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Scientists map the complete genome of an important agricultural bacterium

Peer-Reviewed Publication

Stanford University

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An international research team has decoded the genome of an important microbe that provides an essential source of nitrogen for plants, people and other living organisms on Earth. Researchers say that the new genome map could provide the foundation for improving crop yields, while reducing the use of nitrogen-based fertilizers by farmers.

Scientists from Stanford and seven European and Canadian institutions began sequencing the DNA of the bacterium, Sinorhizobium meliloti, in 1998. Their results – a complete map of the S. meliloti genome – appear in the July 27 issue of the journal Science.

S. meliloti is one of several bacterial species with the remarkable ability to transform atmospheric nitrogen into other chemicals – a process called nitrogen fixation. All living things need nitrogen – a basic ingredient of proteins, DNA and other organic molecules. But obtaining usable nitrogen from nature is a complicated process, despite its abundance: Nearly 80 percent of the atmosphere consists of nitrogen gas, which – unlike oxygen – cannot be absorbed by most living organisms. Nitrogen-fixing bacteria in the ground chemically convert atmospheric nitrogen into ammonia – a nitrogen-based compound that plants can use to produce proteins. Animals and people, in turn, obtain nitrogen by consuming protein from plants and herbivorous animals.

"Nitrogen fixation is essential to life on Earth. Without it, there would be no proteins, for example," says Sharon R. Long, the William C. Steere, Jr. – Pfizer Inc. Professor of Biological Sciences at Stanford and a lead co-author of the Science study.

"All nitrogen fixation is carried out by bacteria," she adds. "The specific attraction of studying the S. meliloti bacterium is the symbiosis."

S. meliloti is one of several symbiotic nitrogen-fixing bacteria known as Rhizobia that live in the roots of legumes – a major plant family that includes peas, beans, soybeans, peanuts, alfalfa and clover.

S. meliloti has a symbiotic relationship with alfalfa -- an important commercial crop grown throughout the world. Alfalfa roots send out chemical signals that attract S. meliloti in the soil. The bacteria respond by infecting the plant, causing its roots to develop swellings or nodules.

Each nodule consists of specialized plant cells that allow S. meliloti to thrive in a mutually beneficial relationship: The bacteria supply the alfalfa plant with nitrogen in the form of ammonia, and the alfalfa provides the bacteria with sugar and other essential nutrients. Because S. meliloti has been extensively studied through biochemistry and genetics, its complete genome sequence is expected to have a major impact in the field of symbiosis research.

Unusual genome

Although similar in function to other symbiotic bacteria, S. meliloti has a "very unusual genome," according to Long. "It breaks all the rules of bacteria," she notes. "The old view of a bacterium carrying a single, main circular chromosome has been changed. S. meliloti actually has three huge circular genetic elements, and this raises interesting questions about gene inheritance and function."

The mapping of S. meliloti’s main chromosome was conducted by a consortium of six European research institutions funded by the European Union and headed by French researcher Francis Galibert, a lead co-author of the Science study. A second genetic element – called pSymB – was mapped by a research team headed by Science lead co-authors Turlough M. Finan of Canada’s McMaster University and Alfred Pühler of the University of Bielefeld in Germany.

Long and her colleagues at Stanford mapped the third strand of DNA known as pSymA, which carries the nitrogen-fixing genes S. meliloti needs for symbiosis with alfalfa.

"There may also be genes in pSymA that provide antibiotic resistance to S. meliloti or help it survive in different soil conditions," notes Melanie J. Barnett, a life sciences research assistant in Long’s lab and co-author of the Science study.

Barnett coordinated the pSymA sequencing effort, in collaboration with Nancy Federspiel, Caridad Komp and Ted Jones from the Stanford Genome Technology Center (SGTC). "It took less than a year to sequence pSymA," says Long. "Purifying the DNA was the most time-consuming part of the effort."

Sustainable agriculture

Long and her colleagues say that the map of the S. meliloti genome will serve as a model for understanding other symbiotic bacterial species. "Many important plants, in agriculture and in natural ecosystems, are legumes," Long observes, "and many of them are infected by specific Rhizobia that carry out nitrogen fixation."

Improved understanding of Rhizobia-legume symbiosis has implications for sustainable agriculture, write the authors of the Science study, noting that it is the scarcity of usable nitrogen that frequently limits plant growth. To improve crop yields, farmers around the world use tons of nitrogen-rich fertilizer every year. But manufacturing fertilizer requires burning large amounts of coal and other fossil fuels, which contribute to the buildup of carbon dioxide in the atmosphere.

"Fertilizers also produce runoff that ends up in lakes and streams, causing other environmental problems," notes Long.

A more sustainable approach to agriculture includes inoculating legume seeds with the appropriate nitrogen-fixing bacteria before planting, along with crop rotation in which clover and other legumes are planted and plowed under in alternate years to improve the nitrogen content of the soil.

Another alternative to fertilization is to breed peas, beans and other legumes that can produce large yields in nitrogen-poor soils. "We can improve symbiotic plants by breeding more efficient, stable and ecologically versatile crops," Long maintains. "Knowing the sequence of the S. meliloti genome is going to give us the opportunity to understand symbiosis in far more precise detail than before."

Long points out that having a map of the S. meliloti genome could help scientists solve several fundamental mysteries about symbiotic plants and bacteria:

* How does the bacterium stimulate the growth of root nodules?

* How does it invade the plant without triggering host defenses?

* Why does the microbe produce nitrogen for the host rather than for itself?

"I began working on this bacterium in 1979, and the field is completely transformed now," Long concludes. "The S. meliloti genome map marks the beginning of a new era."

In addition to her Stanford professorship, Long is an investigator with the Howard Hughes Medical Institute. In September, she will become dean of the School of Humanities and Sciences – the largest of Stanford’s seven schools.


Other Stanford co-authors of the Science study are Ronald W. Davis, professor of biochemistry and director of SGTC; Leah Bowser and Andrea Hong, who recently received their undergraduate degrees; Robert F. Fisher, senior research associate; Richard W. Hyman, Lucas Huizar, Raymond Surzycki, Pia Abola, Sue Kalman, Mani Gurjal and Curtis Palm of SGTC; postdoctoral fellows David Keating and Kuo-Chen Yeh; and graduate students Melicent C. Peck and Derek H. Wells. Stanford alumnus Michael L. Kahn, now a professor at Washington State University, also contributed to the study.

COMMENT: Sharon R. Long, Department of Biological Sciences 650-723-3232;

EDITORS: "The Composite Genome of the Legume Symbiont Sinorhizobium meliloti" appears in the July 27 issue of Science magazine. Photographs are available at (slug: "Microbe 1-5.jpg"). A related study in the Proceedings of the National Academy of Sciences is available for reporters online. For more information on the PNAS study, contact Craig Hicks or Chris Dobbins at or call 202-334-2138.

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