Deepa’s AGU Poster “Connecting H2 consumption to life cycles of soil microbes”

Read Deepa Rao’s Blog Post

It’s a wonderful piece (highlighted on the EAPS department website) about her first the AGU experience written through her uniquely balanced scientific and artistic perspective. For example, she writes, “Science, nature, life, emergence, and the universe have always inspired my art. And it is the unnecessary beauty of science that makes it deeply mysterious and so inviting to my mind… AGU was an incredible week of reconnecting with friends, advisors, professors, fellow researchers. It was also unexpectedly a way for me to connect a path to a foreseeable future where my two passions can be combined, perhaps even muddled, into an exciting career.”

I was thrilled to give a talk this year at AGU in the full-day, highly subscribed Biosphere-Atmosphere Greenhouse Gas Fluxes in Terrestrial Ecosystems IV session organized by Paul Stoy, Christopher Williams, and Todd Scanlon. I’m looking forward to publishing these results very soon!

AGU 2012 Talk

I defended my thesis entitled “Field Measurement of the Fate of Atmospheric H2 in a Forest Environment: from Canopy to Soil” on October 4, 2012.

It was an incredible relief to finish the thesis document itself (link to .pdf). I really enjoyed preparing and giving my thesis defense presentation. It’s not often that one gets to present the culmination of six years of hard work and personal development to colleagues, family, and friends. I am grateful for mentorship from my advisor Ron Prinn, my thesis committee (Steve Wofsy – Harvard, Bill Munger – Harvard, Tanja Bosak – MIT, Colleen Hansel – WHOI, Shuhei Ono – MIT), and many others along the way!

I am continuing at MIT for a short (approximately 9 month) postdoctoral position with Ron Prinn to translate the work described in my thesis to publications. I am currently exploring possibilities for a postdoctoral position at the intersection of microbial ecology and atmospheric chemistry (trace gas cycles or aerosols) by searching advertised positions and writing fellowship proposals.

Presenting a poster on “Physiology of the microbe-mediated soil sink for atmospheric H2″ at ISME in Copenhagen, Denmark. Deepa Rao contributed greatly to this work.

Last week I attended ISME 14 (International Symposium on Microbial Ecology) in Copenhagen, Denmark. It was a delight to see the city – its juxtaposed giant modern, cool, sterile buildings surrounding the historic old city. More of a delight was unexpectedly running into friends from the MBL Microbial Diversity summer school (2010) and realizing they are now my colleagues.

Wind turbines and modern architecture outside of Copenhagen

The conference itself was quite good. I appreciated the range of content from very big picture and abstract to focused experimental projects. One message I took away from the community was a sort of -omics backlash, or perhaps whiplash, to the idea that generating more and more -omics data is the sole future for microbial ecology. It seems that presenters coming from both the -omics and experimental side were acknowledging the importance of both tools, and especially of using them together. Those seem to be a lot of tools for any one scientist to master, so I am encouraged that the tone was of collaborative holistic approaches for tackling scientific questions.

Tuborg beer and the Royal Copenhagen porcelain company

I really enjoyed a somewhat unique session. It was a discussion entitled “Frontiers in microbial ecosystem science: Energizing the research agenda” sponsored at this and other conferences by the US National Science Foundation. All sorts of issues were raised in a discussion of “what needs to be done” – what are the important topics and how should we advance microbial ecology. I was struck by how strong the arguments were that microbial ecology is important for understanding, and possibly mitigating, climate change. This is my main interest, but I often find the microbial ecology literature and research interests so focused on minute points (I think my own project included), that it is difficult to see the link between the microbial and global scales. At this session I learned that it is not only because it is difficult to do, but also because the funding agencies seem to push scientists to write grants in one or the other. It is difficult to be interdisciplinary (falling under more than one NSF department). It has been a (fun) challenge for me to try to get a foot in both atmospheric and microbial ecology science, and it was encouraging to hear from the community that the intersection of the two is valued.

Deepa Rao accepting the award from her academic advisor Sam Bowring

At the 2012 EAPS Student Awards Ceremony Deepa Rao received the Christopher Goetze Prize for Undergraduate Research for her thesis entitled : “Exploring the Microbe-mediated Soil H₂ sink: A lab-based study of the physiology and related H₂ consumption of isolates from the Harvard Forest LTER.” The award recognizes “ innovative experimental design, care in data collection, and sensitive application of results to research problems.”

