One of the most daunting challenges facing science in the 21st Century is predicting the response of Earth’s ecosystems to global climate change. Although the global carbon cycle plays a central role in regulating atmospheric carbon dioxide (CO₂) levels and thus Earth’s climate, our understanding of the interlinked biological processes that drive this cycle remains limited. Whether ecosystems will capture, store, or release carbon is highly dependent on how changing climate conditions affect processes performed by the organisms that form Earth’s biosphere. Advancing our knowledge of biological components of the global carbon cycle is crucial to predicting potential climate change impacts, assessing the viability of climate change adaptation and mitigation strategies, and informing relevant policy decisions.
Greater insight particularly is needed into the role microbial communities play in many critical carbon cycle processes. In many cases, these microbially mediated processes are only minimally represented in carbon cycle models, which may limit their predictive capability and scale of resolution. Elimination of these so-called “black boxes” will require innovative approaches aimed at linking structural and functional characterization of microbial communities with quantitative measurement of carbon cycle processes.
Understanding and predicting processes of the global carbon cycle will require bold new research approaches aimed at linking global-scale climate phenomena; biogeochemical processes of ecosystems; and functional activities encoded in the genomes of microbes, plants, and biological communities. This goal presents a formidable challenge, but emerging systems biology research approaches provide new opportunities to bridge the knowledge gap between molecular- and global-scale phenomena. Systems-level research emphasizes studies on the underlying principles of intact, complex systems and facilitates scaling of concepts and data across multiple levels of biological organization. Applying this approach to the global carbon cycle will require multifaceted but highly integrated research that incorporates experimentation on model organisms and systems, collection of observational data on communities and ecosystems, and mechanistic modeling of processes ranging from metabolic to global scales.
*Items taken from 2008 Carbon Cycling and Biosequestration Report.
In 2013, BER solicited applications for omics-driven basic research in three areas focused on the contribution of prokaryotic and eukaryotic microbes and microbial communities to carbon cycling processes in terrestrial ecosystems:
Systems biology studies on regulatory and metabolic networks of microbes, microbial consortia, and microbe-plant interactions involved in biogeochemical cycling of carbon. Proposed studies should focus on systems biology research using model microbes or microbial consortia relevant to large-scale carbon cycling processes in terrestrial ecosystems. Model systems should be carefully chosen to facilitate development of metabolic and regulatory network models that ultimately could inform larger-scale biogeochemical models of microbial processes in the environment.
Development of omics approaches to investigate microbial community functional processes involved in carbon cycling in terrestrial ecosystems. Applications should address adapting genome-enabled techniques (e.g., metagenomics, metatranscriptomics, and metaproteomics) to interrogate relevant functional processes of microbes in terrestrial environments—either at field sites or using model micro- and mesocosms—and integrating resulting data into process understanding at the ecosystem scale. Applications are encouraged that target key microbially mediated carbon cycling processes in terrestrial systems to predict responses to shifts in temperature, carbon dioxide (CO₂) concentration, or other climate change variables.
Development of omics-enabled methods and technologies for imaging and analyzing microbially mediated carbon cycling processes in terrestrial ecosystems. New approaches are needed for high-resolution characterization of microbial community structure and function in soils and other terrestrial environments. Applications are encouraged that will enable in situ analysis of functional processes of microbial communities and characterization of physical and chemical microenvironments at interfaces between microbes and biotic or abiotic surfaces (e.g., plant roots and soil aggregates).
In addition to addressing these three focus areas, researchers also were encouraged to incorporate project elements aimed at developing data-driven systems biology applications in collaboration with the DOE Systems Biology Knowledgebase. Key points of emphasis in this area included building tools for integrating and visualizing omics data at the microbial community scale and developing methods that link dynamic regulatory and metabolic networks to higher-scale biogeochemical process understanding.
See the full listing of 2013 awards.
Related, complementary research is also being funded by DOE BER's Climate and Environmental Sciences Division (CESD), which focuses on a predictive, systems-level understanding of the fundamental science associated with climate change and DOE’s environmental challenges—both key to support the DOE mission.
For more information, contact Joe Graber, 301-903-1239.
In July 2009, BER solicited proposals for basic research on the contributions of microbes and microbial communities to carbon cycling processes in the following areas:
Systems-level studies on regulatory and metabolic networks of microbes and microbial consortia involved in biogeochemical cycling of carbon. Studies are focused on systems biology research using environmentally relevant model microbes or microbial consortia. Funded projects are examining the impacts of shifts in environmental variables—such as temperature, CO₂ concentration, and availability of water and nutrients—on microbial carbon processing. Investigators were asked to carefully model systems choose that would facilitate development of metabolic and regulatory network models that could ultimately inform larger-scale biogeochemical models of microbial processes in the environment. Interdisciplinary collaboration was encouraged to link laboratory studies of the chosen model system with environmentally relevant conditions.
Development of metatranscriptomic, metaproteomic, and other genome-enabled approaches to understand how shifts in environmental variables impact microbially mediated carbon cycling processes in terrestrial ecosystems. Research is focused on addressing the adaptation of genome-enabled techniques to the interrogation of terrestrial environments, either in situ or using model micro- or mesocosms. Funded projects are targeting key microbially mediated carbon cycling processes in terrestrial systems to predict responses to shifts in temperature, CO₂ concentration, and nutrient availability, among other things. Also encouraged were projects that use genome-enabled techniques to identify and predict the impact of potentially beneficial associations between plants and microbes or microbial communities (both prokaryotic and eukaryotic) on overall ecosystem productivity.
Development of methods and techniques for imaging and analyzing microbially mediated carbon cycling processes in terrestrial ecosystems. New approaches are needed for high-resolution characterization of microbial community structure and function in soils and other terrestrial environments. Research is focused on enabling in situ analysis of the functional processes of microbial communities and characterization of physical and chemical microenvironments at interfaces between microbes and biotic or abiotic surfaces (e.g., plant cells and soil aggregates).
See a full listing of the 2010 awards.
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