Genomics:GTL

Carbon Cycling and Sequestration continued

Microbial Ocean Communities

Photosynthetic Capabilities

Microbial communities living near the surface layers of oceans are the primary photosynthetic organisms driving the biological pump. Absorbing CO₂ and sunlight to produce most oceanic organic materials, the organisms make up the foundation of the marine food chain. Photosynthesis of such phytoplankton as diatoms, dinoflagellates, and cyanobacteria converts about as much atmospheric carbon to organic carbon in the ocean as plant photosynthesis does on land. Large variations in phytoplankton abundance, therefore, can greatly impact the oceans’ ability to take up atmospheric carbon.

Oceans currently have a net absorption of about 2 Gt of carbon per year, offsetting about 30% of carbon emitted to the atmosphere by the burning of fossil fuels. Understanding the interactions and dynamics underlying this natural CO₂ sink is necessary to explain past shifts in global climate and to predict future environmental changes. Microbes drive these processes by converting atmospheric CO₂ into organic matter, some of which remains in the oceans (see sidebar, Carbon Cycling in the Oceans).

Dominant organisms in surface waters include such cyanobacteria as Synechococcus species and Prochlorococcus marinus, which capture CO₂ and light to carry out photosynthesis. Prochlorococci now are thought to be the most abundant photosynthetic organisms on earth. Eukaryotic diatoms such as the recently sequenced Thalassiosira pseudonana also live in surface waters and convert CO₂ and other nutrients into hard silicates. This process carries organically complexed carbon to ocean depths, thus converting its relatively rapid cycling in surface waters (where it is returned to the atmosphere) to a considerably slower one in ocean sediments.

Strategies for Increasing Ocean CO₂ Pools

Ocean carbon-sequestration strategies aim to increase the deep-ocean inventory of CO₂. Two approaches typically are considered: Direct injection of a CO₂ stream into the ocean interior depths and iron fertilization to enhance photosynthesis by phytoplankton in the biological pump and thus increase carbon uptake. The potential effectiveness and adverse impacts must be evaluated for both approaches. According to the Climate Change Technology Program (CCTP) strategic plan, due for publication in 2005: “A research portfolio is required that seeks to determine, via experimentation and computer simulations, the ability of the world’s oceans to effectively store anthropogenic CO₂ without negative environmental consequences” [CCTP, www.climatetechnology.gov].

DOE has sponsored genomic sequencing of several of these organisms. Additionally, recent GTL-sponsored metagenomic approaches have involved researchers sequencing DNA fragments isolated from samples taken from ocean (and terrestrial) environments. These studies have for the first time allowed direct insights into the makeup and functionality of these natural systems, revealing an amazing diversity. Analyses from Sargasso Sea samples, for example, turned up more than a million previously unknown genes, including almost 800 rhodopsins (the light-absorbing antennae of microbes essential for photosynthesis) (Venter et al. 2004). Metagenomic studies of soil samples show an even greater amount of genetic material (Riesenfeld, Schloss, and Handelsman 2004). Results suggest that microbial communities have an extraordinarily wide range of mechanisms and pathways that could offer new applications to meet DOE carbon-management missions.

GTL will use these data as starting points for explorations into molecular processes underlying microbial photosynthesis. The goal is to ascertain fundamental principles of photosynthetic systems’ molecular design. These principles will reveal the dynamics of carbon-assimilation pathways and those that degrade organic matter and ultimately either sequester carbon or return it to the atmosphere.

GTL research will enable us to begin identifying critical organisms and their capabilities and responses to stress. These data will provide the foundation for developing biological rate constants that can be incorporated into detailed models of carbon cycling. When these models are extended to the global ecosystem, the potential impact of carbon-cycle perturbations on climate-change models can be assessed. Ultimately, this knowledge will guide decisions about acceptable levels of change and hence acceptable atmospheric levels of GHGs.

In addition to elucidating carbon-cycling nuances, such detailed biological data can lead to the development of increasingly sophisticated microsensors that can detect changes in the levels of biomolecules (DNA, RNA, proteins, metabolites) and serve as indicators of microbial-community response to environmental stressors (see sidebar, Ocean Monitors).

GTL’s Vision for Ocean Systems

The GTL Knowledgebase ultimately will provide in silico models of microbial systems in oceans, with supporting data and experimental capabilities that can be used to inform policies and develop methods and applications relevant to DOE missions in carbon management.

Gaps in Scientific Understanding

Understanding carbon cycling and sequestration requires knowledge about the underlying mechanisms controlling microbiological systems. Investigations will include defining key players and their roles; determining how systems change as a function of climate, CO₂, nutrients, and biogeochemical cycles; and enabling predictions of atmospheric CO₂ and climate impacts on marine communities over time. Specifically, these analyses will enable us to begin exploring the following types of questions:

• What happens to carbon in the oceans, and how is it portioned among various life forms?
• How does this portioning vary in rate as a function of location, depth, salinity, nutrient availability, temperature, proximity to population centers and coastlines, currents, and seasons?
• How far do carbon and carbon dioxide migrate from their “points of entry” into the ocean, and what impacts their travel and processing?
• What are the elements of the biological pump?
• What happens to growth rates of phytoplankton as a function of carbon entry into the oceans in light of the variables noted above?
• What would happen to carbon absorption if growth rates for phytoplankton were altered either up or down?
• What are the dynamic community structures of ocean microbes, and how do they impact carbon processing?
• How reversible would be the effects of actions that we might take to alter ocean carbon sequestration (and on what time scales)?

Scientific and Technological Capabilities Required

Defining communities and their genomic potential will require capabilities for rapid and accurate sequencing of single cells, key organisms, and environmental communities. Also needed are methods to perform comparative genomic analyses and capabilities for gene synthesis and manipulation. Specific needs include the following:

• Metagenomic approaches to aid in sifting through millions of genes and determining which proteins are produced by ocean communities and when.
• Capacity to make and study the proteins determined by the ocean’s metagenome to understand ocean microbial functionality and processes. Because these microbes are essentially unculturable, protein analysis initially will be achieved only by synthesis directly from genome sequence. A high-throughput approach would permit simultaneous, highly parallel production and characterization tests on hundreds of thousands of proteins.
• Molecular tags (or affinity reagents) for proteins with established critical roles to use as probes for determining the structure and function of natural ocean ecosystems.
• New sampling and analysis tools to investigate the natural dynamics of relationships among microbial, biogeochemical, and physical processes.
• Technologies to measure environmental responses, including ecogenomic sensors of sentinel organisms; biochemical assays of cells, communities, and ecosystems; and environmental assays.
• Detailed studies of proteins, multimolecular machines, and metabolites to aid in understanding key microbial responses in terms of photosynthesis, transporters, and biomineralization processes; development of functional assays and technologies, including imaging, to measure system responses.
• Information on microbial mechanistic behaviors (cellular, community, ecosystem) for incorporation into more-accurate climate models.
• Database of genes, pathways, microbes, and communities to explore the structure and function of ocean ecosystems, and, in particular, the roles of ocean microbes in carbon processing and their impact on global climate processes.

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.