The Bowman Lab

In the weeks leading up to starting at Scripps Institution of Oceanography, where I am now a first year PhD student, I often found myself – for better or worse – turning to Google for advice on navigating the next five years. I would google any anxiety-fueled question that popped into my brain, from “What is the hardest year of a PhD?” to “How competitive is a PhD cohort?” I found the best answers online were from older students, who used the space to reflect on their recent experiences and offer up what they had learned along the ride. In that spirit, I hope some recently accepted graduate student stumbles onto this as they furiously google, and that it offers comfort and (hopefully) wisdom for a fun and tumultuous transition.

Below is a list of five things I really learned – and relearned – as a first quarter grad student. I am only one quarter done with a potentially six-year degree (which if we do some quick GRE math, means I am one quarter of one sixth done, which is a little over 4 percent), so this is by no means an exhaustive list. I’m actually really interested to see which of the five becomes more important as the years go on, and please comment if as a graduate student you think I missed something important.

Five lessons from the first quarter of graduate school:

Find help.  This I think was the most often repeated piece of advice I saw going into my first year, and it really holds up. Finding people who I could be myself around – to whom I could ask stupid questions and lament about failed experiments with— was essential to my first quarter survival. My best memories from a packed schedule of lab and class are from study groups and group lab coding sessions. I also got involved on campus once I felt settled, which was a great way to meet and work alongside older students and mentors.

Planning ahead saves money. I worked in a lab as an undergrad and as a tech once I graduated, but I was never in charge of purchasing lab equipment or supplies. This quarter marked the transition for me between being an ignorant consumer of lab supplies to a conscientious one, now that I know exactly how expensive it all is and how much money you can waste by doing a poorly designed experiment (extra hint: include controls!). More generally, the application process for PhDs includes applying for grants, which is just the beginning in learning to apply for and manage money as a researcher. I’ve realized I have a lot to learn about budgeting and management in my journey to become a successful scientist.

Grades aren’t everything anymore.  It was a hard habit to break, but all of your time shouldn’t be spent studying for your general first year classes. I learned to diversify how I obtained knowledge. Reading scientific papers and attending seminars from visiting professors were places where I learned the most this quarter. An afternoon spent reading a paper closely related to your research or an hour attending an interesting seminar often meant more to me than studying for a midterm in my more general oceanography classes.

Say yes. I am writing this from a ship off of the coast of Antarctica, where I am conducting field work, all because my advisor asked if I wanted to go and I said yes. Saying yes to collecting samples in the field is one example, but even to something simpler but still scary – like a surfing class or going to a social event where you don’t know anyone – just say yes.  

You will make mistakes. I think the biggest lesson I learned from the first few months of grad school was how often you make mistakes. It is a daily (sometimes hourly) part of life, in both lab and in class. I am still working on how to learn from and move past mistakes, both large and small.

I think since I am still in my first year I have yet to really experience burnout or writer’s block, which I know happen often to older PhD students. I feel so fortunate to be able to study and do science as a Bowman lab member at Scripps, and I hope my insight from a great first quarter help put any prospective students that are reading this at ease.

Over the last few months volunteer diver Caitlyn Webster has been putting together a quick outreach video on our CURE-ing Microbes on Ocean Plastics project with National University. In addition to highlighting the project, Caitlyn provides a nice overview of the issue of plastics in the ocean, and some common misconceptions.

The San Diego Union Tribune published an article on our work at the South Bay Salt Works, part of the larger NASA-funded OAST project. Check it out here: https://www.sandiegouniontribune.com/news/environment/story/2019-11-05/seeking-life-in-the-solar-system.

We have a new paper published this week in Frontiers in Environmental Science on estimating ecosystem services along the western Antarctic Peninsula (WAP). This was one of the most challenging academic efforts I’ve been involved in, and is the culmination of nearly 5 years of effort since co-author Barbara Neumann and I conceived the idea during a serendipitous meeting at a Columbia-Kiel University workshop on marine science back when we were both postdocs.

Ecosystem services, the direct and indirect contributions of ecosystems to human well-being, is a concept that’s received a lot of attention as a critical abstraction at the interface between science and policy. Scientists have gotten very good at understanding ecosystem processes and relating them to other ecosystem processes. Economists and social scientists are getting better at quantifying the social and economic costs of environmental change. What’s frequently missing, however, is a framework for linking specific ecosystem processes to social or economic outcomes. This becomes really important if you want to effectively manage resource use; ecosystems perceived as being more socially and economically valuable (i.e. providing more ecosystem services), for example, might warrant more nuanced management.

