Genomics:GTL

Carbon Cycling and Sequestration continued

Terrestrial Microbial Communities

Influence on Plant Growth

Terrestrial ecosystems absorb CO₂ directly from the atmosphere, mainly via plant photosynthesis. The carbon is stored in plant biomass and soil organic matter or respired back to the atmosphere. Terrestrial ecosystems can help reduce concentrations of CO₂ in the atmosphere by increasing carbon stores in biomass, soils, and wood products.

Some microbial populations influence carbon storage in plants by enhancing their growth through interactions with organic compounds around the root (the rhizosphere), by providing nutrients such as phosphorous and nitrogen, or by suppressing plant pathogens in the soil. Other microbial communities exert neutral or even harmful effects. A better understanding is needed of the molecular mechanisms that enable microbes to colonize root surfaces, interact with organic compounds in the rhizosphere, and cooperate with other organisms.

Microbes impact carbon storage in soils by transforming carbon in decaying plants into other forms of organic matter, with varying degrees of recalcitrance. Soils thus are a complex mixture of compounds having different residence times, with more-stable compounds being the most important for carbon sequestration because their turnover times can be hundreds to thousands of years. Soils contain about 75% of the carbon in the terrestrial ecosystem, and knowing more about the microbial processes taking place there will lead to a better understanding of long-term carbon storage in soils.

Carbon dioxide is emitted from soils through soil respiration, a result of the metabolic activity of plant roots and soil microbes decomposing plant material and soil organic matter. Most plant material entering the soil is respired relatively quickly as CO₂; a small fraction becomes humus, which remains in soils for a longer time. Soil respiration is a major component of the global carbon cycle, returning nearly 10 times as much CO₂ to the atmosphere as emissions from fossil-fuel combustion (Rosenberg, Metting, and Izaurralde 2004). The shift in the ability of microbes to respire carbon to the atmosphere during environmental stresses such as climate change (e.g., more carbon is released by decomposition when stress causes plants to die) is a serious complicating factor in determining the permanency of these pools for sequestration. Physical influences such as agricultural tillage practices and fire contribute greatly to the amount of carbon released to the atmosphere from soils. As we understand microbial species and specific processes that create recalcitrant forms of carbon and those that metabolize carbon rapidly to carbon dioxide, we can manage terrestrial ecosystems in better ways, including low-till and no-till agriculture.

Strategies for Increasing Stable Carbon Inventories

Gaining a fundamental understanding of biological mechanisms of carbon cycling and sequestration in an ecological context can help us understand and predict effects of climatic change on key ecological processes. Genomics and, even more so, proteomics and metabolomics will become valuable tools for developing a biological systems understanding and reducing uncertainty about effects of future (potential) climate changes on the terrestrial biosphere’s structure and function. They also will be useful for increasing the likelihood of successful human responses to such climate-change contributors as carbon sequestration and ecosystem management (see sidebar, Integrated Assessment Program).

Augmenting natural microbial activities may be a promising option to optimize the inventories of stable carbon forms. DOE has sponsored successful field experiments that remove uranium from contaminated groundwater by stimulating the growth of particular microbial communities known to precipitate (and immobilize) that contaminant. We also can envision potentially altering some plants (notably cellulosic energy crops needed to produce bioethanol) in ways that stimulate them to produce larger fractions of more-recalcitrant organic matter that would lead to increased carbon sequestration in the terrestrial biosphere (see sidebar, Poplar Tree Offers Potential for Greater Carbon Storage). An added benefit could be improved soil quality because of increased carbon. Natural carbon fluxes are large, so even small forced changes resulting from sequestration strategies can be very significant.

Terrestrial Systems Vision

GTL science will generate the knowledge to incorporate, for the first time, models describing the global ecosystem into climate models to provide foundations for a more robust science base for policy and engineering. It also will enable evaluation of potential biology-based strategies for terrestrial carbon sequestration. The national goal is to develop these policies and strategies substantially over the coming decade.

Carbon Cycling and Sequestration Challenges, Scale, and Complexity

Research and Analytical Challenges

Scale and Complexity

Analysis of ocean and terrestrial microbial-community makeup and genomic potential Analysis of carbon and other cycling processes Photosynthesis and respiration in oceans Storage and decomposition in soil: microbial, fungal, and plant communities Modeling and simulation of microbe biogeochemical systems

Thousands of samples from different sites, consisting of millions of genes, thousands of unique species and functions Functional analysis of enzymes involved-potentially tens of thousands; hundreds of regulatory processes and interactions; spatially resolved community formation, structure, and function Models at the molecular, cellular, and community levels incorporating signaling, sensing, metabolism, transport, biofilm, and other phenomenology into macroecosystem models

 

Gaps in Scientific Understanding

Understanding the global ecosystem and its climatic effects requires learning about key microbial processes involved in carbon and nitrogen cycling, maintaining soil fertility, and increasing soil carbon content. Understanding how microbes and their ecosystems respond to a variety of environmental factors will allow for more accurate assessments and predictions of carbon inventories in terrestrial systems and their impacts on climate change to enable more-effective strategies to manage these inventories.

As part of a broader science base for understanding effects of climatic change on terrestrial ecosystems, GTL systems biology will support studies on interactions among terrestrial ecosystems and on changes in atmospheric composition and the climate system. In particular, advanced hardware and software capable of rapidly sequencing genomes will provide the foundation for performing systems biology analyses and quantifying climate effects on key protein functions to understand the following:

• How do microbes contribute to carbon transformation in soils, and what is their potential for sequestering meaningful amounts of carbon (gigatons per year) in more stable forms? This knowledge will provide decision makers, including the public, with information on designing and evaluating options for responses to potential climatic effects of future carbon-based energy production.
• How do microbial genomes adjust mechanistically to climate change? This understanding will allow more realistic prediction of future climate-change effects (or explain effects of recent climate change) on the structure and functioning of ecosystems.
• What is the genomic-mechanistic basis for biological feedbacks to the climatic system brought about through the terrestrial carbon cycle? The potential exists for significant releases of CO₂ or CH₄ to the atmosphere in response to rising temperatures and changes in precipitation.
• With a “simple” understanding of the underlying biology of ecosystems, how can we develop a modeling framework to put systems biology information into a usable context for predicting feedbacks to climate and atmospheric CO₂?

Scientific and Technological Capabilities Required

Defining communities and their collective genetic functional potential requires both single-cell and community sequencing (in situ and in vitro), systems biology studies, and the ability to relate microbial activities to soil processes. Capabilities to accomplish these goals include:

• Methods to understand processes by which carbon is transformed into long-lived forms and to design technical and management strategies for enhancing advantageous processes and mitigating negative responses.
• Methods to measure biomolecular inventories correlated with environmental conditions; characterizations of microbial-system interactions with soils, rhizosphere, and plants; and imaging of microbial functional activities (e.g., proteomes and metabolomes) at cellular and community levels—all to understand processes that impact production of GHGs (CO₂, methane, nitrous oxide, and dimethyl sulfide).
• Methods to detect and measure microbial responses to manipulation of plant inputs to the carbon cycle, to human inputs to soils, and to other environmental changes.
• Methods to use microbes as sentinels of climate-induced change in the environment. Research will determine the biomarkers that correlate with specific environmental parameters. Biomarker signatures include combinations of RNAs, proteins, metabolites, and signaling elements; community genomic makeup brought about by population shifts; and functional assays (Tringe et al. 2005).

Text adapted from Genomics:GTL Roadmap: Systems Biology for Energy and Environment, U.S. Department of Energy Office of Science, August 2005. DOE/SC-0090.