Microbe's Genome Reveals Insights Into Ocean Ecology

Unexpected findings about the genetic makeup of a marine microbe have given scientists a new perspective on how bacteria make a living in the ocean - a view that may prove useful in wider studies of marine ecology. The analysis by TIGR and collaborators of the DNA sequence of Silicibacter pomeroyi found that the metabolic strategies of marine bacterioplankton are more diverse and less conventional than previously thought.

December 15, 2004

Rockville, MD - Unexpected findings about the genetic makeup of a marine microbe have given scientists a new perspective on how bacteria make a living in the ocean - a view that may prove useful in wider studies of marine ecology.

By deciphering and analyzing the DNA sequence of Silicibacter pomeroyi, a member of an important group of marine bacteria, scientists found that the metabolic strategies of marine bacterioplankton are more diverse and less conventional than previously thought.

In one surprise, the study found that S. pomeroyi has the genetic tools to enable it to use inorganic compounds (such as inorganic sulfur) for energy, which allows the microbes to use organic carbon more efficiently in low-nutrient ocean environments.

Analysis of the genome sequence also showed that the microbe has adapted in ways that allow it to take advantage of so-called ocean "hot spots" - microscopic areas of the ocean that are rich in organic matter, typically related to living and dead microbial cells.

The study, which appears in the December 16 issue of Nature, was led by scientists at The Institute for Genomic Research (TIGR) and the Department of Marine Sciences at the University of Georgia (UGA), along with several collaborators. The project was sponsored by the National Science Foundation.

S. pomeroyi is a member of an important group of marine microbes, the Roseobacter clade, found in both coastal and open oceans. Those bacteria account for an estimated 15 percent of the production of new microbial cells in the ocean.

The S. pomeroyi genome offers the first real glimpse at the genetic material harbored by the Roseobacter group of bacteria, which have evolved metabolic strategies that allow them to flourish in marine environments. While scientists knew from laboratory studies that the microbe would metabolize sulfur, the genome sequence offered several surprises about how bacteria make a living in the ocean.

One unexpected finding from the genomic analysis was evidence of "lithoheterotrophy," the ability of marine bacteria that typically rely on organic carbon fixed by primary producers as their source of cell material to also use inorganic compounds (in this case, carbon monoxide and sulfur) for energy. In that way, the microbes can save more of the organic compounds for biosynthetic processes - allowing more efficient use of organic carbon in an environment that has little to go around.

"The microbe's predicted ability to use such inorganic compounds was surprising," says TIGR's Naomi Ward. "This study demonstrates how genome analysis allows us to propose new hypotheses of biological activity for a well-studied organism. We were able to test and confirm some of those hypotheses in the lab, providing more evidence for this lithohetrotropic strategy."

Another significant finding was that S. pomeroyi has numerous adaptations to living in association with ocean particles, so that it can take advantage of marine "hot spots," which feature rich areas of organic matter floating in an otherwise nutrient-poor ocean environment. The "hot spots" concept was first proposed more than a decade ago by Farooq Azam of the Scripps Institution of Oceanography.

The Nature paper's first author, UGA's Mary Ann Moran, says the S. pomeroyi sequence "demonstrates that genomes of ecologically relevant cultured microbes have enormous potential to move marine biogeochemical research forward at a rapid pace, both by generating hypotheses about how the ocean works and by providing tools to investigate these hypotheses in the ocean."

TIGR's role in the project was led by Ward and Associate Investigator John Heidelberg. The DNA libraries were constructed by Grace Pai; closure of gaps in the genome sequence was performed by Matt Lewis, Shivani Johri, and Bruce Weaver; the contact bioinformatics analyst was Lauren Brinkac; the megaplasmid was analyzed by Jane Carlton and David Rasko; the transporters were analyzed by Ian Paulsen and Qinghu Ren; and the metagenomic data sets were analyzed by Jonathan Eisen and Heidelberg.

Other than Moran's UGA group, collaborators in the project included: Ron Kiene of the University of South Alabama; Gary King of the University of Maine; Clay Fuqua of Indiana University; Robert Belas of the University of Maryland Biotechnology Institute's Center of Marine Biotechnology; and José González of the University of La Laguna in Spain.