Ecosystem services are most useful when we can consider their distribution in space and time. However, linking ecosystem services to specific places and times is methodologically challenging. One way to do this is to use expert elicitations via the matrix method. In this approach a collection of experts is formally interviewed in a consistent, scripted fashion to identify “consensus” estimates of service supply from specific ecological units. This approach is typically applied to landscapes, where the ecological units are geographically fixed (think about a mosaic of forest and grassland, each providing different services, but fixed in space).

But what about the marine environment? Certain ecological features, such as a shoal, gyre, or recurrent eddy can be geographically fixed, but away from such features the marine environment is a fluid mosaic that is not fixed in time or space. We decided to try an approach that was agnostic to location, and instead elicited expert opinions of service supply from the seascape units derived from an objective analysis of macronutrients, chlorophyll, temperature, and salinity in Bowman et al., 2018.

For our group of experts we tapped the investigators of the Palmer Long Term Ecological Research (LTER) project (many thanks to all of you!). It was quite a challenge to reconcile the divergent methods – when we conducted the interviews we hadn’t worked out all the details of the seascape unit classification system – but we got there in the end. The approach could use some further refinement before it’s ready to produce a data product for resource managers, however, we hope the proof-of-concept will stimulate further effort at LTERs and elsewhere in the marine environment!

Natalia Erazo and I are on our way back from an amazing week of sampling in the Cayapas-Mataje Ecological Reserve in northern Ecuador. We first visited the reserve in 2017 and have been anxious to return ever since. Our objectives on this trip were to collect water column and sediment samples to test hypotheses about how shrimp aquaculture impacts mangrove forest health and biogeochemical cycling in mangrove-dominated estuaries. Cayapas-Mataje is an ideal place for this study. The reserve is the largest of its kind along the Pacific Coast of Latin America. The presence of the reserve has prevented the large-scale conversion of mangrove forest to shrimp aquaculture (as has happened further south in Muisne and other parts of the country), however, there are a number of facilities – some quite large – that existed prior to the establishment of the reserve. Thus relatively “pristine” forest can be found immediately adjacent highly impacted forest.

Congratulations to Natalia for receiving a National Geographic Young Explorer award to make this trip a reality! Here are a few choice pictures from the week.

Hello! It’s Emelia again – to learn more about me and my research in the Bowman Lab check out this post. I have recently returned from 2 weeks in the Canadian Arctic where I attended an absolutely incredible summer field course entitled “Arctic Microbiomes: From molecules and microbes to ecosystems and health” through the Sentinel North International PhD School at Universite Laval in Quebec, Canada. This course emphasized an interdisciplinary approach to asking (and answering) questions about the role of microbiomes in the Arctic. A microbiome represents the complex interactions of microscopic life (bacteria, archaea, phytoplankton, fungi, viruses, etc.) within a specific habitat. And just as the community that makes up a human gut microbiome can give insights into the health of a person, the diversity of Arctic – soil, pond, sea-ice etc. – microbiomes can give insights into the health of Arctic ecosystems. The Arctic is one of the most rapidly changing places on Earth with warmer temperatures and less ice each year. Key to understanding the broader ecosystem (including human) impacts of this rapid change we must first understand the dynamics of these microbial worlds and how they might buffer, accelerate, or shift in response to, the changing Arctic climatic state.

The course was based out of the Center for Northern Studies in Whapmagoostui-Kuujjuarapik. Not entirely remote, there are about 1,400 inhabitants between the Cree First Nation and Inuit communities living in the adjacent villages of Whapmagoostui and Kuujuarapik. The research complex is located at 55º N along the coast of Hudson Bay and is one of 10 stations in the Canadian Network of Northern Research Operators. This field school was fun and informative for many reasons, but here I will briefly recite the top of the list.

1. It really was an International PhD school

18 students from all around the globe came together to study the microbiota of the Arctic. Every continent was accounted for (and we’ll include Antarctica, considering that many of these polar researchers have spent quite a bit of time there) and there was the possibility that ~5 languages were being spoken simultaneously at any given time. The diversity of this group also extended to scientific expertise – between students and mentors there was a spectrum of research experience, from medical studies of the human gut microbiome to soil microbial ecology and astrobiology. However, while scientific interest may have brought us together, after 10 days of dorm life, sharing meals, and surviving long days in the field, the personal connections and budding cross-continental friendships are what made this school truly unique.  

2. Collaborations with the Cree First Nation

Speaking of a cross-cultural experience – as the research complex is on Cree land, it is run in collaboration with the Cree First Nation of Whapmagoostui. Upon our arrival at the station, we were addressed by the Chief – who also happened to be the first female Chief elected in Cree history! She emphasized the importance of learning from the land and provided a human perspective to how we think about research in the North and the challenges facing their community. This type of knowledge exchange continued throughout the school from a science & microscopes workshop held at the local grocery store to traditional tipi building at the research complex. Led by locals, we chopped and prepared the trees ourselves; finally constructing the tipi on our last day at the base. The school also coincided with a yearly heritage festival and we were honored to be included in the local gathering. I learned a lot from the Cree elders, particularly the many changes that they’ve seen in the environment during their lifetimes; an important reminder that climate change is just as much (in fact more of) a human issue as an environmental one.

