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My summer research students Rebecca Lightman, Miranda Seixas, and I had the pleasure of sampling onboard the R/V Folger, with extra help from the Allen Lab. We were collecting samples for a new research project where we hope to investigate harmful cyanobacterial bloom dynamics in Lake Champlain.

Eggleston Lab Summer 2018 (L to R Miranda Seixas, Rebecca Lightman, Prof Eggleston)

Harmful algal blooms caused by cyanobacteria (CHABs) produce toxins that pose a major public health threat globally. The genes coding for these toxins are predicted to be acquired through a variety of mechanisms, including horizontal gene transfer. Viruses play an important role in shaping cyanobacterial populations and the exchange of genetic material. Transduction, the process whereby viruses transfer DNA between bacteria, is one horizontal gene transfer mechanism that could play a role toxin gene mobility. It has been suggested that cyanophage (viruses of cyanobacteria) may impact harmful algal bloom dynamics, and they may also mediate toxin gene exchange between cyanobacterial species.

Prepping the CTD Rosette (Miranda Seixas, Rebecca Lightman, Harper Baldwin)

Collecting water samples from the CTD Rosette

Eutrophication has led to increased incidence of CHABs in Lake Champlain, VT, which serves as a freshwater drinking supply and recreational attraction. The degree to which cyanophage mobilize cyanotoxin genes has implications for public health, as well as CHAB monitoring and management. This study aims to characterize cyanobacterial, cyanotoxin, and cyanophage diversity and dynamics to inform these public health and management decision making processes. While cyanotoxin gene transduction by cyanophage has been predicted, this will be this first study to directly test this hypothesis.

Miranda and Rebecca fixing samples for microscopy.

Miranda preparing slides for microscopy while Rebecca filters water.

At Middlebury College we are very lucky to have access to this amazing research vessel, the R/V David Folger which allows us to gain access to sampling areas all around Lake Champlain. For this trip we cruised up to Shelburne Bay, with Captain Rich Furbush and crew member Chris Goodrich, as well as some crew trainees. We collected water using the CTD rosette with niskin bottles (a specialized set of water bottles, with probes that detect conductivity, temperature and depth). Once we had the water on deck it was portioned out for a variety of downstream applications. We filtered and stained small volumes of water to count bacteria and viruses in the water. Additional samples were collected on filters and stored for future work extracting and identifying bacterial communities to study their DNA. The final aspect of the sampling was to collect a large volume of water for viral precipitation, which we we also analyze DNA from, to determine all of the types of viruses present in the water sample. We hope to be able to focus our DNA analysis on cyanobacteria and cyanophage (their viruses) to better understand the role of viruses in the bloom dynamics.

Femina Sciscitator

Venus_shell_large_V2_square.pngPresenting Femina Sciscitator, an online space that promotes the empowerment of women in science, both personally and professionally. The purpose of Femina Sci is to:

  • share our science experiences

  • develop our identities

  • build community

  • support each other

  • process what it means to be a woman of science today

We plan to accomplish our mission through a series of panel discussions, personal essays, and interview blog posts. We welcome additional voices! If you are interested in contributing to this discussion, please send us a message.

Check out our website:

Moving to the “North Country”

As some of you already know, Sam and I have moved to Canton, NY. Where did you say? Until this past August I had never heard of Canton, NY either. We’re NORTH of the Adirondack State Park, about 20 min from Canada, and fairly close to both Ottawa and Montreal.

Canton_blogMore excitingly, Sam has a tenure-track Assistant Professor position at St. Lawrence University in the Department of Environmental Studies. His position focuses on the intersection of health and the environment, and he’ll be teaching and continuing his research in environmental public health. I have a Visiting Assistant Professor position in the Department of Biology at St. Lawrence, where I will co-teach a microbiology course with lecture and lab components. I am also starting a research collaboration with Dr. Michael Twiss at Clarkson University (up the road ~20 min) examining microbial communities in the St. Lawrence River.

We are both excited about these next steps for our research and teaching. I’m also feeling extremely fortunate to have this opportunity to start positions in the same geographical location, that play to our disciplinary strengths, and at a school with such talented and friendly colleagues.

