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Grad student blog

By Mia Phillips

Hi EEES Crew!

this course gets a seal of approvalI just got back from an amazing two-week summer course on animal acoustic communication hosted by the University of Southern Denmark (SDU). This course is offered every other year to PhD students from across the globe. For 10 years now, bioacoustics experts from SDU and elsewhere have come together to provide students with training in both marine and terrestrial animal acoustics research. Before attending, I had heard that the course was known for being good, and I was not disappointed.

The first week of the course took place at the Marine Biological Research Center in Kerteminde, Denmark, and was all about measuring and producing sound underwater. Technical lectures and hands-on practicals were given by professors Magnus Wahlberg (SDU), Coen Elemans (SDU), Lasse Jakobsen (SDU), Jakob Tougaard (Aarhus University), Colleen Reichmuth (UC Santa Cruz), and Mark Johnson (University of St. Andrews). This week we were introduced to the dB sound pressure level scale, the physics of sound propagation in water, theoretical and practical psychophysics, and the basics of underwater sound calibration. Although I work in air, most of the material presented was readily applicable to terrestrial animal systems, and was also just fascinating to learn. Practical exercises included hydrophone calibration, measurement of aquatic sound transmission, prevention of errors in sound recording, and even measurement of captive porpoise echolocation behavior!

Before moving to the next field site, we spent one day at SDU in Odense learning techniques for studying animal sounds and hearing in the lab. We were shown techniques like laser-Doppler vibrometry (LDV), auditory brainstem response measurement, microphone array recording, and analysis of acoustic motifs. We then packed up our things and traveled to Faaborg, where we spent a sunny day-off lounging near the beach.

The second week took place at the Svanninge Bakker field station and was filled with lessons in airborne sound measurement. The primary lecturers were Coen Elemans (SDU), Lasse Jakobsen (SDU), Jakob Christensen-Dalsgaard (SDU), Iris Adam (SDU), Ole Larsen (SDU), Sue-Ann Zollinger (Manchester Metropolitain University), and Peter Narins (UCLA). The most important lesson I learned during this week was that calibration is everything. We created and analyzed sounds in Matlab, measured sound attenuation over different surfaces, experimented with LDV, learned about near and far field sounds, and measured reflectance of sound in different sized rooms. All of this requires proper calibration of equipment, or else all your data will be useless (as I learned the hard way).  At the end of the week, we celebrated with a bat observation excursion and a party to conclude the course.

If you’re using or measuring sound in your research, this course is incredibly useful. Other courses that dig deep into the physics of sound and the logistics of measurement are hard to find. This course gave me essential training to perform acoustic playbacks to animals and measure the sounds my animals make. The funds provided by EEES made my participation in this course possible, and I am truly grateful for this wonderful experience.

 

By Melissa DeSiervo

Hey EEES-ers!

The past two weeks I have been taking a summer course at the Flathead Lake Biological Station (FLBS) located on the shores of gorgeous Flathead lake in Montana. FLBS is one of the oldest field stations in the US and has a focus on aquatic ecosystems. It is an active research site with about ~30 faculty, grad students, postdocs, and techs there year-round who work on things like periphyton and invertebrate species interactions, vertical migrations of Mysis shrimp, methane production in lakes, and much more! The assistant director (Tom Bansak) is a Dartmouth alum who was inspired to be a field ecologist in part by his experience on the Biology FSP many years ago!

FLBS hosts summer courses run through the University of Montana which include topics such as: Stream ecology, Lake ecology, Landscape ecology, and the course that I took, Aquatic Microbial Ecology. For 2 weeks I stayed in a cabin on the shore of Flathead lake, ate meals with other students, staff, and faculty, adventured around the Flathead valley, and got experience using world-class lab facilities at the station. I truly can’t believe how much I learned in only two weeks, all while having fun and connecting with other scientists.

The aquatic microbial ecology class is taught by Associate professor Matt Church who has a background in oceanography and microbial ecology and is especially jazzed by the role of microbes aquatic nitrogen cycling. In the first week, we paddled out on 3 nearby lakes, measured parameters such as temperature and dissolved oxygen across depth profiles and collected water samples. We also went on a white-water rafting trip on the middle fork of the Flathead river, right outside Glacier National Park, and collected water samples in different river habitats such as upwelling zones.

By far the most beneficial part of the course for me was learning about the variety of lab techniques you can use to study aquatic microbes. We analyzed our water samples for chlorophyll fluorescence, prepared slides using a staining technique called DAPI to count bacterial cells, and learned about flow cytometry. We got hands on experience using elemental analyzers to measured nutrients like N and P in our water samples. We also extracted DNA from our samples and went through the entire process of PCR to look for the presence of specific genes involved in processes like denitrification and methane oxidation. One of the coolest things we discovered was the presence of purple sulfur bacteria thriving in anoxic conditions on the bottom of one of the lakes we sampled.

