Cover of Incorporating Microbial Processes Into Climate Models

It is difficult to imagine 2 fields more different in their methods, tools and objectives than climate science and microbiology, and yet there is a vital connection between these 2 endeavors. Microbes are critical players in every geochemical cycle relevant to climate including carbon, nitrogen, sulfur, and others. The sum total of microbial activity is enormous, but the net effect of microbial activities on the concentration of carbon dioxide and other climate relevant gases is currently not known. The past 2 decades have witnessed an explosion in our recognition of the diversity of the microbial world, as new technologies have made it possible to characterize microbial communities in ever greater detail. Modeling, too, has experienced tremendous advances in its capabilities. For all the progress, however, we are not able to measure microbial processes in such a way as to allow climate scientists to include them in models of global climate.

Determining how to measure the rates, fates, and fluxes of climate-relevant gases through microbial communities and the environment is a task that falls between climate science and microbiology and is the focus of neither. While the gap between the 2 disciplines is daunting, the need to bridge it is urgent and the science and technology needed to begin to do so is within reach. By breaking the task down into tractable parts, strategically developing needed tools, methods and community resources, and facilitating the establishment of interdisciplinary teams with well defined, shared goals, the task of incorporating microbial processes into climate models can begin to be tackled, to the benefit of both fields.

Common Ground:

The differences between climate science and microbiology are considerable, but they have something quite powerful in common, the use of models. Indeed, both Earth’s climate and microbial community processes are too complex to study without models. In both fields, models represent logical syntheses of assumptions and boundary conditions, can identify gaps in understanding, and are useful for revealing amplification and dampening effects. The development of methods to quantify microbial impacts on climate so that they can be incorporated into climate models is a major interdisciplinary challenge.

Connecting the pieces:

For the first time, an accurate, quantitative census of microbes inhabiting any environment can now be taken. Knowing which microbes are present is useful for suggesting the community potential, what processes might be going on now, or might be possible in other circumstances, but that information cannot yet be turned into fluxes and rates. The challenge will be to simplify complex community dynamics so that net inputs and outputs that accurately reflect reality can be incorporated into climate models.

The group recommended a multi-pronged approach to breaking the challenge into manageable parts.


  • Choose a few specific biogeochemical cycles to serve as demonstration projects

    Because the task is currently unmanageable in its entirety, the best approach would be to begin with in-depth characterization of particular biogeochemical transformations that are important, microbially driven, and tractable. Three examples meeting these criteria were identified at the colloquium.
    • Methane:
      Microbes play important roles on both sides of the methane cycle—they both produce and consume methane. Human activities like cultivation and deforestation have substantial effects on methane fluxes. Furthermore, methane production from thawing permafrost in the Arctic could be large enough to be significant on a global level.
    • Carbon storage:
      Microbes produce and break down an infinite variety of carbon compounds. Their activities are a primary determinant of whether any terrestrial or marine environment acts as a net carbon source or sink.
    • Nitrous oxide:
      Nitrous oxide (N2O) has more than 300 times the heat-trapping ability of carbon dioxide and human practices like agricultural fertilization have contributed to significant increases in nitrous oxide emissions over the last century. The actual rate of N2O flux from agricultural soils varies enormously, due in large part to the activities of soil microbial communities.
  • Assess current data collection and develop a monitoring/data collection strategy

    A great deal of pertinent data has been and continues to be collected that could be useful in efforts to understand microbial roles in geochemical processes. Unfortunately, these data are not organized in such a way as to make them accessible across the scientific community. Opportunities to leverage current activities are being lost.
  • Implement validation processes to integrate data collection, modeling, and experimentation

    Bottom-up experimentation will have to scale from individual microbial physiologies in laboratory culture through to small-scale environmentally realistic mixed cultures. Top-down observation will require measuring relevant rates and fluxes while treating microbial community dynamics as a black box. Both will be needed to validate the inclusion of microbial processes in climate models.
  • Facilitate and provide incentives for collaborations and interdisciplinary training

    Progress will require close interaction among communities that do not work together currently, and stable, long-term funding will be needed to lower the risk of participation. Interdisciplinary short-term training and long-term degree programs are key.
  • Address Technology Needs

    Technologies like real-time remote sensing and improvements in pure and mixed laboratory culture techniques are needed to make it possible to collect data more inexpensively, more often, in more places, and to study microbes and microbial communities in new ways.

Major events of the distant past illustrate the need to incorporate microbial activities into existing climate models. They demonstrate that the microbial processes that affect climate do not necessarily balance each other out. Billions of years ago, changing microbial community composition resulted in the shift to an oxygenated atmosphere. The organisms that had inhabited the Earth for at least a billion years were no longer able to survive on the Earth’s surface. In the past, such profound change took millions of years, a time span well beyond that with which current climate models are concerned. Today, changes due to human activity are causing similar large scale global effects in as little as 100 years. There is clear evidence that microbes can have an enormous impact on climate but their responses and impacts cannot currently be measured. In light of ongoing global change and the centrality of microbes in global biogeochemical cycles, their specific responses and activities in the context of climate change modeling can no longer be ignored.


Incorporating microbial processes into climate models: ​Report on an American Academy of Microbiology Colloquium held on Feb. 21-23, 2011. Washington (DC): American Society for Microbiology; 2011.

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