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 art!

Soil composition by Luke Williams (UA art student). Laser cut pattern on wood filled in with some of my soil samples.
Soil composition by Luke Williams (UA art student). Laser cut pattern on wood filled in with some of my soil samples.

I’ve had the pleasure of working with two fantastic UA art students (Luke Williams and Melissa Yepiz) through an Infographics class with Prof. Karen Zimmerman. Stay tuned for our infographic on carbon cycle tracers! As a side project, I’ve given the students some of each of the 20 soil samples from my recent study to constrain soil fluxes of carbon cycle tracers (COS and 18O-CO2, see story). I asked them to make a creative piece with the soils, highlighting differences in color, texture, etc… Luke’s piece nicely contrasts soil color using red Colorado river, gray Moab soils, and black Hawaiian soils within a geometric framework burned into wood. I’ll look forward to sharing more soon!

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.

Soil systems – the challenges of complexity and scale

Soils are complex systems, in which physical, geochemical and biological processes interact in aggregate structures situated in dynamically shifting air- and water-filled spaces. It is difficult to adequately sample soil properties and to model processes related to those soil measurements. These challenges were discussed in a stimulating three-day conference on Complex Soils Systems in Berkeley a few weeks ago. Attendees came from an incredible diversity of backgrounds with a common interest in tackling issues in soil science. The need to better understand soils was motivated by the importance of soil processes in climate and for figuring out “How to feed the soil and the planet?” in the anthropocene – a question posed early on by Professor John Crawford. 

Issues of scale were brought up explicitly or were evident implicitly in many of the presentations. Namely, that relevant processes in biogeochemical cycles occur over a wide range of spatial (nano- to mega-meter) and temporal (seconds to millennia) scales, but our observations are typically limited to a much narrower scope given measurement and resource constraints. These issues were elegantly summarized in the recent article “Digging Into the World Beneath Our Feet: Bridging Across Scales in the Age of Global Change” by Hinckley, Wieder, Fierer and Paul in Eos, Transactions American Geophysical Union 95 (11), 96-97. In a real sense, the scale issue presents problems when societal decisions regarding soil sustainability and ecosystem services are made using data and models derived from different (often smaller) spatial scales than are relevant to the policies and issues themselves.

One illustration of the concept of a spatially complex soil system is illustrated with the figure below by California College of the Arts (CCA) student Sakurako Gibo. The image depicts a theoretical assemblage of soil microbes with different morphologies (for instance round spores versus string-like mycelia). In the second figure, the complex system is “pulled apart” into bins that might represent the effect of a sampling strategy that subsamples components of the whole system. The information about the original complex assemblage and connections is not retained, and as a result, data and rules based off of the binned samples may be different from the case in the real intact community.

Spatially complex microbial community
Spatially complex microbial community
Spatial ordering is lost in measurements and models
Spatial ordering pulled apart

What to do? I walked away from the meeting in awe of the amount of unanswered questions on soil complexity and scale. However, with the increasing technical capability in soil and microbial measurements, and efforts at meetings like this one, made it evident that progress will continue in this area.

I’ll end with another neat set of figures produced by CCA student Leslie Greene who illustrated an emergent pattern of predicted H2 consumption (o) based on the availability of H2 (•) from the atmosphere (distributed) and from N2-fixing root nodules (gray filled circles). She created the pattern of H2 consumption based on one rule, soil moisture had to be above 10% and below 50%, as indicated by the concentric rings around water-logged soil sites (red filled circles). From this simple scheme, an irregular pattern emerges of the location where H2 consumption occurs. When faced with the complexity of soil, it is easy to feel paralyzed, and perhaps starting with a simple approach like this will help me embrace the system and its questions.

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Emergent H2 system
Predicted H2 consumption (o) based on the availability of H2 (•) from the atmosphere (distributed) and from N2-fixing root nodules (gray filled circles) that occurs when soil moisture is above 10% and below 50%, as indicated by the concentric rings around water-logged soil sites (red filled circles), by Leslie Greene

 

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

Undergraduate Researcher Shersingh’s SURGE Experience

Congratulations to visiting undergraduate researcher Shersingh Joseph Tumber-Davila on completing and thriving in the demanding eight-week Summer Undergraduate Research in Geoscience and Engineering (SURGE) program! Shersingh came to the Welander lab with a strong background in environmental research (news article) from his home institution of the University of New Hampshire. SURGE is a competitive earth science research and graduate school preparation program, which is specifically designed to recruit students of diverse backgrounds from other universities across the country. I was amazed at the number of activities the program had for the students including GRE test preparation, faculty seminars, career and grad school panels, and field trips. This was all while performing graduate-level research including a oral and poster presentation at the end of the program. Shersingh approached all these demands with amazing energy and attitude, which we’d really like acknowledge!

SURGE student Shersingh
SURGE student Shersingh

In Shersingh’s research, he asked whether microbe-mediated hydrogen (H2) uptake support C mineralization in soils. Soils are a strong sink for atmospheric H2, which is presumably used by soil microorganisms to fuel their energy metabolism. In addition, emissions of H2 have grown since the industrial revolution, so the availability of H2 energy to soil microbes likely also increased. Shersingh tested the influence of excess H2 on the ability of soil microbes to mineralize soil carbon for a variety of carbon substrates, especially those that can be energy intensive (e.g., lignin and lignocellulose). He used Streptomyces ghanaensis as a model organism containing high affinity hydrogenase (H2 uptake) and laccase (lignin breakdown) genes. By measuring carbon dioxide respiration rates and intermediate products involved in the breakdown of lignin and lignocellulose, we found evidence for increased breakdown of lignocellulose (straw) with elevated levels of H2. This may point to a  link between the H2 and C biogeochemical cycles in soils that will be interesting to pursue further. This project is in collaboration with Stanford postdoc Marco Keiluweit who specializes in soil carbon cycling.

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.

 

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”