AGU 2013 Session: Linking Microbial Communities and Biogeochemistry to Ecosystem Processes and Environmental Change

I am co-organizing a session at this year’s annual AGU meeting in San Francisco focusing on the microbial influence on atmospheric chemistry and ecosystem processes. We are bringing together a group with diverse disciplinary backgrounds and scientific approaches to share approaches and ideas. We hope to see you there on Friday!

Sessions: B51D (poster), B53D (oral), B54B (oral)

-search the sessions-


Section/Focus Group:



Laura Meredith, MIT,

Catherine Febria, University of Maryland,

Jake Hosen, University of Maryland,

Ed Hall,


Microbial communities are mediators of all biogeochemical cycles, controlling ecosystem responses to human-induced change. Advances in the molecular characterization of carbon and microbial communities have produced novel datasets that capture large spatiotemporal dynamics. Researchers are now able to address questions about the interactivities of nutrient flux from the microbial community to ecosystem scale. This session will highlight ressearch on the functional role of microbial communities in ecosystem-level biogeochemistry. We encourage contributions that investigate C, N, P, small-scale experiments and syntheses that can inform understanding of ecosystem-level responses to environmental change.

Index Terms:

[0439] BIOGEOSCIENCES / Ecosystems, structure and dynamics
[0470] BIOGEOSCIENCES / Nutrients and nutrient cycling
[0465] BIOGEOSCIENCES / Microbiology: ecology, physiology and genomics
[0428] BIOGEOSCIENCES / Carbon cycling

Deepa attends AGU and blogs about her experience

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

The EAPS department website shares Deepa’s blog about her first the AGU experience. 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.”

Thesis Defense!

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

I was honored to receive the 2012 Carl-Gustaf Rossby Prize for my thesis  (link to .pdf).

It was an incredible feeling to defend. 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!

ISME conference on “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.

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, 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.”

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
Deepa Rao accepting the award from her academic advisor Sam Bowring

Spotlight on H2 fluxes at Harvard Forest

PAOC Spotlight: Back to the forest Interview

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.

The MIT Program in Oceans, Atmospheres, and Climate interviewed me on the current state of my work with a custom instrument deployed at 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 “I survived the AGU 2011 Fall meeting”

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 “Helping deploy Anita’s instrument to Darjeeling, India”

Field tripping around Boston – 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.

Experimental Atmospheric Chemistry course collage
Experimental Atmospheric Chemistry course collage

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!

Teaching plant biogeography for the EAPS Extreme Weather and Climate course

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 vegetation at 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 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.