Manuscript presenting first yearlong study of carbonyl sulfide fluxes

Harvard Forest EMS tower
Harvard Forest EMS tower

Our manuscript on the “Seasonal fluxes of carbonyl sulfide in a midlatitude forest” was just recently published in PNAS (document online). Lead author Róisín Commane and I met at Harvard Forest where she installed an Aerodyne Research Inc., laser spectrometer to study the seasonal behavior of carbonyl sulfide (interchangeably called OCS and COS by different groups). Of particular interest are the common pathways to both CO2 and OCS, for example both trace gases react with carbonic anhydrase enzymes in leaves. This commonality may provide a quantitative, independent measure of the photosynthetic pathway for carbon assimilation.

In this study, we find that vegetative uptake accounted for 72% of annual uptake of OCS, and nighttime uptake through stomata and soil uptake accounted for the remainder. Emissions of OCS from the forest canopy and soils were observed episodically at the forest, and by an unknown mechanism.

We find that OCS and CO2 are in certain cases affected by different processes, making their relationship variable. Thus, OCS cannot be used as a direct tracer of photosynthetic activity, but can probe various aspects of ecosystem activity, such as stomatal conductance, which will be useful for constraining aspects of carbon cycling models.

Manuscript evaluating a suite of flux-gradient methods for determining ecosystem H2 fluxes

A manuscript I’ve been working on entitled “Ecosystem fluxes of hydrogen: a comparison of flux-gradient methods,” was now been published in Atmospheric Measurement Techniques (view paper online). Our goal was to present a detailed experimental approach for measuring ecosystem fluxes of H2 and to test different so-called “flux-gradient methods” for calculating the H2 fluxes. Some common trace gas flux methods, e.g. eddy covariance, are not available for species like H2 that cannot be measured precisely at high frequencies (<1 Hz). We hope this paper will help inform the design of future studies for which flux-gradient methods might be the best option for measuring trace gas fluxes.

Here are a couple videos on the instrument deployment and design for more information.

H2 fluxes were measured at Harvard Forest, MA
H2 fluxes were measured at Harvard Forest, MA

BioDesign course – bridging science and art

Biologist/architect team Tobi Lyn Schmidt and Mike Bogan created a course linking artists, designers, architects, and biologists from the California College of the Arts (CCA) and Stanford University. I served as a postdoc mentor to help inspire and guide the process of cross-hybridizing biology and design (some examples) with three really talented undergraduate CCA students: Leslie Greene, Sakurako Gibo, and David Lee.

The students were first charged with creating designs to illustrate scientific concepts in my field of research. I challenged them think about the issue of scale with respect to the biogeochemical cycles I study. The processes I investigate occur over a wide range of spatial and temporal scales, which is a challenge for their measurement and interpretation. David focused on a selection of atmospheric trace gases with a wide range of abundances, and that interact with each other through key reactions. In his image, the hydroxyl radical (OH) is illustrated by the white dot from which orange and blue strings respectively represent the path length to molecules of  hydrogen (H2) and methane (CH4) in the surrounding space. The density of the strings is representative of the concentration of H2 and CH4 relative to OH. I love the sense of competition in this image. These reduced molecules compete for reaction with OH, and with other trace gases not shown, which helps explain the relatively their long lifetimes of H2 (~2 years) and CH4 (~10 years) in the atmosphere.

Concentration Burst, by David Lee
Concentration Burst, by David Lee

The second task for the students was to manipulate a biological system for design or artistic ends. All three students visited the Welander geobiology lab at Stanford and the Berry lab at Carnegie on campus where atmospheric trace gases are measured. For her project, Leslie was interested in manipulating microorganisms to reveal art. Using a combination of strains from the lab and purchased online, Leslie created competitive interactions between organisms and against antibiotics to reveal structures that were both patterned and complex. In the example below, she laid a cross-pattern of Streptomyces ghanaensis and Bacillus subtilis colonies and let them grow and compete. Intriguing features arose, appearing as if the Streptomyces strain grew on top of the Bacillus strain, perhaps antagonistically or not. Leslie overlaid emergent patterns in topology and color from microbial cultures with and without competition to create an amazing image that reveals some very aesthetic order in the systems.

Bio-manipulation of Streptomyces ghanaensis and Bacillus subtilis
Bio-manipulation of Streptomyces ghanaensis and Bacillus subtilis
Emergent patterns from competition
Emergent patterns from competition, by Leslie Greene


Finally, the students illustrated various concepts related to my work including artistic renditions of Streptomyces colonies and concepts of complexity (see related post). I really love the feel of the image created by Sakurako Gibo showing the atmospheric H2 concentrations that I measured between the ground and top of a measurement tower (y-axis) over the year-long experiment (x-axis) at Harvard Forest as an ephemeral curtain. Higher concentrations of H2 are represented with a deeper intensity of blue. The impact of the soil sink is illustrated by the lightening of the color near the base of the image caused by high rates of soil microbial H2 consumption in summer and fall.

Curtain of H2 Harvard Forest
Curtain of H2 at Harvard Forest, by Sakurako Gibo


Manuscript linking consumption of atmospheric H2 to the life cycle of soil-dwelling actinobacteria

The presence (left) or absence (right) of aerial hyphae in Streptomyces may influence their atmospheric H<sub>2</sub> consumption
The presence (left) or absence (right) of aerial hyphae in Streptomyces may be linked to atmospheric H2 consumption

Microbe-mediated soil uptake is the largest and most uncertain variable in the budget of atmospheric hydrogen (H2). In Meredith et al. (2014) in Environmental Microbiology Reports, we probe the advantage of atmospheric H2 consumption to microbes and relationship between environmental conditions, physiology of soil microbes, and H2First, we were interested in whether environmental isolates and culture collection strains with the genetic potential for atmospheric H2 uptake (a specific NiFe-hydrogenase gene) actually exhibit atmospheric H2 uptake. To expand the library of atmospheric H2-oxidizing bacteria, we quantify H2 uptake rates by novel Streptomyces soil isolates that contain the hhyL and by three previously isolated and sequenced strains of actinobacteria whose hhyL sequences span the known hhyL diversity. Second, we investigated how H2 uptake varies over organismal life cycle in one sporulating and one non-sporulating microorganism, Streptomyces sp. HFI8 and Rhodococcus equi, respectively. Our observations suggest that conditions favoring H2 uptake by actinobacteria are associated with energy and nutrient limitation. Thus, H2 may be an important energy source for soil microorganisms inhabiting systems in which nutrients are frequently limited.

Much of this work was done with the help of Deepa Rao, an undergraduate researcher at MIT at the time who wrote an award-winning senior thesis on the topic and presented results in a number of venues, including at AGU 2012.


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!

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”

Instrument deployment at Harvard Forest

Instrument deployment to Harvard Forest
Instrument deployment – Harvard Forest

After over a year of designing, building, and testing a custom instrument system to measure fluxes of molecular hydrogen (H2), I deployed the system to the Harvard Forest Long Term Ecological Research site in Petersham, Massachusetts ( With the instrument installed, I will measure hydrogen fluxes for a year to determine the seasonal dynamics of H2 cycling in this mixed deciduous forest, and in particular, to characterize the strong soil sink for atmospheric H2.

The instrument shed was tight, and I was packing a lot of equipment. But the move in day was a successful and fun experience thanks to the help of colleagues at Harvard University.

This short documentary created by fellow PhD student Ryan Abernathey highlights the challenges and excitement of move-in day. But the work has only just begun…

Laura at Harvard Forest from Ryan Abernathey on Vimeo.