Microbiomes: What USGS Research Is Learning from the Invisible World

USGS Fact Sheet 2017–3074, September 2017.

What microbiomes are

Microbiomes are communities of microorganisms — bacteria, viruses, fungi — living on, in and around people, plants, animals, soil, water and the air. They help ecosystems work: shaping water quality, how plants take up nutrients and handle stress, and the stability of soil and water.

When conditions change, a microbiome can go wrong: some microbes turn pathogenic (disease-causing) or some groups overgrow. The results include coral disease, poorer crops and contaminated waterways. Understanding microbiomes helps with clean water, food, energy and the health of people and ecosystems.

In 2016, the White House Office of Science and Technology Policy announced the National Microbiome Initiative, a 5-year effort with federal agencies and private partners to study microbiomes across ecosystems — work USGS scientists had already been doing for more than a decade.

Where USGS microbiome research happens: permafrost, wildlife, energy, water, soil, invasive species, ecosystems and bioremediation. Illustration: USGS.

Why the USGS

As the Department of the Interior's only science agency, the USGS studies hazards, resources from water to minerals, ecosystem health and climate and land-use change. There is no single microbiome program; the research sits within many mission areas, and serves the EPA, Fish and Wildlife Service, Park Service, Bureau of Ocean Energy Management, NOAA, NASA, the Department of Energy and many local, state and Tribal agencies.

Seven examples

Invasive plants. More than 5,000 invasive plant species have displaced natives in the U.S., and billions of dollars go each year to control invasives — about $100 million on aquatic weeds alone. The USGS Great Lakes Science Center, with the Great Lakes Commission and universities, is targeting the partnership between invasive reeds such as Phragmites and their microbiomes.

Sampling invasive Phragmites. Photo: Kurt Kowalski, USGS.

Bat disease. White-nose syndrome, a fungal disease, has killed about six million hibernating bats in the U.S. and Canada since 2007. Bats save U.S. farmers more than $3 billion a year by eating crop pests, and help pollinate and spread seeds. The National Wildlife Health Center is collecting baseline data on bats' skin microbiomes to find natural defenses and possible biocontrols.

Antibiotic resistance. Drug-resistant bacteria cause at least 2 million illnesses and more than 20,000 deaths a year in the U.S. Alaska Science Center researchers, with colleagues in Sweden, found urban gulls in Alaska more likely than remote gulls to carry antibiotic-resistant E. coli — suggesting spread from landfills or wastewater, and raising questions where people and gulls meet.

Gulls at a landfill. Photo: Andrew Reeves, USGS.

Deep-sea corals. More than 3,000 species of deep-sea coral live hundreds to thousands of feet down; some are centuries old and shelter commercial fish. The St. Petersburg Coastal and Marine Science Center is recording their baseline microbiomes, key to judging impacts as energy, fishing and mining move deeper.

A deep-sea coral. Photo courtesy of Deepwater Canyons 2012–Pathways to the Abyss, Bureau of Ocean Energy Management and NOAA.

Natural gas from coal. Coal-bed gas is about 7 percent of U.S. natural gas, mostly methane, some made by microbes. USGS scientists are stimulating coal-bed microbiomes to boost it, work that could couple photosynthesis and methane production to make gas and algal biofuels while storing carbon dioxide.

Microbes on coal under a scanning electron microscope. Image: Elliott Barnhart, USGS.

Permafrost. Frozen soils store vast carbon that warming could release, and they are a model for exobiology, the study of possible life on other planets. Researchers at the USGS Menlo Park campus, with Lawrence Livermore National Laboratory, NASA and universities, study how microbes survive frozen over geologic time.

Coring permafrost. Photo: Mark P. Waldrop, USGS.

Cleanup. Energy, military and industrial activity have left chlorinated solvents, hydrocarbons, heavy metals and radionuclides in water, sediment and soil. Some microbes can break down or remove them; the USGS Reston Microbiology Laboratory studies these natural cleanup crews, including at oil and gas sites.

Culturing bacteria from a contaminated site. Photo: Andrea Fraser, USGS.

Sources

Based on USGS Microbiome Research, USGS Fact Sheet 2017–3074, U.S. Geological Survey; a work of the United States government in the public domain. The illustration and photographs are taken from the fact sheet's PDF; a bat photograph by the Pennsylvania Game Commission is not reproduced, and the illustration appears without its labels.