Benefits of Microbial Genome Research
Imagine! A future in which we can
- use "super bugs" to detect chemical contamination in soil, air, and water and clean up oil spills and chemicals in landfills;
- 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 modest-sized 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:
- The cyanobacteria Prochlorococcus and Synechococcus, 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 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.
- 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.
- 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.
