of which over look the Pacific and have rocks the create huge waves.  It was so beautiful to be perched up above the beach and to look out and only see the ocean.

Next week I am looking forward to spending the 4th of July along the Oregon Coast and hope to do some more sight seeing around the area.


Hello, Oregon!

Hello everybody, my name is James Kralj and I am so glad to be an Oregon Sea Grant summer scholar this year! I am a junior at the University of Wisconsin – Madison where I am majoring in microbiology. I am also an undergraduate researcher in the Department of Atmospheric and Oceanic Sciences where I help create and use computer models to study the ecology of Lake Michigan.  For as long as I can remember I have wanted to be an oceanographer and I cannot wait to start learning about marine science this summer!


As part of my internship, I will be working with the United States Environmental Protection Agency in the Pacific Coastal Ecology Branch at the Hatfield Marine Science Center in Newport, Oregon studying soil oxidation rates in salt marshes along the Oregon coast.  I will be doing a lot of fieldwork this summer and I cannot wait to get started but before the fun begins, the EPA requires quite a bit of training.

This past week I have been working my way through the EPA’s health and safety training where I learned everything from how to properly hold a ladder to the correct usage of air filtration masks. Exciting, I know! But now that I have finished with that, I can start working in the field. Next week I will be going to two marshes with EPA researchers to set up our experiments.

In addition to getting started at the EPA, I have been having a great time so far in Newport. I am staying in the dorms at the Hatfield Marine Science Center and have met a ton of awesome people from all over the country. It has been great to meet so many people, each from such different backgrounds.

Also, everything here is so beautiful! We have been down to the beach many times already and each time I see the water I can’t get over how great it is to be living on the coast. Even if the weather isn’t perfect, it is still amazing to see the mountains and the waves through the fog and rain. Plus, I’d take a cool Pacific breeze over the hot and humid Wisconsin summers any day!


I have already done a lot of great things in Newport. A group of students from Hatfield and I have gone to the Oregon Coast Aquarium and were given a behind the scenes tour which was really great to see. I have also had some pretty amazing seafood like clam chowder, fish and chips, and clam strips. I love to cook and can’t wait to try my hand at cooking some local seafood.

Although it has been just a week, I have already been having such a great time. I cannot wait to start my fieldwork next week and I am really excited to learn all about the coastal salt marshes of Oregon. And of course, I can’t wait to share all of my experiences with you!