UNOLS Training Cruise Update 2

Day 4

We all got up at 02:30 to experience passing through the lock. It was big enough, barely, for the large ore barges that carry ore from Duluth to Chicago to fit through, so there was plenty of space for our smaller vessel. The gates closed and water was pumped in from the bottom, until the boat gained about 20 feet to level off with the water level of Lake Superior. The river is fairly narrow at this point, so we could wave to Canada who’s far shore was cast in yellow middle-of-the-night light. From here we continued our transit to our next station, the deepest point in Lake Superior. This was our most involved science station along the cruise track since all of us were interested in sampling here. We deployed the instruments for collecting water, filtering large volumes of water to analyze proteins in the water column, acoustic sampling equipment, and I tried to collect sediment samples. After three failed coring attempts we decided the bottom of the lake was too solid to sample, and I changed my plans to sample at a later station. We left station 4 at sundown to continue on our transit.

Day 5

When I woke up the map of our transit, that was displayed on a few screens around the ship, was showing a possible detour to land in along the Keweenaw Waterway. The captain came down to inform us we were going to need to stop to get our sewage tank pumped. Apparently there was either a water leak, or the gauge for the sewage system was off, and we needed to offload sooner than Duluth. This detour allowed Andrew, one of the other trainees on board the boat, to get off a bit early since he was done with his sampling, and the detour location was only a few miles from his home. It also meant we got to swim from the shore in the Keweenaw Waterway. The surface temperature was about 15C (59F) and dropped to 4C (39F) in the top 2 meters. Needless to say, it took my breath away, but was quite refreshing! After saying goodbye to Andrew, we departed the Keweenaw Waterway and continued on to our next station. Once there, two of the other trainees took samples and we continued on our way to our final three stations.

Day 6

The final day of sampling was a busy one. Our last three stations were a transect that covered three depths (250m, 150m and 90m), but were quite close together, only allowing about 30 min between stations for sample processing. I took my final cores at the first of these stations, and we also deployed the gear for water sampling and large volume pumps. We had off and on squalls with a bit of rain and wind, and it was really amazing to watch these storms move in and then past us. Our science was only delayed about 20 minutes for weather when there was lightening and it wasn’t safe to operate on the back deck. At lunch we celebrated Katy’s birthday with a delicious cake. It’s fair to say that the food on this research vessel, prepared by our steward Lisa, is the best food I’ve ever had on board a ship. The crew jokes about gaining the “Blue Heron 15,” (like the freshman 15) and now I know why! Every meal was amazingly creative, and prepared in a nook of a kitchen. Lisa is incredible, I hope to work on board the R/V Blue Heron again in part because of the delicious food. After wrapping up our last station we started steaming for port in Duluth. We made a quick stop to recover another scientist’s small mooring that was having battery issues, and then crossed under the aerial lift bridge into the harbor. There’s a waterfront trail along the lake that was filled with people waving to us as we arrived, which made us all feel like celebrities. After parking the boat on the dock, there was a frenzy of activity as the crew departed, and we were sad to see them go. They were a phenomenal group to work with, and with the commotion of the last three stations back to back we weren’t quite prepared to see them go. After a bit of science cleaning up and packing, we made our way into the downtown touristy area of Duluth to the Canal Park Brewing Company for a birthday pint.

Day 7

I woke up early to continue packing and cleaning up my science. Arranged for shipping my samples, and started helping the others to pack up their gear. We took a break at about 14:00 to walk into town and made our way to the Great Lakes Aquarium, which is the first freshwater aquarium I remember ever going to. We were there at 15:00 for the river otter feeding which was quite adorable, and then made our way back to the boat. I said my goodbyes, for now, to the other trainees, and caught a taxi to the airport. My taxi driver told me all about his agate collection and was showing off a few of his favorites. The flight back was mostly smooth, with about an hour delay in Minneapolis. I struck up a conversation with a guy at a charging station in the airport who turned out to be a St Lawrence University alumnus (where Sam and I will be working in the fall), who used to be a motorcycle dealer in area of CT where my mom grew up, and who’s family donated the land for a state park close to Albany. So many crazy connections! Sam picked me from the the airport in Albany, and it was great to make it home to my own bed. Hopefully the land will stop rocking soon as I get my land-legs back! Overall I had a fantastic time on board the R/V Blue Heron. The crew was amazing, so generous and flexible. Doug, who organized this training program, was so helpful prior to, and on board, the boat. To top it all off, I met four remarkable scientists who I hope to continue collaborating with in the future. Science friends, if you have the opportunity to apply for this program I would highly recommend it. Please get in touch if you want more information.


