Many thank to atmospheric chemist extraordinaire Jessie Creamean for participating in our NSF project on MOSAiC Leg 1. Jessie’s participation allowed us to have a physical presence during the critical setup phase and freeze in. Her participation was a double win; she has her own DOE funded project with MOSAiC that didn’t include ship time, while our project needed a capable hand for Leg 1. I’ll be picking up where she left off when Leg 3 starts in just a couple of weeks. Jessie shared a few photos from Leg 1.
Jessie Creamean with Akademic Federov in the background.Checking out a crack in the ice. The ice has been much more dynamic than expected, creating some problems for installing the various observational instruments.A beautiful view of Polarstern at the onset of the polar night.Frost flowers! Still a special place in my heart after all these years…The Russian icebreaker Kapitan Dranitsyn, which will be ferrying the Leg 2 and Leg 3 personnel to Polarstern.
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.
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).
From Jacobs et al., 2015. Expert based estimates of ecosystem service apply can be mapped to ecological with a known spatial distribution, yielding a spatial map of ecosystem service supply.
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.
From Neumann et al., 2019. The distribution of objective defined seascape units at different depths along the central west coast of the Antarctic Peninsula. Bowman et al. 2018 identified a total of 8 seascape units that varied in time and space, though most exhibited a tendency toward a certain depth range or location along the onshore-offshore gradient.
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!
From Neumann et al., 2019. Service supply categorizations for tradition, “landscape” based service providing units and objectively defined seascape units, derived from expert elicitations from the Palmer LTER investigators.
From the tropics to the Arctic… I spent last week in Tromsø , Norway helping prepare the German icebreaker Polarstern for the MOSAiC year-long polar drift expedition. As I’ve written in past posts, I’ve been waiting for this moment since 2012 and it’s hard to believe it’s finally here. MOSAiC is a true coupled ocean-ice-atmosphere study, and the first such study of its scope or scale. There have been modern overwintering expeditions in the Arctic before – most notably the SHEBA expedition of the late 1990’s – but none have approached the breadth or scale of MOSAiC.
The start of the MOSAiC expedition in Tromsø, Norway.
The basic idea behind MOSAiC is to drive Polarstern into the Laptev Sea and tether the ship to an (increasingly rare) large floe of multiyear sea ice. As we move toward winter, the floe and Polarstern will become encased in newly forming sea ice. The ship will drift with this ice through the full cycle of seasons, allowing a rare opportunity to study the physical, chemical, and biological characteristics of sea ice through its full progression of growth and decay.
The German icebreaker Polarstern tethered to an ice floe in the Arctic. Image from https://www.mosaic-expedition.org/expedition/drift/.
But MOSAiC is about more than sea ice. Sea ice is – for now – a dominant ecological feature of the central Arctic, and it exerts a strong influence on both the atmosphere and the upper ocean. Better predicting the consequences of reduced sea ice cover on these environments is a major goal of the expedition.
With support from the National Science Foundation, for our own little piece of MOSAiC PhD student Emelia Chamberlain and I are collaborating with Brice Loose and postdoctoral researcher Alessandra D’Angelo at the University of Rhode Island, along with colleagues from the Alfred Wegener Institute in Germany. We’ll be looking at how the structure of prokaryotic and eukaryotic communities in sea ice and the upper ocean influence the oxidation of methane (a potent greenhouse gas), and the production and uptake of CO2. I’m looking forward to joining Polarstern in late January for a long, cold stint at the end of the polar night!
Our lab on Polarstern.We searched in Tromsø for a totem for the lab, but ran a bit short on time and settled for Igor. Trolls are troublesome creatures and not, I think, particularly emblematic of our project team. Cavity ring-down spectrometers and mass specs, however, can be a bit trollish at times. So the totem is for them. Igor will be in charge of our little group of instruments. We can direct our frustrations at him, and hopefully by placating him with offerings we can keep things running smoothly.The Akademik Federov, a Russian research icebreaker that will sail with Polarstern and help establish the drifting observatory. Federov will return in a few weeks.Dancing on ice floes. The MOSAiC launch was quite an event with lectures, a party, and a hi-tech light show. The show included an interactive ice floe field – step on the floes and they crack to become open water, slowly freezing after you pass. It was well done.It’s the Polarstern projected on the Polarstern. So meta.And they’re off! waving good-bye to the Polarstern.
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.
