BioEd Online

Researchers scouring the world's oceans have been forced to drastically revise estimates for the number of microbial species residing there after a census indicated up to one hundred times the expected diversity may be present.

When the International Census of Marine Microbes (ICoMM) kicked off in 2003, microbiologists had identified 6,000 kinds of microbe and predicted that they might find as many as 600,000.

After collecting samples at more than 1,200 sites around the world, ICoMM researchers compiled a database of 18 million microbial DNA sequences and identified hundreds of thousands of different microbes. They conservatively estimate that there must be at least 20 million kinds of microbe in the oceans. The true number may even be billions or trillions.

"The findings have dramatically expanded our understanding of microbial life in the oceans," says microbiologist Norman Pace at the University of Colorado in Boulder, who was not involved in the census. "They have opened the door to an entirely new world we didn't know before."

The ICoMM is one of 14 projects that make up the Census of Marine Life, which involves over 2,000 scientists from more than 80 countries.

Some of the microbial habitats discovered in the oceans by the census are astounding. A patch of microbes identified on the sea floor off the west coast of South America covers an area roughly the size of Greece. Meanwhile, even the deepest mud brought to the surface by the project — from more than 1,600 metres below the sea floor off Newfoundland in Canada — still teemed with microbes.

Ecological wild cards

The surprising wealth of species presents researchers with fresh questions, says Mitch Sogin of the Marine Biological Laboratory at Woods Hole, Massachusetts, who leads the ICoMM. "The overwhelming majority of the novel diversity comes from microbes that are rare and present in low abundance," he says. "Why are there so many different kinds of low-abundant microbes? What roles do they have in ecological processes in the oceans?"

Some researchers speculate that these organisms have important functions in the ecosystem — perhaps in producing certain essential compounds. Others suspect that low-abundance microbes represent a reserve of genetic and genomic innovation for different environments. When ecological conditions change, the relative abundance of marine microbes may shift.

The future of those microbes in a warming world is unclear. "They are basically wild cards," says Sogin. "We don't know what they do or how they are going to respond, but they could have an enormous impact."

As a major constituent of marine biomass, microbes continue to serve as the primary engine of Earth's biosphere, driving biogeochemical cycles that shape our planetary atmosphere and environment. Despite this, "we know very little of the microbial world in the oceans", says Ian Poiner, chief executive of the Australian Institute of Marine Science at Cape Ferguson in Queensland.

"Wherever we look in the oceans, we see a great diversity of life," says Poiner, who chairs the Census of Marine Life's scientific committee. "With new technologies, researchers have dramatically revised their estimates of diversity and improved understanding of the key role microbes play in maintaining the health of the planet."

Sequencing step-change

The census focused on sequencing of an evolutionarily conserved gene that encodes ribosomal RNA in seawater samples. The low sequencing power of early technologies meant that researchers were able to pick up only the most abundant organisms.

The breakthrough came in 2005, when the researchers found that a rapidly evolving region of the ribosomal RNA gene could serve as a proxy for the evolutionary divergence of microbes.

With the advent of high-throughput sequencing technologies, the census team has been able to get hundreds of thousands of sequences of that evolving region in one day, as opposed to the mere one thousand sequences of the entire gene that were attainable previously. It is this higher sequencing power that has allowed researchers to pick up on the vast diversity of low-abundance microbes — doing for the field what the Hubble Telescope has done for astronomy. "This has really changed the dynamics of what we can do," says Sogin. "The results just blow the wheels off all estimates of microbial diversity."

The full report of the census will be unveiled at a symposium in London in October. However, there is still much work to do. "We don't see this as the end but as the first of a series of censuses," says Poiner.

In the next stage, one of the greatest challenges will be getting a better handle on the abundance of marine organisms and how it is changing. "We also need to better understand how species interact and how one depends on another," Poiner says.