Researchers discover 1.2 million new genes in Sargasso Sea microbes

Department of Energy-funded researchers at the Institute for Biological Energy Alternatives (IBEA) have sequenced microbes in the Sargasso Sea and have discovered at least 1,800 new species and more than 1.2 million new genes. The results will be published in the journal Science. IBEA researchers’ discoveries include 782 new rhodopsin-like photoreceptor genes (only a few dozen have been characterized in microorganisms to date).

“What excites the Department and our Office of Science about this project is its range of potential benefits,” Secretary of Energy Spencer Abraham said. “Scientists have used DOE funds to determine the genetic sequences of all the microorganisms occurring in a natural microbial community, which may lead to the development of new methods for carbon sequestration or alternative energy production. This will offer a direct and early test of one of the central tenets of DOE’s Genomics: GTL program – that microbes can be used to develop innovative solutions to address national energy needs.”

DOE’s Office of Science has awarded $12 million to IBEA since 2001 for microbial genomics research. DOE funds IBEA as part of its Genomics: GTL program that includes over 70 research projects to universities, national laboratories and private companies. Dr. Venter’s research team at IBEA is addressing three scientific challenges: research on photosynthesis and hydrogen production to determine if the efficiency, and thus the utility, of these natural microbial processes can be greatly improved; strategies to create a synthetic minimal genome that may speed our ability to develop biology-based solutions for some of our most pressing energy and environmental challenges; and environmental genomics research that uses genomics approaches to discover new microbial capabilities that can be used to address DOE energy and environmental needs.

Obtaining the DNA sequence of the entire human genome, along with those of scores of microbes and other organisms, stands as one of the greatest achievements of the 20th century. Yet these complete genome sequences, the “recipes for life,” serve merely as a foundation for the biology of the 21st century, the departure point for an effort aimed at the most far reaching of all biological goals: to achieve a better understanding of life. The Genomics: GTL program within DOE’s Office of Science is an important part of this effort. The program aims to develop the knowledge base and the national infrastructure for systems biology — both experimental and computational — needed to achieve this understanding.

The enormous amount of data to be collected by Genomics: GTL researchers dwarfs the data collected in the Human Genome Project. However, no amount of additional information will in itself yield the understanding sought. There remains a second, much deeper and complex challenge, that of deriving underlying theoretical and mathematical principles for biology and the development of sophisticated computer simulation and modeling tools to understand biological systems. Thus, the Genomics: GTL program will also depend on the department’s leadership in high performance computing to build the computational infrastructure needed for the new biology of Genomics: GTL.

While we know that the individual cells in a complex organism, like a plant or a human, work together to give those organisms life, even the simplest microbes often work together in complex microbial communities to perform their many functions including those of interest to DOE. Thus, a key component of Genomics: GTL is environmental genomics where researchers will characterize at the molecular level the functions of complex microbial communities in their natural environments.

As part of their contribution to the Genomics: GTL program, IBEA scientists determined the genetic sequences of all the microorganisms occurring in a natural microbial community. Microbes are prevalent in the environment — there can be many thousands of different organisms in a teaspoon of soil or water — but the Sargasso Sea was thought to be an environment with a manageable number of microbes.

IBEA, a nonprofit scientific research institution located in Rockville, Md., is seeking ways to use biology and genetics to reduce the amount of carbon dioxide that is released into the atmosphere by current sources of energy such as petroleum and coal. It also will seek to produce clean fuels.