Download Energy Sources and Environmental Applications: Today, scientists

Energy Sources and Environmental Applications:
Today, scientists have in hand the complete DNA sequences of genomes for many organisms—from
microbes to plants to humans. The U.S. Department of Energy's Genomic Science program (formerly
Genomics:GTL) uses microbial and plant genomic data, high-throughput analytical technologies, and
modeling and simulation to develop a predictive understanding of biological systems behavior
relevant to solving energy and environmental challenges including bioenergy production,
environmental remediation, and climate stabilization. Learn More »
Biofuels
Alternative fuels from renewable cellulosic biomass are expected to
significantly reduce U.S. dependence on imported oil while enhancing national
energy security and decreasing the environmental impacts of energy use.
Developing a cost-effective, commercial-scale cellulosic biofuel industry will
require transformational biological research in feedstock development,
biomass deconstruction, and fuel synthesis. Learn More »
Knowledgebase
Driven by the ever-increasing wealth of data resulting from new generations of genomics-based technologies, systems biology is
demanding a computational environment for comparing and integrating large, heterogeneous datasets and using this information to
develop predictive models. To address this challenge, the Genomic Science program is developing the DOE Systems Biology
Knowledgebase. Learn More »
Carbon Cycling and Climate
The global carbon cycle plays a central role in regulating atmospheric carbon
dioxide levels and thus Earth’s climate, but our basic understanding of the
tightly interlinked biological processes driving the carbon cycle remains limited.
Advancing our knowledge of these processes is crucial to predicting potential
climate change impacts, assessing the viability of climate change adaptation
and mitigation strategies, and informing relevant policy decisions.Learn More »
DOE JGI Community Sequencing Program accepting letters of intent. Details athttp://1.usa.gov/JGI-CSP13
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Winter 2012 edition of JGI newsletter The Primer now available
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2012 Genomic Science Meeting was held February 26-29, 2012. Abstracts now available.
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National Laboratories and Universities Team up to Build a Community Systems Biology Knowledgebase. DOE
announced the selection of a collaboration of top scientists from across the Nation to lead development of a computer-based Systems
Biology Knowledgebase.
Citation and Credit
Unless otherwise noted, publications and webpages on this site were created for the U.S. Department of Energy Genomic Science program by Biological and Environmental
Research Information System (BERIS). Permission to use these documents is not needed, but credit the U.S. Department of Energy Genomic Science program and provide
the URL http://genomicscience.energy.gov. Materials provided by third parties are identified as such and not available for free use.
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Last modified: Tuesday, April 03, 2012
Microbial Genomics
at the U.S. Department of Energy
 Research Programs
 Sequencing Candidates
 Organisms & Progress
 Research Highlights
 DOE Publications
 Other Microbial Publications
 Web-Based Resources
 Links
Why Microbes?
 Benefits
 Landmark Discoveries
The U.S. Department of Energy (DOE) Office of Science supports innovative,
high-impact, peer-reviewed biological science to seek solutions to difficult
DOE mission challenges. These challenges include finding alternative sources
of energy, understanding biological carbon cycling as it relates to global
climate change, and cleaning up environmental wastes.
Through its (now-completed) Microbial Genome Program (MGP), the Genomic
Science Program (GSP), and the DOE Joint Genome Institute's
(JGI) Community Sequencing Program, DOE’s Office of Biological and
Environmental Research (BER) has sequenced hundreds of microbial genomes
and tens of microbial communities having specialized biological capabilities.
Identifying these genes will help investigators discern how gene activities in
whole living systems are orchestrated to solve myriad life challenges.
Why Microbes?
Microbes, which make up most of the earth’s biomass, have evolved for some
3.8 billion years. They have been found in virtually every environment,
surviving and thriving in extremes of heat, cold, radiation, pressure, salt,
acidity, and darkness. Often in these environments, no other forms of life are
found and the only nutrients come from inorganic matter. The diversity and
range of their environmental adaptations indicate that microbes long ago
“solved” many problems for which scientists are still actively seeking
solutions.
