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

Carbon cycle tracers, an infographic

Carbon cycle tracer infographic

I’m happy to present an InfoGraphic on Carbon Cycle Tracers created by University of Arizona art students Melissa Yepiz and Luke Williams in Prof Karen Zimmerman’s course on infographics. Creating this infographic on complex scientific concepts was not an easy task, but Melissa and Luke did an incredible job. Through this collaboration they have provided me with an invaluable resource for sharing my research to a range of audiences (and in a much more aesthetically pleasing way than usual). I learned a lot in the process, including how to better explain my science and to get down to the fundamentals of the message I wanted to share. I was blown away by the talent in the UA art department!

The Carbon Cycle Tracers Infographic in poster form:

Carbon cycle tracer poster

 

 

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

 

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.

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

 

Move to Stanford University!

Stanford life

Boston to the Bay Area! This October I began a new academic life at Stanford University where I am a NSF postdoctoral fellow working on questions regarding the microbiology underpinning large trace gas fluxes between the atmosphere and biosphere. I am working under the guidance of Professor Paula Welander who recently joined the Environmental Earth System Science faculty. I am looking forward to learning from her expertise and from the rest of our group. With this new move, I also began a new social life, which (after many years in tech schools) included my first-ever college football game and tailgating. Should be a great couple of years.

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!

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