If you work in aquatic ecosystems, or want to gain a stronger background in field ecology, you should not miss the opportunity to take a course at FLBS. And if you work on aquatic microbes, I highly recommend the microbial ecology course! This was a great use of the funds provided to EEES grad students to take a course outside of Dartmouth.  To top off the experience, I spent a few days in Glacier National Park (which is just about an hour away) and had an awesome time hiking through alpine meadows, over giant mountains, and seeing wildlife including grizzlies and big-horned sheep. What an experience!

By Madi Gamble

The University of Washington hosts short courses on a range of subjects each year through its Summer Institutes program. The course I attended, “Mixed Models for Quantitative Genetics,” is part of the Summer Institute for Statistics and Genetics. The course was two and a half days long and covered a staggering amount of material in that time. The course was taught by Bruce Walsh (University of Arizona), one of the authors of a classic textbook on quantitative genetics, and Guilherme Rosa (University of Wisconsin), who specializes in the biostatistics behind plant and animal breeding.

We began with a review of vectors and matrices and how to use them to store multi-dimensional information. We then reviewed matrix algebra, discussed eigenvalues and eigenvectors as characteristics of matrix geometry and dimensionality, how to express systems of equations in matrix form, and then on to general linear models, generalized linear models, and finally the uses of fixed and random effects in linear mixed models.

Throughout, the course was fast paced but welcoming of questions and discussion. I really appreciated that the instructors encouraged us to ask questions and never expressed surprise or disappointment at more basic questions (that said, one instructor did refer to the second edition of his book as “the new testament” – whether he was referring to its length or its perceived impact on the world was unclear).

While I learned a lot about the mathematics behind linear models, I wish that we had spent less time on the math and more on the applications of those models. For example, I would have liked more concrete examples relative to biology when discussing the use of certain models, and more practice using the models to analyze data with tangible variables.

Perhaps the best part of the course was the people I met, who I will certainly remain in touch with as I use mixed effect models in my research. The participants in the course ranged from mathematicians, to statisticians, to biologists working with humans, livestock, crops, and other plants and animals. The diverse perspectives of the students in the course helped to make the material more accessible to everyone. I would highly recommend this course and others that are part of the Summer Institutes at UW to other students!

Did you know New Hampshire has no native earthworms? 

After glaciers receded from this part of the country at the beginning of the Holocene, the land was scoured and effectively soil-free. This habitat was unwelcoming to soil-dwelling earthworms, which cannot migrate far without human intervention. . .

Enter explorers! After Europeans arrived in North America, earthworms hitching a ride on their ships were able to colonize New England. These days, earthworms are still moving around New Hampshire with the help of humans--as fishing bait, in soil on the wheels of logging equipment, and more.

So how does the introduction of earthworms into forests across New Hampshire affect soil properties? This is the question our students in Ecology lab here at Dartmouth are going to investigate! But before we set them loose, we decided to see for ourselves just how many earthworms live at the local forest across from the Dartmouth Organic Farm...  

It takes a team to successfully search for worms

Sure enough, we found a fair few! We identified at least five species.

Worms in our collection bucket after they were counted and identified

Nightcrawlers are great for catching fish...and teaching assistants!

Our trip was a roaring success--worms galore, beautiful fall weather, and great enthusiasm for introducing our Ecology students to this interesting study system!

Posted by Ashley

This June, Fiona and I got the chance to travel to Colorado State University and learn about all aspects of soil ecology from the awesome researchers in the CSU Natural Resource Ecology Lab in Fort Collins, CO. We were excited to learn all about the different dimensions of soil ecology that might be important to our research, but that we don’t usually think much about.

Using a hammer corer to collect surface soil from a montane pine forest impacted by wildfire and mountain pine beetle

We learned about techniques for sampling soil and felt a little bit jealous of the lack of rocks in the forest and grassland soils of Colorado.

We also learned about the various invertebrates that live in soil, their functions, and how to quantify their abundance in space and time.

Ashley with former lab-mate Melanie Taylor investigating the soil invertebrates of a grassland soil sample

We noticed dramatic differences in the soil from Colorado compared to New England, and we’re feeling quite proud of our beautiful soil horizons in the northeast!

A soil profile from a shortgrass steppe in Colorado

 

We also had some time to travel around the region, and we stopped for a bit to camp in beautiful Wyoming.

At the end of the trip, we rounded off the Colorado experience with a quick hike up to Emmaline Lake near the CSU Mountain Campus. We saw some beautiful landscapes and looked a little closer and the plant and fungal communities we were hiking past.

Emmaline Lake, a glacial lake near the border of Rocky Mountain National Park
A lovely waterfall on the way up to the lake
Cirque Meadow on the way back down from the lake (after the morning fog had cleared).

