The World's Smallest Whistle-Blowers, Microbes Warn of Ecological Damage

Microbes warn of impending problems in ecosystems.

Researcher Forest Rohwer collects bacteria samples almost a half-mile below ground in the Soudan Mine in Minnesota.
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Long before the people, plants or animals of a community detect brewing ecological threats, such as increasing pollution or harmful algae blooms, one type of resident invariably warns of impending problems—microbes, the simplest but most-sensitive members of every community.

But if microbes are so sensitive, why haven't they been incorporated into early warning systems that could, for example, tip off aquaculture managers to the presence of disease-causing organisms before their investments go belly up, or flag marine environments stressed by climate change? Because warnings from microbes come not as megaphoned evacuation shouts but as subtle, telltale adjustments in the growth rates, sizes and compositions of microbial communities—characteristics that are instructed by the organisms' genes.

Scientists have been sequencing the DNA of individual bacteria and viruses for decades to determine what their genes do. That information has led to valuable new strategies for manufacturing medicines and combating infectious diseases. But getting at the DNA of communities of microbes inhabiting entire ecosystems has proven more difficult. More than 99 percent of microbes cannot be grown and studied in laboratories.

Now, scientists have inventoried and analyzed the presence of almost 15 million DNA sequences from dozens of bacteria and viruses that control some two dozen metabolic functions—indeed, all of the functions microbes are genetically programmed to conduct in many types of ecosystems, ranging from vibrant ocean coral reefs to deep, dark mines. They say the study represents the first definitive inventory of microbial functions across so many different ecosystems and will significantly advance efforts to identify and interpret microbial warnings of ecological changes.

Rather than conducting laboratory studies of individual strains of microbes, Elizabeth Dinsdale, Rob Edwards and Forest Rohwer of San Diego State University led a large team of biologists, computer scientists, ocean scientists and other experts in applying the new science of metagenomics, which analyzes the DNA composition of microbial communities en masse. Metagenomics enables scientists to quickly assess microbial responses, Rohwer said.

And, because metagenomic studies sample microbial communities in their natural habitats, "they get about as far away from a Petri dish as you can get," said Dinsdale.

According to the study, each type of ecosystem has its own microbial DNA profile that is as unique as a signature or a fingerprint. The uniqueness of each ecosystem's profile reflects the fact that in order to stay healthy, each ecosystem needs a particular suite of microbes to perform specific jobs. A coral reef, for example, needs certain microbes to fight diseases common to tropical marine environments. These microbes are different from those needed by a lake to fight diseases common to fresh-water environments.

Without its unique, beneficial microbes, an ecosystem can be overrun by harmful microbes and therefore decline. For instance, catalogues the researchers developed of the microbial DNA of a dying coral reef in the Pacific Ocean and a contaminated fresh-water pond in San Diego differed significantly from those of their healthy counterparts. The study thereby showed that microbes of stressed ecosystems change in measureable and predictable ways.

Scientists look forward to eventually incorporating microbial monitoring into large scale environmental sensing networks. But before they can do so, additional insights into microbial signaling are needed and new technology supporting real- time monitoring of various environments must be developed.

The study appeared in the April 3 issue of the journal Nature. It was supported by the National Science Foundation and other federal and non-profit organizations.

—Lily Whiteman/NSF

This report is provided by the National Science Foundation, an independent federal agency that supports fundamental research and education across all fields of science and engineering, in partnership with U.S. News and World Report.