3. Fieldwork

I am a sucker for field work, to me it is the best (and most fun) way to explore the natural world. Even with a rigorous and scientific sampling scheme, there is always the chance to see something new. And this school provided a TON of it in an absolutely GORGEOUS environment – mosquitos and all. One of my favorite days was when we sailed out onto the Great Whale River to take water samples and measure the river’s chemical properties using a hand-held CTD. The water and mist warded off the worst of the mosquitos and I had the opportunity to try out new, state of the art sampling equipment! (Plus I always enjoy a good day on the water.) Some of the other highlights were sampling the local ponds and lakes for cyanobacteria – a type of photosynthetic bacteria that, in these regions, grow in thick filamentous mats. (Formerly known as blue-green algae). It was especially neat because nearby there were some stromatolites – ancient fossilized cyanobacteria from early Earth. These ancient cyanobacteria are responsible for filling the atmosphere with oxygen and making Earth habitable for life like us. In one day we touched the past and collected samples from the present to ask scientific questions about the future.

While the weather didn’t cooperate enough for us to actually sample there, we were also able to get a helicopter tour of some of the local permafrost sites! Permafrost encompasses any ground (soil, rock, etc.) that is completely frozen (<0ºC) for at least two consecutive years. However, most permafrost has been frozen for much, much longer than that. The soils are held together by ice and, historically, have been so solidly frozen in some areas that builders considered it more stable to construct on than concrete. In the northern hemisphere, about 1/4 of the land area is made up of permafrost and it is currently melting at unprecedented rates. This not only poses a threat to shorelines and infrastructure but is rapidly and unpredictably changing the microbial communities that live in this unique environment.

4. Scientific Expertise & Laboratory Work

As this was a microbiology field school, a good portion of our time was spent analyzing samples in the lab. Many of the techniques we used were similar to the ones we employ here in the Bowman Lab but there was still a lot for me to learn. The first step in most microbiome studies is to simply see who is there. To do this, we extracted genetic material from our samples for DNA sequencing. The first step in this process requires breaking apart the cells from your environmental samples, releasing their genetic material. Then, through a series of chemical reactions and washing steps, this material is extracted from the sample and ready to be amplified and sequenced. Using field-kits and portable sequencing devices, this process can be long and arduous, but thankfully we had many hands in the lab and an excellent cell-phone DJ. By the end of the week we were able to sequence the metagenomes from several of our sampled sites. Then, even without internet (the horror), through the incredible expertise of our mentors, we were able to analyze the diversity of the microbial communities. By pairing who is there with environmental parameters and rate measurements like gas fluxes, we are able to paint a picture of the current functionality and ecosystem services that microscopic life provides.

Based on the rotational schedule of this field school I spent most of my days in the lab following those cyanobacteria mats through their subsequent analyses. First we measured the amount of oxygen in each layer of the mats using a micro sensor. This probe allows us to measure O2 gas on the micro-meter scale, giving us an in depth profile for each mat. The top of the mats are photosynthetic, with the highest concentration of chlorophyll just below the surface layer. Towards the bottom of the mats however, respiration becomes the dominant process, and some of the mats even had anoxic bottom layers. This distinct layering would indicate a change in community composition with depth (both cyanobacteria species and other bacteria & viruses that call this mat structure home). To test this, we dissected the mats vertically, separating out layers based on the depth where we saw a distinct change in the oxygen profile. These layers could somewhat be characterized by color which created an easily visible distinction for dissection. These layers were then placed in tubes and analyzed separately in all further analyses.

At the end of the course, we worked on synthesizing all of our results to draw some conclusions about the microbial ecosystems we had been studying for the past week and a half. Each presentation turned into an exciting scientific discussion relying heavily on the diverse expertise and research experience of the mentors and students. I feel incredibly lucky to have been able to learn from these experts and practice the full scientific process in such a unique place.

5. Exploring the North

The North is a fascinating place to do research. We know so little about its environmental processes and there are many scientific questions still begging to be asked. More than that however, the stunning and surprisingly diverse environment, rapidly shifting weather conditions, and richly unique flora and fauna make it a true adventure to explore. Here are some of the pictures I took which I think best capture the north’s wild beauty and ecological diversity.

That’s all for now, folks! To learn more about what I and the rest of this year’s students were up to during the Sentinelle Nord IPS you can check out the group’s field blog here, or follow me on twitter @Antarctic_Emma (see #SNAM19).