Table 2. Science Roadmaps for Natural Systems: Relationship to Science Milestones and Facilities

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Table 2. Science Roadmaps for Natural Systems:
Relationship to Science Milestones and Technologies

Progression of GTL Science Milestones and Technologies	Conceptual Science Roadmaps for Natural Systems
Oceans: Photosynthetically Driven Biological Pumps for Carbon and Energy in Aquatic Systems	Terrestrial: Microbes in Ecological Communities, Carbon and Nutrient Cycles	Deep Subsurface: Microbial Community Processes for Mitigation of Toxic Chemicals and Metals
Milestone 1: Determine the Genome Structure and Potential of Microbes and Microbial Communities Production and Characterization of Proteins and Molecular Tags Characterization and Imaging of Molecular Machines	Single-cell and environmental community sequence Heterotrophs, autotrophs, viruses, and "twilight zone" organisms Comparative analyses of rhodopsin, hydrogenase genomes Gene synthesis and manipulation	Single-cell and community sequence in situ and in vitro Organisms related to processes in soils Genome annotation	Single-cell and community sequence in situ and in vitro to identify members, functions Superannotation, genome plasticity effects Metagenomics, gene transfer Tags to ID microbes, proteins, metabolites
Milestone 2: Develop a Systems-Level Understanding of Microbial and Community Function and Regulation Whole Proteome Analysis Analysis and Modeling of Cellular Systems	Photosynthesis, transporters, biomineralization Proteins, machines, metabolites, and functional assays Systems responses Imaging	All GHGs: CO₂, methane, nitrous oxide, dimethyl sulfide Molecular inventories vs cues Systems interactions with soil, rhizosphere, plants: Inputs and outputs (e.g., stable isotope probes) Proteome and metabolome imaging at cellular and community levels	Community structure and relationship to function Pathways and networks: Mechanisms of intercellular communication and function Stoichiometry and kinetics of intercellular fluxes
Milestone 3: Develop the Knowledgebase, Computational Methods, and Capabilities to Advance Understanding of Complex Biological Systems and Predict Their Behavior GTL integrated computational environment for biology	Modeling of climate-based and mitigational perturbations Individual and multiple life-scale models (cellular, community, ecosystem): Metabolic budgets Multiple photosynthetic processes	Modeling of microbial responses to manipulation of plant inputs into carbon cycle Human inputs directed to soils Response to environmental change understood	Four-dimensional reactive transport models based on genomic, geochemical, and hydrological data Scaling of processes through molecular, cellular, community, and environmental levels; and molecular to long time scales
Missions Outputs Measure environmental responses via sensors	Ecogenomics of sentinel organisms Cellular, community, and ecosystem biochemical assays Accompanying environmental assays	Biomarkers: RNAs, proteins, metabolites, signaling Ecogenomics, functional assays, environmental conditions Carbon and nutrient inventories	Biology and geochemistry: DNA, RNA, proteins, metabolites, geochemical from single-cell to field scales Mesoscale simulation of field conditions Regulatory levels of contaminants
Robust Science Base for Policy and Engineering	Natural behaviors of ocean ecosystems, impact on and of climate change scenarios incorporated into IA models Assessment of efficacy and impacts of intervention strategies	Biological processes for carbon and nitrogen cycling, impact on and of climate change scenarios incorporated into IA models Assessment of potential and strategy for terrestrial carbon sequestration	Predictions of transport and fate Assessment of need for remediation Remediation strategies, designs, and tests

Progression of GTL Science Milestones and Technologies

Conceptual Science Roadmaps for Natural Systems

Oceans: Photosynthetically Driven Biological Pumps for Carbon and Energy in Aquatic Systems

Terrestrial: Microbes in Ecological Communities,
Carbon and Nutrient Cycles

Deep Subsurface: Microbial Community Processes for Mitigation of Toxic
Chemicals and Metals

Milestone 1: Determine the Genome Structure and Potential of Microbes and Microbial Communities

Production and Characterization of Proteins and Molecular Tags

Characterization and Imaging of Molecular Machines

Single-cell and environmental community sequence

Heterotrophs, autotrophs, viruses, and "twilight zone" organisms

Comparative analyses of rhodopsin, hydrogenase genomes

Gene synthesis and manipulation

Single-cell and community sequence in situ and in vitro

Organisms related to processes in soils

Genome annotation

Single-cell and community sequence in situ and in vitro to identify members, functions

Superannotation, genome plasticity effects

Metagenomics, gene transfer

Tags to ID microbes, proteins, metabolites

Milestone 2: Develop a Systems-Level Understanding of Microbial and Community Function and Regulation

Whole Proteome Analysis

Analysis and Modeling of Cellular Systems

Photosynthesis, transporters, biomineralization

Proteins, machines, metabolites, and functional assays

Systems responses

Imaging

All GHGs: CO₂, methane, nitrous oxide, dimethyl sulfide

Molecular inventories vs cues

Systems interactions with soil, rhizosphere, plants: Inputs and outputs (e.g., stable isotope probes)

Proteome and metabolome imaging at cellular and community levels

Community structure and relationship to function

Pathways and networks: Mechanisms of intercellular communication and function

Stoichiometry and kinetics of intercellular fluxes

Milestone 3: Develop the Knowledgebase, Computational Methods, and Capabilities to Advance Understanding of Complex Biological Systems and Predict Their Behavior

GTL integrated computational environment for biology

Modeling of climate-based and mitigational perturbations

Individual and multiple life-scale models (cellular, community, ecosystem): Metabolic budgets

Multiple photosynthetic processes

Modeling of microbial responses to manipulation of plant inputs into carbon cycle

Human inputs directed to soils

Response to environmental change understood

Four-dimensional reactive transport models based on genomic, geochemical, and hydrological data

Scaling of processes through molecular, cellular, community, and environmental levels; and molecular to long time scales

Missions Outputs

Measure environmental responses via sensors

Ecogenomics of sentinel organisms

Cellular, community, and ecosystem biochemical assays

Accompanying environmental assays

Biomarkers: RNAs, proteins, metabolites, signaling

Ecogenomics, functional assays, environmental conditions

Carbon and nutrient inventories

Biology and geochemistry: DNA, RNA, proteins, metabolites, geochemical from single-cell to field scales

Mesoscale simulation of field conditions

Regulatory levels of contaminants

Robust Science Base for Policy and Engineering

Natural behaviors of ocean ecosystems, impact on and of climate change scenarios incorporated into IA models

Assessment of efficacy and impacts of intervention strategies

Biological processes for carbon and nitrogen cycling, impact on and of climate change scenarios incorporated into IA models

Assessment of potential and strategy for terrestrial carbon sequestration

Predictions of transport and fate

Assessment of need for remediation

Remediation strategies, designs, and tests

U.S. Department of Energy Office of Science

Genomics:GTL

Table 2. Science Roadmaps for Natural Systems:
Relationship to Science Milestones and Technologies

	Human Genome Project Information Genomics:GTL DOE Microbial Genomics home

U.S. Department of Energy Office of Science

Genomics:GTL

Table 2. Science Roadmaps for Natural Systems: Relationship to Science Milestones and Technologies

Table 2. Science Roadmaps for Natural Systems:
Relationship to Science Milestones and Technologies