R/V Blue Heron in port in Milwaukee


First sunset on Lake Michigan


My last sediment core samples, ready to be frozen.

UNOLS Training Cruise Update 1

Milwaukee Arrival

I arrived in Milwaukee and made my way to Ben Balcom’s, a Hampshire College friend, apartment. My super friendly cab driver agreed to pick me up again in the morning. After getting to Ben’s I figured out how to make my way by bus to the Haggerty Museum of Art at Marquette University to check out Ben’s current exhibition. It was really fun to see his work, especially since it’s been about 8 years since I had seen his Div III project at Hampshire College!

After checking out the exhibit I wandered around the downtown area, walked around the public library for a bit which was beautiful, and made my way to a great lunch spot. Build-a-Burger filled me up with a delicious portabella mushroom sandwich and I was on my way. I had noticed an Urban Ecology Center on the map while I was figuring out how to make it to the museum and decided to check it out. I had a very nice walk along the Riverside Park trails, found the center before it closed, and got to check out their exhibit of native Wisconsin animals, tanks with various turtles, snakes, and fish. It was also really amazing to see so many people commuting around by bicycle. Milwaukee seems to have many bike lanes, as well as non-motorized vehicle paths, for bikes and pedestrians.

From the Urban Ecology Center, I made my way back “home” for a bit before meeting up with one of the other members of the science party on the cruise, Julia Gauglitz, who is a post-doc at WHOI. After meeting up at the Lakefront Brewery we wandered to a less rowdy restaurant nearby called Wolf Peach. It was a lovely restaurant with farm-to-table flare. Then I made my way home again to prepare for the cruise training the next day.

UNOLS Chief Scientist Training Day 1

I arrived at the Freshwater Sciences Building, a part of the University of Wisconsin Milwaukee, Saturday morning to start the day of land training prior to our cruise. A woman from the UNOLS Office, as well as our training coordinator presented information about the UNOLS fleet, equipment and cruise planning process. I got a lot of useful information out of the presentations in the morning and afternoon, and then we got to take our first tour of the R/V Blue Heron and start moving onboard and mobilizing for our departure. We ended the day with dinner at the Milwaukee Ale House.

Day 2

We spent the morning mobilizing for cruise, tying equipment down, and getting all of our research equipment set up. At noon we headed out of port and are in transit to our first research station. We should reach our station by about midnight tonight.

Day 3

The first two stations went well. At station 1 we sampled the water column, acoustics, and sediments at the deepest point in Lake Michigan. I successfully sampled with a multi-corer for the first time! We deployed the multi-corer and got three really good, intact, cores. From there I spent ~7 hours extruding the samples. This entails pushing the core up from the bottom, like a push-pop ice cream treat made of mud, 1cm at a time; collecting that layer of the core, and then freezing them for later analyses. The three cores were all extruded in time for breakfast, and then I took a good nap. We reached station 2 about 16:00. At this station the science party collected water column samples and took acoustic measurements. We’re now steaming up river between Lake Michigan and Lake Superior and should reach the lock around 02:15. Should be pretty cool, I’ve never been through and operational lock before!

(I will post pictures once I’m back on land with a stronger internet connection!)

A Great Lakes Adventure

I was recently accepted to a UNOLS Chief Scientist Training program on the Great Lakes. We’ll be on board the R/V Blue Heron, and our transit will take us from Milwaukee, WI to Duluth, MN. That’s approximately 800 miles in 4 days! This doesn’t leave much time for sampling, but we’ll make the best use of the time we have. My focus for this research cruise is to investigate sulfate-reducing bacteria, as well as bacteria that mediate mercury-methylation, in sediments in both Lake Michigan and Lake Superior. My colleagues on this cruise will investigate a number of interesting topics, including: greenhouse gas flux from surface waters, acoustic pollution, and cyanobacteria populations and dynamics. Stay tuned for pictures and details when the cruise commences on June 26, 2016!