Making a plan. Jesse (blue hat) was our guide in 2017. This trip we were lucky to be joined by Santos, a local fisherman with deep knowledge of the area.Tambillo. Best village in Cayapas-Mataje.Bringing the coconuts to market.You don’t see many dugout canoes in Cayapas-Mataje, though I understand that they’re more common among the indigenous villagers up-river.Shrimp farm in Cayapas-Mataje. So much nitrogen…Measuring tree height. Some of the mangroves in Cayapas-Mataje are so high that you wouldn’t believe it if I told you how high (64 meters).Crabs. Ecologically important. Very camera shy.Natalia with Jesse’s boat “Los Reyes del Manglar” (The Kings of the Mangroves)Santos with cockles. Cayapas-Mataje supports a major artisinal cockle fishery (see here).It’s a jungle…Where’s Natalia?After a hard days work.Borbón, our home for the week. Town motto: We make every night an all-night dance party because we can!Sampling in the mangroves.Mangroves!
These guys are a bit bigger than the microbial organisms we usually study in the Bowman Lab, but are absolute models under a standard light microscope. Here you can see two rotifers (far left with egg sac, and top center) a type of microscopic invertebrate commonly found in freshwater. (PC: E.J. Chamberlain)
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.
(PC: Charles W. Greer) Great learning can happen anytime, anywhere. From the classroom……to the Great Whale River! (PC: E.J. Chamberlain)
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.
Locations of some of the CEN stations, including Whapmagoostui-Kuujjuarapik. PC: CEN
Full Research Complex, taken in the evening (~9 PM) with kitchen (center) and dorm/lab buildings (right). (PC: E.J. Chamberlain)
Main CEN building, run in collaboration with the Cree First Nation of Whapmagoostui as a community center. (PC: E.J. Chamberlain)
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
Learning about the native plants of the area and their traditional medicinal & household uses by the Cree community. (PC: E.J. Chamberlain)
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.
The finished product! The next group of base-bound researchers will be in charge of adding canvas for the walls. (PC: E.J. Chamberlain)
Sunny – our leader through the tree cutting process helps students place their trim poles into the right position (PC: E.J. Chamberlain)
3. Fieldwork
While sailing to our sample sites we are able to test equipment and ensure that collections will run smoothly. Here I help test out the depth finder while we make our way through the mist. (PC: Flora Amill)
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.
This sedimentary rock is actually a stromatolite formed from layers of ancient cyanobacteria growth. Cyanobacteria secretes a sticky mucus that binds sediment grains into fine mineral layers that fossilize into the rings seen here. (PC: E.J. Chamberlain)
Sampling microbial mats is all about having the right tools – from bug nets to your good ‘ole Canadian Tire spatula… It’s all in the wrist. (PC: E.J. Chamberlain)
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.
Permafrost mounds seen from the helicopter. As the permafrost melts, organic carbon (frozen ancient plant biomass) is released into the adjacent meltwater ponds where it is consumed by hungry bacteria and archaea. The activity rates of this Arctic ~microbiome~ determines how much of this carbon is released into the atmosphere as carbon dioxide or methane – both greenhouse gases. (PC: E.J. Chamberlain)
4. Scientific Expertise & Laboratory Work
Running a qPCR (quantitative polymerase chain reaction). PCR is a technique to make copies of, or amplify, targeted genetic material. qPCR quantifies that material. Here we looked to quantify the amount of toxin-producing genes in our cyanobacteria samples. (PC: E.J. Chamberlain)
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.
Measuring the oxygen profile of a microbial mat. (PC: E.J. Chamberlain)
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.
The dissection station and colorful results (right). (PC: E.J. Chamberlain).
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.
Rapidly shifting and unpredictable weather makes planning for the field difficult and often delays flights south. (PC: E.J. Chamberlain)
This photo was only taken an hour before the one to the right. The fog rolled in and out constantly most days. (PC: E.J. Chamberlain)Even in mid July, Hudson Bay was still thick with melting sea ice. It was otherworldly to see the rotted ice washed up on the beach, particularly in contrast to the lush fields & forests nearby. (PC: E.J. Chamberlain)
(PC: E.J. Chamberlain)
(PC: E.J. Chamberlain)A birds-eye (helicopter) view of the Great Whale River. (PC: E.J. Chamberlain)
Fauna: An adolescent black bear eyes us from the riverbank. (PC: E.J. Chamberlain)
Flora: Cladonia stellaris, or my new favorite lichen. While it looks plant-like, lichen is actually made of two types of microbes – algae and fungi – living in symbiosis. This lichen is an important food source for caribou and reindeer, giving it the common name “reindeer lichen”. (PC: E.J. Chamberlain)
Exploring the Great Whale River during a fieldwork pit stop! (PC: Ligia F. Coelho)
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).