Potential Microbial Applications
Researchers have only scratched the surface of microbial biodiversity.
Knowledge about the enormous range of microbial capacities has broad and
far-reaching implications for environmental, energy, health, and industrial
applications.
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Cleanup of toxic-waste sites worldwide.
Production of novel therapeutic and preventive agents and
pathways.
Energy generation and development of renewable energy sources
(e.g., methane and hydrogen).
Production of chemical catalysts, reagents, and enzymes to
improve efficiency of industrial processes.
Management of environmental carbon dioxide, which is related to
climate change.
Detection of disease-causing organisms and monitoring of the
safety of food and water supplies.
Use of genetically altered bacteria as living sensors (biosensors) to
detect harmful chemicals in soil, air, or water.
Understanding of specialized systems used by microbial cells to live
in natural environments with other cells.
Last modified: Wednesday, July 21, 2010
Base URL: microbialgenomics.energy.gov
Site sponsored by the U.S. Department of Energy Office of
Science, Office of Biological and Environmental Research
Benefits of Microbial Genome Research
Imagine! A future in which we can
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use "super bugs" to detect chemical contamination in soil, air, and
water and clean up oil spills and chemicals in landfills;
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cook and heat with natural gas collected from a backyard septic
tank or bottled at a local waste-treatment facility;
obtain affordable alcohol-based fuels and solvents from cornstalks,
wood chips, and other plant by-products; and
produce new classes of antibiotics and process food and chemicals
more efficiently.
These scenarios represent only a few of the possible ways that microbes—the
invisible bacteria, archaea, protozoa, and fungi that inhabit our environment,
our bodies, our food and water, and even the air we breathe—can be
harnessed to serve humankind. Technological advances, particularly in genetic
research conducted as part of the international Human Genome Project, are
enabling researchers to learn about microbes at their most fundamental level
and to ask questions about how the basic parts work together to form a
functioning organism. The answers may challenge accepted scientific thought
and offer beneficial applications in areas important to DOE's Biological and
Environmental Research (BER) program, among them bioremediation, global
climate change, biotechnology, and energy production. BER's Microbial
Genome Program helped shape microbial research and lead to BER's Genomic
Science Program .
Why Microbes?
By some estimates, microbes make up about 60% of the earth's biomass, yet
less than 1% of microbial species have been identified. Because most do not
cause disease in humans, animals, or plants and are difficult to culture, they
have received little attention. Identifying and harnessing their unique
capabilities will offer us new solutions to longstanding challenges in
environmental and waste cleanup, energy production and use, medicine,
industrial processes, agriculture, and other areas. Scientists also are starting
to appreciate the role played by microbes in global climate processes, and we
can expect insights about both the biological underpinnings of climate change
and the contributions of microbes to earth's biosphere. Their capabilities soon
will be added to the list of traditional commercial uses for microbes in the
brewing, baking, dairy, and other industries.
A Vast and Genetically Rich Resource
Microbes and their communities make up the foundation of the biosphere and
sustain all life on earth. These single-celled organisms are masters at living in
almost every environment and harvesting energy in almost any form, from
solar radiation to photosynthesis-generated organic chemicals to minerals in
the deep subsurface.
Microbes have evolved over 3.5 billion years, transforming the atmosphere
with oxygen (a by-product of photosynthesis) more than a billion years ago to
create the environment for life as we know it. Some microbes can thrive in
either aerobic (with oxygen) or anaerobic (without oxygen) conditions.
Microbes also capture nitrogen from the atmosphere, make it available to
plants (and other life forms), and carry out processes responsible for soil
fertility. Most do not cause disease. The unique microbial biochemistries
amassed over eons in every niche on the planet now offer a deep and virtually
limitless resource of capabilities that can be applied to national needs,
including DOE energy and environmental missions.
Although immense, the microbial world remains largely unexplored, a frontier
of truly astronomical dimensions: The estimated nonillion or 1030 individual
bacteria on earth are 109 times more than the number of stars in the
universe. The vast majority, however, cannot be studied using standard
techniques. While 2000 to 3000 species are estimated to be present in a
single gram of soil, we can cultivate for study only some 0.1 to 1% of the
species in that or any other environment. About 5700 species have been
described thus far.