Click here for a description of her Senior Thesis Presentation 

It has been a pleasure to supervise Deepa’s thesis research and her results will contribute to our research efforts to understand the mechanisms driving the soil sink for atmospheric H2. Professor Ron Prinn acts as the faculty advisor for both Deepa and I.

Article describing the expansion of the atmospheric chemistry program at MIT over the past five years with a short feature on our work to understand the H2 soil sink in the field and in the lab.

Micro-organisms have produced dramatic shifts in the composition of the Earth’s atmosphere and continue to be important drivers of ocean- and land-atmosphere exchanges of gases that have a strong influence on atmospheric composition and climate. An interesting example is the microbial influence on atmospheric molecular hydrogen (H₂), which dominates the fate of this gas in the atmosphere. H₂ is emitted to the atmosphere by about half natural and half anthropogenic, or human-induced, processes but it is predominantly removed from the atmosphere by microorganisms in the soil, which makes this process the most important, yet least understood, player in the atmospheric H₂ budget.

In this video graduate student Laura Meredith shares her thesis work to build and deploy an instrument to the Harvard Forest Long Term Ecological Research site in central Massachusetts. Laura is in the Climate Physics and Chemistry Program. Her advisor is Ron Prinn.

Presenting my poster at AGU - one of 12,000+ posters

First stop was San Diego, where I attended the 44th Meeting of Advanced Global  Atmospheric Gases Experiment (AGAGE) Scientists and Cooperating Networks at the Scripps Institute of Oceanography in La Jolla. Anita Ganesan’s instrument in Darjeeling may pave the way for the first AGAGE site in India, so the crowd was eager to hear her describe our success in deploying her instrument. Her dedicated and diligent work is paying off as she is collecting some of the first high precision direct greenhouse gas measurements in India.

I gave a talk at the AGAGE meeting on my recent work on the flux of H2, CO2 and COS between the soil and atmosphere at Harvard Forest. I focus on the persistence of soil-atmosphere exchange of trace gases across snowpack, which insulates the soil microbial community from freezing air temperatures while allowing trace gases  to diffuse through the porous snow matrix. I’m interested in how strongly the biogeochemical cycling continues throughout the winter and in comparing the behavior of the different cycles in the low temperature ‘incubator’ beneath the snow.

This is also the subject of the poster I presented at the American Geophysical Union (AGU) Fall meeting, which is available via their new ePoster website. AGU, with its 20,000+ attendees, was overwhelming, but very enjoyable this year. I met great people and I learned a lot – some connected to my research, some completely random and fun.

I enjoyed both presentations and was happy to get feedback on the project. I was happy to discover the large interest the COS, carbonyl sulfide, community has in my H2 measurements. I have been working closely with Roisin Commane, a postdoc with Steve Wofsy at Harvard, to understand the relationship between the soil sinks of H2 and COS because we have observed a strong correlation between the two. COS has high potential to be used as a tracer of photosynthesis because it is taken up by the photosynthetic machinery of plants, but unlike CO2, it is not re-released by respiration. The respiratory release of CO2 makes partitioning out the photosynthetic component from bulk changes in CO2 very difficult. COS can be used as a tracer of just photosynthesis provided it does not have any other strong production or loss processes. However, COS has a soil sink, and recent observations suggest it may be too large and complex to ignore completely. Roisin and I are hoping to address this with our measurements and to provide information for modellers who investigate this question on larger scales.

I’m in my second week in India, where I am helping fellow Prinn-group graduate student Anita Ganesan deploy her gas chromatograph to Darjeeling, a town high on a ridge in West Bengal in the foothills of the Himalayas (Anita has a blog now!). It’s quite a trek to get to the Bose Institute where her instrument will be housed. We spent a few days adjusting to the change in time and culture in the hectic city of Kolkata. A haze hung over the city, making the day seem darker and the nights lighter, and there was a constant smell of burning. It was not unpleasant, but the concerns about the impact of particulate levels on air quality and health that we are taught in the classroom were made real. Two million people in this city and its surroundings breathe this local atmosphere daily, until it is exported to the globe.