A couple of months ago I was fortunate to have the opportunity to give a lecture at the Birch Aquarium at Scripps in the Perspectives on Ocean Science lecture series. The lecture covered some emerging topics in Arctic Oceanography and provided a brief intro to the upcoming MOSAiC expedition. The lecture was broadcast by UCTV and can be found here. Matthias Wietz – sorry for botching your introduction on the title slide! (Matthias was a PhD student at the Technical University of Denmark when the picture was taken. The record has been set straight.)
Last week we were busy hosting the inaugural Oceans Across Space and Time (OAST, @Space Oceans OAST on Facebook) combined first year meeting and field effort. It was a crazy week but a huge success. The goal of OAST is to improve life detection efforts on future NASA planetary science missions by better understanding how biomass and activity are distributed in habitats that mimic past or present “ocean worlds”. Ocean worlds is a concept that has gained a lot of traction in the last few years (see our Roadmap to Ocean Worlds synthesis paper here). We have a lot of past or present ocean worlds in our solar system (Earth obviously, but also Mars, Europa, Enceledus, and a whole host of other ice-covered moons), and oceans are seen as a natural feature of planetary bodies that are more likely to host life. Our first year effort focused on some open-ocean training for the Icefin robot, designed for exploring the protected spaces below floating ice shelves, and a multi-pronged investigation of the South Bay Salt Works.
The South Bay Salt Works in Chula Vista, CA. A truly amazing site for exploring how microbial activity and biomass are distributed across environmental gradients.
The Salt Works are an amazing environment that my lab has visited previously (see here and here). Our previous work in this environment has raised more questions than answers, so it was great to hit a few of our favorite spots with a top-notch team of limnologists, microbiologists, geochemists, and engineers.
Part of the OAST team setting up next to some very high salinity NaCl-dominated lakes. The pink color of the lakes is the true color, and is common to high salinity lakes. The color comes from carotenoid pigments in the halophilic archaea that dominate these lakes.This is what I love about NASA – it’s an agency that develops the most sophisticated technology in the history of human civilization, but isn’t afraid to use a rock when the situation calls for it. Spanning several millennia of technological advancement is Maddie Myers (LSU), with Natalia Erazo (SIO) and Carly Novak (Georgia Tech) in the background.Carly Novak (Georgia Tech) sampling salts with Peter Doran (LSU) and his “surfboard of science” in the background.Doug Bartlett (SIO), a little out of his element at only 1 atm.
I’m thrilled to learn that my CAREER proposal was just funded by NSF-OPP, though I’m slightly disappointed that they made me change the title from IM-HAPPIER: Investigating Marine Heterotrophic Antarctic Processes, Paradigms, and Inferences through Research and Education to Understanding Microbial Heterotrophic Processes in Coastal Antarctic Waters. Apparently NSF is the only federal agency that doesn’t like a good acronym. This project will address open questions regarding the diversity and ecological function of heterotrophic bacteria and protists in coastal Antarctica. In particular there will be an emphasis on better understanding the mechanisms of bacterial mortality (i.e. protist bacterivory and viral lysis) and the implications for carbon flow through Antarctic marine ecosystems.
We’re coming for you! An unidentified protist (likely mixotrophic member of the genus Teleaulax) captured by microscope at Palmer Station in 2015. Heterotrophic bacteria and protists are ubiquitous in Antarctic waters, but we know surprisingly little about their genetic makeup or ecology.
This project means that after heading north for MOSAiC in 2020, the lab will be heading south for two field seasons in Antarctica. That work will be spearheaded by incoming PhD student Beth Connors. Although several lab members have or will soon be participating in the Palmer LTER cruise along the western Antarctic Peninsula, I haven’t been to the WAP since 2015. Looking forward to going back!
Palmer Station and the ARSV Laurence M. Gould.
CAREER proposals emphasize both education and research, so in addition to field, laboratory, and modeling work we will be developing a new summer Junior Academy course for Sally Ride Science on polar ecology and oceanography.
