Microbial drivers of N2O emissions in the Biosphere 2 Tropical Rainforest

B2 Rainforest floor

Post by Juliana Young

The Rainforest at Biosphere 2 is a unique study system because it operates under very high temperatures and has adapted to the Arizona heat. In 2002, Dr. Joost van Haren studied nitrous oxide (N2O) flux in the Rainforest at Biosphere 2 and found that there is a high and low pulse zone of emissions of this gas under the condition of post-drought (van Haren et al., 2005). Our study builds from the foundations of this experiment. We are testing what could be responsible for the spatial difference in N2O gas fluxes. While there are many facets of the Rainforest to study, my interests and area of research focuses on the climatic parameter of drought and rewetting responses of the microbial community in the soil of the Rainforest. Currently, with the help of Dr. Laura Meredith and Dr. Aditi Sengupta, I am characterizing the soil microbial communities of the Rainforest and how their abundance or metabolism can be related to the N2O gas flux.

B2 Rainforest waterfall

Our data includes five sites and 3 depths at each site in the Rainforest that were sequenced using 16S rRNA gene for bacteria and archaea and ITS2 for fungi. We consider these data alongside edaphic factors like soil moisture, average pH, average electric conductivity, total carbon, total nitrogen and carbon to nitrogen ratio and gas fluxes including nitrous oxide, methane, and carbon dioxide concurrently collected during the 60-day experiment. Current analysis is focused on linking microbial metabolism or abundance to pulses in nitrous oxide in the Rainforest at Biosphere 2. Correlations between abiotic factors are also being related to microbial communities within each specific sampling site.

Tropical environments generate a lot of the Earth’s nitrous oxide through biogeophysical processes that are not well understood; therefore, studying the microbes and nitrous oxide emissions could potentially give insight into the complexity of this greenhouse gas. To complement our current data, we are planning metagenomic or targeted amplicon sequencing for genes that are shown to be highly conserved for nitrification and denitrification in our original samples or a new drought experiment to explain the microbial drivers of high and low N2O pulse regions.


Juliana Young
Biochemistry and Molecular and Cellular Biology double major
Junior at the University of Arizona

Soil survey: microbial, chemical and physical drivers of carbon cycle tracers

soil samples
19 of the 20 soils included in the soil survey study (peat soils not shown).

Two trace gases (carbonyl sulfide and the oxygen isotopes of CO2) show promise to help disentangle carbon cycle processes, but their soil fluxes need additional characterization. As in leaves, we anticipate that carbonic anhydrase (CA) enzymes in soil microbes drive uptake of atmospheric COS by soils (COS + H2O -> CO2 + H2S) and exchange of the oxygen isotopic signature between atmospheric CO2 and water (CO2 + H2O <-> HCO3 + H+). We performed a soil survey to test whether soil microbial CA drive the soil fluxes of these two potential carbon cycle tracers. By measuring the microbial, chemical, and physical properties of a diverse set of soils, we set out to determine the best predictors of exchange of COS and 18O-CO2, and specifically whether the abundance or diversity of microbial CA was the top predictor.

soil sample map
Sampling locations include a range of biomes.

With the help of a large number of colleagues*, we collected and processed 20 soil samples from sites around the United States (including Hawaii) and from two sites in Cambodia. These soils represented a range of biomes and land use, as a number of soils came from sites used for agriculture.

working with soil
Working with soils is fun! Sieving soil replicates, air drying, incubating at 30% water holding capacity, and quantifying gas fluxes!

This was my first experience working with soils, and I had a fantastic time! Soils are the result of coevolving biotic and abiotic components, and the results can be incredibly diverse. This diversity is evident in the range soil color and texture (see photo above), and was mirrored in our physical and chemical measurements. With support from a DOE Joint Genome Institute Community Science Program, we will be characterizing the microbial communities and their carbonic anhydrase expression to test whether soil microbial CA are linked with the soil exchange of these potential carbon cycle tracers.

*Max Berkelhammer, Ken Bible, Sebastien Biraud, Kristin Boye, Nona Ciariello, Ingrid Coughlin, Ankur Desai, Pat Dowell, Evan Goldman, Tom Guilderson, Paul Hanson, Marco Keiluweit, Kehaulani Marshall, Amy Meredith, Jesse Miller, Bharat Rastogi, Ulli Seibt, Christian von Sperber, Chris Still, Wu Sun, Jonathan Thom, Mary Whelan, Peter Vitousek.

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

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

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”

How much energy does H2 supply to soil microbes?

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

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 (http://harvardforest.fas.harvard.edu/). 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.