We flew above haze spotted by convection clouds yesterday en route to Bagdogra, where we chartered a ride to Darjeeling. The road up through the mountains to Darjeeling was narrow and winding. Anita found the hairpin turns flanked by precipice most stressful because her instrument will make that journey in a delivery truck in just a few days. I was more worried about us, but I do know how it feels to worry about your custom creation being transported on bumpy roads. The cool mountain air was refreshing, but our lungs were aching by the end of the journey after following a chain of cars belching black smoke from their exhaust pipes. Happy to arrive, we entered the Darjeeling campus of Bose Institute in the dark, ready to start work the following day.

On our first full day on the site, Anita showed me around the site. We surveyed the site to decide on the best route for the inlet tubing, which will run from an inlet mounted on a small tower of one building to a different building in which her instrument will be housed. The site operator provided us with a table to support her instrument, and we picked out a spot for it in their instrument room.

Anita has done an incredible amount of work not only on the instrument design and construction but also on developing collaborations to use this site and on the monumental task of shipping everything to this remote site. We hope the instrument will arrive soon.

Experimental Atmospheric Chemistry course collage

It’s my fourth year as a TA for our ‘Experimental Atmospheric Chemistry’ undergraduate and graduate course at MIT, and today we have loaded up the department’s van with nitric oxide (NO) and ozone (O3) monitors, a uv radiometer, and three particulate monitors (PM 10, 2.5, and 1.0 um). As part of the ‘Pollution Exposure’ unit, we will synchronize the monitors and drive around Boston noting changes in pollutant levels and keeping notes to identify possible pollutant sources. The field trip is a good time, and this year our class has grown to ten students, which is the biggest class we’ve had since I helped develop the course in 2007 with my advisor Professor Ron Prinn and group alumnus Arnico Panday, now at University of Virginia.

We explore tunnels (Boston’s Big Dig provides miles of them), construction sites, urban sites with high traffic congestion, and cleaner beach sites. The students note changes in particulate levels at different sites, which often have distinct particulate size distributions as you would expect from a variety of types of aerosol sources. We follow cars, trucks, and buses of all shapes and sizes. Diesel buses and accelerating vehicles have much higher particulate emissions than clean natural gas buses and stationary vehicles; we might already expect this, but students are able to witness it first-hand and real-time.

Tunnels provide a unique photochemical ‘experiment’. Outside air, under uv light from the sun, has certain levels of pollutants that are created and destroyed by ‘photochemical’ reactions. When this air is swept into a one-way tunnel by the traffic and moved slowly through the tunnel, the tunnel blocks the sun and air is no longer being acted on by uv light, so the photochemical reactions cease. Students can then watch what happens if certain reactions that don’t need uv light proceed (such as NO+O3-> NO2 + O2, which will decrease concentrations of O3) and certain reactions that need uv light are halted (such as NO2 + uv -> NO + O leading to O + O2 + M -> O3 + M, which would have regenerated concentrations of O3). In the tunnels, ozone concentrations decrease because O3 reacts with NO, and because there is no uv light, ozone cannot be regenerated; the students clearly see ozone concentrations fall to nearly zero by the end of long tunnels, such as the Ted Williams Tunnnel in Boston.

The study of atmospheric chemistry is often the study of invisible reactions producing invisible products in the atmosphere, so driving around with instruments and observing these phenomenon real-time have been invaluable teaching tools for students (and myself). Over the semester, the course includes the following sections and field exercises; 1) CO2 and climate, in which students deploy a CO2 monitor to Harvard Forest to understand the carbon cycle, 2) Pollution exposure, in which students monitor their own daily particulate exposure and also observe pollution around Boston as described here, 3) Photochemical cycles, in which a wide range of instruments are deployed to MIT’s Green Building roof, which is the tallest building in Cambridge, and the concentrations of chemicals linked by photochemical reactions are studied in detail, and 4) Isotopes and the carbon cycle, in which students learn the value of the added information provided by measuring the isotopic composition of atmospheric molecules, not just concentrations, and measure the isotopic composition of some atmospheric trace gases. Isotope expert, professor Shuhei Ono, has joined the course and spearheads this fourth topic on isotopes. I have enjoyed helping develop and teach this course, and along with the students I learn something new every year!