We had such a great time in Colorado, and now that we’re back home, it’s time to apply our new knowledge to our research questions!

 

Learning Excursion: Cary Institute Fundamentals of Ecosystem Ecology Course 2017 by Morgan E. Peach

Every winter, the Cary Institute of Ecosystem Studies in Millbrook, NY offers a two-week intensive course in the Fundamentals of Ecosystem Ecology, led by the knowledgeable, accomplished, and approachable scientists of the Institute. The EEES program supported my enrollment in the class, which was an enriching and stimulating experience.

The course, of a slightly modified structure year to year, provided comprehensive exposure to both the fundamentals and cutting edge of ecosystem science. Topics, to name only a few, ranged from primary production, to urban ecology, disease ecology, and the new paradigm of conservation science. Each class meeting featured a Cary scientist, a leader in their field, that led lecture as well as facilitated discussion of pertinent primary literature. The course culminated with student group presentations of an NSF-style proposal defense, which was a valuable opportunity to develop grant-writing skills alongside practice at team-building scientific collaboration.

Beyond the classroom, the course experience provided opportunities to develop relationships with classmates from around the world as well as with Cary scientists. This was a rewarding aspect of the class, consisting of many substantive discussions that furthered my PhD research. All Cary scientists made themselves abundantly available to meet with students, and provided useful guidance, helping students to shape a promising career trajectory in the broad arena of ecosystem ecology.

 

I’d recommend this immersive learning experience to any and all students with interest in ecosystem science! Thanks to EEES for making it possible!

Last week several of us in the EEES community were lucky enough to attend the 1st meeting for the Network for Arthropods of the Tundra (NeAT) at the Aarhus Institute for Advanced Studies in Denmark.  NeAT is an academic network of Arctic and Antarctic researchers studying terrestrial and aquatic arthropods. Over 50 scientists from 10 countries were present to share recent research about their favorite study organisms including soil microfauna, invasive midges, and wolf spiders. A highlight of the meeting was keynote speaker Jane Uhd Jepsen’s talk about outbreaking geometrid caterpillars which periodically defoliate entire birch forests in Northern Europe(!).

From our Dartmouth group, we heard an exciting preview of Christine Urbanowitz’s new thesis chapter about Arctic pollinator networks, and an overview of Jess Trout-Haney’s dissertation research on cyanotoxins that transfer through aquatic and terrestrial food webs. Additionally, second year graduate student Melissa DeSiervo and Lauren Culler (PhD, Lecturer of Environmental Studies) presented exciting new research about population dynamics of Arctic mosquitoes. Overall the meeting was a blast, and we made dozens of new friends that we look forward to collaborating with on future projects.  We even got to sing a very special Danish Happy Birthday song to Christine!

Neat_group
Over 50 scientists were present at the 1st Network for Arthropods of the Tundra (NeAT) meeting in Aarhus, Denmark
Chrstine_present
Christine Urbanowitz explains her research on Arctic pollinator networks.
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EEES graduate students Jess Trout-Haney, Christine Urbanowitz, Melissa DeSiervo and post-doc/lecturer Lauren Culler presented research at the first NeAT meeting

From EEES Student Andy Vacca:

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Every year the Cary Institute, an independent environmental research institute located in Millbrook, NY, hosts a course titled Fundamentals of Ecosystem Ecology (FEE).  This course allows a small group of students from around the world the opportunity to learn from and interact with leading experts in the field of ecosystem science.  In fact, a number of researchers at the institution have played pivotal roles in defining this discipline and pushing the boundaries of knowledge regarding ecosystem structure and function.  Cary Institute researchers have substantial expertise in the following fields: freshwater health, infectious disease ecology, urban ecology, invasion ecology, climate change and biogeochemistry.

The 2016 FEE course was loosely organized around four major topic areas: energetics, biogeochemistry, frontiers in ecosystem ecology and professional development seminars.  Subject matter experts held either lecture-based or discussion-based sessions followed by an in depth discussion of related primary literature led by students in the class.  Major topics included primary and secondary productivity, decomposition pathways, an overview of biogeochemistry, coupled elemental cycling and nutrient cycles with the carbon, nitrogen and phosphorus cycles each having their own lecture.  We also explored cutting-edge topics in conservation, human ecological systems, coupled human-natural systems and urban ecology with Cary scientists who are leading the way in these fields.

One aspect of the class that was particularly enjoyable was the professional development sessions.  One of the session was devoted to a mock NSF proposal review panel, led by a Cary scientist and former NSF program officer.  This provided invaluable insight into the proposal review process and allowed students to ask questions regarding review and the organization of funding.

I would strongly recommend this course to other students in EEES.  The class covers a wide range of topics and allows students to solidify their fundamental knowledge and move into high level discussion of each subject area.  The opportunity to interact with leading scientists in ecosystem ecology in both a learning and professional development context was invaluable professionally and personally.