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.


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


AGU 2013 Session: Linking Microbial Communities and Biogeochemistry to Ecosystem Processes and Environmental Change

I am co-organizing a session at this year’s annual AGU meeting in San Francisco focusing on the microbial influence on atmospheric chemistry and ecosystem processes. We are bringing together a group with diverse disciplinary backgrounds and scientific approaches to share approaches and ideas. We hope to see you there on Friday!

Sessions: B51D (poster), B53D (oral), B54B (oral)

-search the sessions-


Section/Focus Group:



Laura Meredith, MIT,

Catherine Febria, University of Maryland,

Jake Hosen, University of Maryland,

Ed Hall,


Microbial communities are mediators of all biogeochemical cycles, controlling ecosystem responses to human-induced change. Advances in the molecular characterization of carbon and microbial communities have produced novel datasets that capture large spatiotemporal dynamics. Researchers are now able to address questions about the interactivities of nutrient flux from the microbial community to ecosystem scale. This session will highlight ressearch on the functional role of microbial communities in ecosystem-level biogeochemistry. We encourage contributions that investigate C, N, P, small-scale experiments and syntheses that can inform understanding of ecosystem-level responses to environmental change.

Index Terms:

[0439] BIOGEOSCIENCES / Ecosystems, structure and dynamics
[0470] BIOGEOSCIENCES / Nutrients and nutrient cycling
[0465] BIOGEOSCIENCES / Microbiology: ecology, physiology and genomics
[0428] BIOGEOSCIENCES / Carbon cycling

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

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

Is H2 an upper atmospheric tracer?

I presented a poster at the 2010 American Geophysical Union General Assembly on H2 as a “mesotracer.” A rare glimpse into the chemical and dynamical evolution of the Arctic polar vortex is provided by a suite of in situ balloonborne measurements. A set of mesospheric tracers observed in the late vortex validate theoretical mesospheric chemical profiles, which is especially valuable for the case of mesospheric H2. Early vortex mesospheric profiles are constructed to explain mixing in tracer-tracer space. Expanding a model to incorporate three mesotracers, H2, CO, and SF6, instead of only one, will increase our ability to constrain estimates of the amount of mesospheric air that descended to stratospheric altitudes by vortex end.

AGU 2010 - Chemical tracers in the upper atmosphere
AGU 2010 Poster – Chemical tracers in the upper atmosphere