Thesis Defense!

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 .pdfCarl-Gustaf Rossby Prize for best PhD thesis in PAOC for the year). 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.

ISME 14 – The power of the small

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.

Presenting a poster that Deepa Rao and I co-authored on the “Physiology of the microbe-mediated soil sink for atmospheric H2” at ISME in Copenhagen, Denmark.

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.

Wind turbines and modern architecture outside of Copenhagen

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.

Tuborg beer and the Royal Copenhagen porcelain company

Deepa receives Goetze Prize for Undergraduate Research

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.

Deepa Rao accepting the award from her academic advisor Sam Bowring

Feature in EAPS article: Atmospheric chemistry redux

Atmospheric Chemistry Redux

MIT Department of Earth, Atmospheric and Planetary Science 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.

PAOC spotlight video

PAOC Spotlight: Back to the forest Video

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.

I survived the AGU 2011 Fall meeting

I just returned to Boston after the six weeks of travelling. My two weeks in California, filled with conferences and colleagues, was quite different from the intensive and somewhat isolated period spent in India.

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. Continue reading

Helping deploy Anita’s instrument to Darjeeling, India

Update: The first publication from Dr. Anita Ganesan’s work in Darjeeling has been published in Atmospheric Chemistry and Physics (view document online).

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. Continue reading

Field trip around Boston for the MIT Experimental Atmospheric Chemistry course

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!

DEAPS Extreme Weather and Climate 2011

This week I traveled up to Mt. Washington with this year’s EAPS FPOP (Freshman Pre-Orientation Program) Discover Earth, Atmosphere and Planetary Sciences: Extreme Weather & Climate. It’s the third time I’ve acted as a TA for the program by heading up the flora and fauna section, or what is now more commonly known as “Flora with Laura.”

Describing the link between vegetation and microclimate in the Alpine Garden

The 3 day program is Spotlighted on the PAOC website, which describes it as being “designed to provide incoming freshmen with the opportunity to explore the science of weather and climate through an exciting combination of lectures and fluids experiments, providing a glimpse into some of the most interesting and challenging aspects of research in PAOC.

I’ve always be interested in plants. My father (and now one of my sisters) is a forester in the diverse mixed forests of Southern Oregon. The flora of trails I’ve hiked always interested me, especially the relationships between plant communities and regional climate (and even micro-climates) that were obvious even to my untrained eyes. Shrubby grasslands cover convex faces of the hills in Big Sur, CA, while coastal redwoods thrive in the moist and cool concave recesses. The towering forests of the North Cascades, WA are a world apart from the flowering cacti of the Mojave. However, it wasn’t until I took the Field Course in Arctic Science, held at both the University of Alaska, Fairbanks and the remote Toolik Field Station on the North Slopes of Alaska, that I formally learned about the adaptations of plants (and animals) to climate. We focused on different strategies plants employ for survival in harsh environments, specifically to arctic environments.

The material from that course translates beautifully to Mt. Washington because, just as plants adapt to the harsher climates found at higher latitudes, the plants found at different altitudes on Mt. Washington must adapt to increasingly harsher alpine conditions. Therefore, the altitude gradient on a mountain in Massachusetts reflects the latitudinal gradient from Massachusetts to the northernmost reaches of Alaska. Interestingly, many of the species on the summits of New England are also found in northern most Alaska – the alpine mountain top climes are the last refuge of arctic plants that extended to mid-latitudes during the last ice age.

The DEAPS group ascends the Mt. Washington auto road from the base near Pinkham Notch at 2032 ft to the peak at 6288 ft. The students make temperature, wind speed and pressure measurements to note how the weather varies up the mountain on that day. I teach them how to use the plant ecosystems as the key indicator of the year-long weather experienced at different altitudes on the mountain. The presence of plants that are adapted to cold temperatures, short growing seasons, ice and wind abrasion, high uv light, low water and nutrient retention, and other environmental stresses are visual indicators of the harshness of the year-round weather on Mt. Washington. Students note how these hardy plants increase in prevalence as we ascend the mountain, which confirms their lessons in how weather up the mountain also becomes more extreme.

DEAPS group at the Mt. Washington summit

Beyond the actual instruction, it’s a unique opportunity to interact with incoming MIT freshman; often we are the first group of MIT students and staff that they interact with upon arrival. Students come from all over the country and the world, and they are eager to start their academic and personal lives at MIT.

Atmospheric H2 energetic fertilization to soil microorganisms in a forest ecosystem

I presented a poster at the at the Ecology of Soil Microorganisms conference in Prague, 2011 on the role of soil microorganisms in dominating the fate of atmospheric molecular hydrogen (H2). Recent work has linked atmospheric H2 uptake to a novel high-affinity [NiFe]-hydrogenase expressed in active Streptomyces sp. cells, and is perhaps not driven by abiotic hydrogenases as was previously thought. Consequently, atmospheric hydrogen may be a 60-85 Tg yr-1 energetic supplement to microbes in Earth’s uppermost soil horizon. To understand the role of this supplement to the soil microbial ecology, this work explores the following questions:

  1. What is the importance of atmospheric H2 energy to soil microbial communities relative to carbon substrates?
  2. How might this energetic supplement change with changes in anthropogenic H2 emissions?
Ecology of Soil Microorganisms poster

Ecology of Soil Microorganisms