Tag Archives: soil

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 both 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. An overarching concern was to better understand soils to know “How to feed the soil and the planet?” in the anthropocene, which was 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), but our observations are typically limited to a much narrower range given measurement and resource constraints. These issues were elegantly summarized in the 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 the policies 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 the whole system or measurements that only count certain members of the communities. 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? Well, let’s just say I walked away from the meeting knowing that there are plenty of unanswered questions on soil complexity and scale. With the increasing technical capability in soil and microbial measurements, and communication at meetings like this one, we’ll get there soon.

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 (for me anyway), and perhaps starting with a simple approach like this will help me embrace the system and its questions.

Emergent H2 system

Emergent patterns of H2 consumption

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At a slightly more macro scale

Thank you for the BioDesign course organizers at California College of the Arts (Tobi Lyn Schmidt and Mike Bogan)!

Manuscript published on flux-gradient methods for ecosystem H2 flux measurements

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 on consumption of atmospheric H2 during 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 a recent study (early view in Environmental Microbiology Reports), we probed 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