Approximate Cruise Track in Red (Google Earth)

Two MOOCs: Pros and Cons

I have now completed two MOOCs: An Introduction to Evidence-Based Undergraduate STEM Teaching, and R Programming. I found the format far more conducive for a programming class than for learning about teaching practices.

Maybe it shouldn’t have come as a surprise that the online format was a challenge for a teaching in STEM course. There were many lecture videos, and although they contained some good information, they often fell into the trap of “do as I say, not as I do.” In other words, there would be a talking head showing lecture slides to discuss the need for peer-interactions and feedback, or classroom engagement.  I hoped to get more out of the homework assignments than the lectures/quizzes, but these were also only vaguely useful since the peer-feedback came from people in various STEM fields. While diverse backgrounds are useful for debate about teaching practices, it made providing (and receiving) useful feedback very challenging. I was asked to give feedback on a physics lesson plan, and while I could judge certain aspects of the design in general, as a microbiologist I couldn’t really speak to the effectiveness of the plan in teaching the subject.

The R programming course was harder than I anticipated since I didn’t realize there had been a recommended prerequisite intro class. The video lectures had variable usefulness, but the homework assignments were quite challenging and pushed me to improve my R coding skills. The online format was well suited to this type of class because the subject doesn’t rely heavily on peer-to-peer interactions. Since everyone was working on the same assignments the peer-feedback format worked well.

With these two MOOCs under my belt, I’m inclined to take more computer science oriented courses in this format, but I’ll continue to pursue teaching development in face-to-face workshops and classes. My skepticism of this format working well for teaching pedagogy was validated in this regard, but I would be curious to hear if you have had positive online learning experiences with teaching in STEM.

My first MOOC: An Introduction to Evidence-Based Undergraduate STEM Teaching

This week I started my first MOOC (massive open online course) in STEM teaching for undergraduates offered through coursera. I’m am intrigued to try out an online course for a few reasons. I’m very interested in undergraduate teaching and curious about the opportunities I might have to reach out to a broader range of STEM teachers through a large online platform, and additionally to see an online course in action to see how effective they can be.

I firmly believe that everyone should have the access to education and be able to pursue their academic interests. There are a variety of avenues through which a student can learn. The most canonical is the path from secondary education to college and then potentially on to graduate studies, all of which are housed on various campuses with interactive, face-to-face encounters with educators. This is my experience with education so far and I have found that it worked extremely well for me. However, there are students for whom, for a variety of reasons (economic, work schedules, family commitments, etc), this is not always an effective model. I would like to believe that online classes, especially those that are available at no, or reduced, cost to the student, present a meaningful alternative. I go into the experience with a bit of skepticism. How can you replace the time spent in class with a group of students and an instructor solely with online content? Can you have relevant and meaningful interactions through online discussion boards and peer feedback on assignments? Whichstrategies are effective for presenting new knowledge and information online? Which fall short? How do you assess learning in an online environment? How do you keep students engaged and motivated to keep up with coursework and complete the class (one of the biggest drawbacks to online courses seems to be low completion rate)?

As I go forward with my academic pursuits, and have the potential to teach in a variety of ways, I would like to reach out to as many students as possible. That could potentially mean developing online courses, and this seems like a good first step: try out an online course and get a handle on the pros and cons from a student perspective. So, here goes!

Erin Eggleston, PhD

I made it! After a well attended defense seminar and an hour and a half of closed door B-exam I passed from PhD candidate to PhD.  I’m feeling a slight sense of relief, and immense amount of gratitude for all the support and help I’ve received along the way. IMG_20150511_152056

Respiratory gene database paper is online

My paper accepted at Environmental Microbiology is now online under accepted articles.  It addresses specific changes in bacteria community respiration using mRNA expression of respiratory genes in Chesapeake Bay. This estuary exhibits seasonal anoxia (oxygen deprivation) and the bacterial communities respond by utilizing different electron acceptors for their respiration (nitrogen ions, metals, sulfate). We analyzed these changes by parsing community mRNA sequencing data with curated gene specific databases.  For more information check out the Environmental Microbiology page.