Investigators now are beginning to apply the tools of genomics to studying
this enormous untapped natural treasure. Because microbes have modestsized genomes (averaging 4 to 5 million bases compared with 3 billion bases
in the human and other mammalian genomes), they represent a tractable life
form we can use to explore and understand life processes at a whole-system
level. Already, limited environmental sampling of microbes and their
communities has led to the discovery of millions of previously unknown genes
and proteins, thousands of species, and innumerable variations in critical
functionalities. As scientists begin to scratch the surface of the microbial
world, they are finding analysis an enormous challenge.
Recent discoveries from projects funded by DOE's Biological and
Environmental Research program highlight the ubiquitous presence and
critical importance of microbes in all ecosystems. For example:
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The cyanobacteria Prochlorococcus andSynechococcus, along with
other ocean phytoplankton, account for about half of global
photosynthesis.
Diatoms, ancient and intricately shaped ocean microbes, store an
amount of carbon comparable to that in all the earth's rainforests
combined. Over geological time, diatoms may have influenced the
earth's climate.
More than a million previously undiscovered genes, possibly
representing new biochemical functions, were the surprising find in
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sequencing DNA fragments from the Sargasso Sea—a region
heretofore thought to sustain little life. This discovery also was
named one of Science magazine's "Breakthroughs of the Year."
Microbes thrive deep within the earth's subsurface and at extremes
previously thought to extinguish life. Growing recognition of
microbial capabilities and potential applications has made a
compelling case for further investigations by DOE and other
agencies and institutions.
Before we can harness their capabilities, microbes must be understood in far
greater detail and in the realistic context of whole living systems—whether as
individuals or communities of interacting microbes—rather than as isolated
components such as single genes and proteins. Microbes already can be
manipulated at the molecular, cellular, and system levels, but understanding
and taking advantage of their complexities and surmounting the technical
challenges of whole-systems biology is a daunting prospect.
Understanding Microbes and Their Communities
Most microbes live in highly organized and interactive communities that are
versatile, complex, and difficult to analyze from many perspectives. Some of
these challenges are outlined below.
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Microbes are exceedingly small—only 1/8000th the volume of a
human cell and spanning about 1/100th the diameter of a human
hair. Investigating processes within this size range is challenging.
The microbial world encompasses millions of genes from thousands
of species, with hundreds of thousands of proteins and
multimolecular machines operating in a web of hundreds of
interacting processes in response to numerous physical and
chemical environmental variables. Gene control is complex, with
groups or "cassettes" of genes (operons) directing coordinated
transcription and translation of genes into interacting proteins.
Microbes adapt rapidly in response to environmental change, an
ability that underlies their survival for billions of years. For
example, various species of "extremophile" microbes have adapted
to great extremes of pressure, temperature, pH, salinity, and
radiation. Their high surface-to-volume ratio enhances interactions
and supports adaptation. Unlike animal cells, they have no
protective nucleus for their DNA, which leaves it more vulnerable to
alteration. Genes move easily among species. Moreover, microbial
communities are awash in genetic material from viruses that confer
additional genetic properties and expand their range of
adaptability.
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Microbial communities can extend in size from cubic millimeters (or
smaller) to cubic kilometers. Even relatively simple communities
can have millions of genes, giving them a genetic diversity
substantially greater than that of higher life forms, even humans.
Recent investigations have focused on collecting DNA fragments
from environmental samples in the sea and other natural
ecosystems. These "metagenomics" studies have given us a
glimpse into the intricacies of these natural ecosystems and their
diverse functions.
See also
The Microbial World: A Challenging Frontier (2005) extracted from the DOE
Genomics:GTL Roadmap, this 8-page section focuses on the vast and
genetically rich resource of the microbes.
Last modified: Wednesday, July 21, 2010
Base URL: microbialgenomics.energy.gov
Site sponsored by the U.S. Department of Energy Office of
Science, Office of Biological and Environmental Research