Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Microbial biofilm yields community genomes, metabolic clues


Research from Iron Mountain mine sheds light on acid drainage

Acidic drainage from a mine flows on the surface after passing through the underground study site at Iron Mountain, near Redding, Calif.
Credit: Gene Tyson, UC Berkeley

This FISH image of the biofilm – showing Leptospirillum in yellow, archae in blue, and Sulfobacillus in green – is surrounded by a representation of a genome sequence that indicates genes by colored bars.
Credit: Gene Tyson and Jill Banfield, UC Berkeley

Examining life extracted from toxic runoff at a northern California mine, researchers for the first time have reconstructed multiple individual genomes from a microbial community taken from an environmental sample rather than from a laboratory culture.

According to Jill Banfield, the leader of the scientific team behind the discovery, "This takes the study of natural biogeochemical systems to a new level."

Announced Feb. 1 in the online version of the journal Nature, the research focused on a sample from a postagestamp- sized patch of pink biofilm taken from a thin microbial layer found growing hundreds of feet underground. (Often slimy, biofilms are communities of microorganisms-such as bacteria and fungi-that grow on surfaces. Think of a kitchen sink left unwiped.) The research team found its biofilm atop a hot, flowing, extremely acidic solution-laden with dissolved iron, copper, zinc and arsenic-emanating from a mine on Iron Mountain, about nine miles northwest of Redding.

According to the Environmental Protection Agency, the mine, which shut down in 1963 after nearly a century of operations, created the most acidic mine drainage in the world, discharging-on average-a ton of toxic metals every day into the Upper Sacramento River until remediation efforts began a decade ago.

Acid mine drainage remains a significant environmental problem worldwide. Banfield, a professor at the University of California at Berkeley, said the new findings enhance scientists’ understanding of the metabolic activity of iron oxidizing microbes that greatly accelerates acid production.

Nine other scientists from Berkeley and the Department of Energy’s Joint Genome Institute in Walnut Creek, Calif., co authored the report. The study was funded by the National Science Foundation’s Biocomplexity in the Environment program and the Department of Energy’s Microbial Genomics Program.

According to Matt Kane, program director in NSF’s Division of Molecular and Cellular Biosciences, the findings shed light on how bacteria and other microbes function collectively.

"This work simultaneously reconstructed the genome sequences for a five-membered microbial community from nature," Kane said. "It goes beyond previous achievements, such as those that sequenced the entire genome of single, isolated species or efforts that gathered genomic content from a microbial community but stopped short of constructing the individual genomes within it."

The researchers first screened several biofilms with a technique called FISH-fluorescence in situ hybridization-before settling on the particular pink sample a soup of several strains typical of acid mine drainages. They then applied to their selected community a genomics approach usually put to an individual species-"random shotgun sequencing."

This meant extracting DNA directly from the sample and a "small insert library." Once the sequences of short pieces of DNA were obtained, computer processing linked them to generate large genomic fragments that could be assigned to specific organisms within the community.

The researchers reconstructed nearly complete genomes of two organisms-strains of the bacterium Leptospirillum and of the archaeon Ferroplasma-and partial genomes of three other microbes. According to the researchers’ Nature article, such recovery "from an environmental sample is an advance in the study of natural microbial communities."

According to Banfield, "The transition to this genome-level study of real populations opens the way for new understanding of speciation and evolution."

Further analysis of each organism’s gene complement yielded clues about which microbes are most likely responsible for which services in this acid-adapted, self-sustaining community.

For example, organic compounds produced by the community allow it to attach to its surroundings; float at the air water interface; and make readily accessible the oxygen, carbon dioxide, nitrogen and iron necessary for respiration and metabolism.

While researchers are unsure which organisms are responsible for creating some key polymers, they found within the Leptospirillum strain-but not in the Ferroplasma strain-the genes for making cellulose and other proteins that prevent drying out and support floatation. The genetic foundation of other critical functions, such as making carbon and nitrogen accessible to the organisms, also appears to be "partitioned among members of the community," Banfield said.

Sean Kearns | NSF
Further information:

More articles from Ecology, The Environment and Conservation:

nachricht Dispersal of Fish Eggs by Water Birds – Just a Myth?
19.02.2018 | Universität Basel

nachricht Removing fossil fuel subsidies will not reduce CO2 emissions as much as hoped
08.02.2018 | International Institute for Applied Systems Analysis (IIASA)

All articles from Ecology, The Environment and Conservation >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Space observation with radar to secure Germany's space infrastructure

Satellites in near-Earth orbit are at risk due to the steady increase in space debris. But their mission in the areas of telecommunications, navigation or weather forecasts is essential for society. Fraunhofer FHR therefore develops radar-based systems which allow the detection, tracking and cataloging of even the smallest particles of debris. Satellite operators who have access to our data are in a better position to plan evasive maneuvers and prevent destructive collisions. From April, 25-29 2018, Fraunhofer FHR and its partners will exhibit the complementary radar systems TIRA and GESTRA as well as the latest radar techniques for space observation across three stands at the ILA Berlin.

The "traffic situation" in space is very tense: the Earth is currently being orbited not only by countless satellites but also by a large volume of space...

Im Focus: Researchers Discover New Anti-Cancer Protein

An international team of researchers has discovered a new anti-cancer protein. The protein, called LHPP, prevents the uncontrolled proliferation of cancer cells in the liver. The researchers led by Prof. Michael N. Hall from the Biozentrum, University of Basel, report in “Nature” that LHPP can also serve as a biomarker for the diagnosis and prognosis of liver cancer.

The incidence of liver cancer, also known as hepatocellular carcinoma, is steadily increasing. In the last twenty years, the number of cases has almost doubled...

Im Focus: Researchers at Fraunhofer monitor re-entry of Chinese space station Tiangong-1

In just a few weeks from now, the Chinese space station Tiangong-1 will re-enter the Earth's atmosphere where it will to a large extent burn up. It is possible that some debris will reach the Earth's surface. Tiangong-1 is orbiting the Earth uncontrolled at a speed of approx. 29,000 km/h.Currently the prognosis relating to the time of impact currently lies within a window of several days. The scientists at Fraunhofer FHR have already been monitoring Tiangong-1 for a number of weeks with their TIRA system, one of the most powerful space observation radars in the world, with a view to supporting the German Space Situational Awareness Center and the ESA with their re-entry forecasts.

Following the loss of radio contact with Tiangong-1 in 2016 and due to the low orbital height, it is now inevitable that the Chinese space station will...

Im Focus: Alliance „OLED Licht Forum“ – Key partner for OLED lighting solutions

Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology FEP, provider of research and development services for OLED lighting solutions, announces the founding of the “OLED Licht Forum” and presents latest OLED design and lighting solutions during light+building, from March 18th – 23rd, 2018 in Frankfurt a.M./Germany, at booth no. F91 in Hall 4.0.

They are united in their passion for OLED (organic light emitting diodes) lighting with all of its unique facets and application possibilities. Thus experts in...

Im Focus: Mars' oceans formed early, possibly aided by massive volcanic eruptions

Oceans formed before Tharsis and evolved together, shaping climate history of Mars

A new scenario seeking to explain how Mars' putative oceans came and went over the last 4 billion years implies that the oceans formed several hundred million...

All Focus news of the innovation-report >>>



Industry & Economy
Event News

New solar solutions for sustainable buildings and cities

23.03.2018 | Event News

Virtual reality conference comes to Reutlingen

19.03.2018 | Event News

Ultrafast Wireless and Chip Design at the DATE Conference in Dresden

16.03.2018 | Event News

Latest News

For graphite pellets, just add elbow grease

23.03.2018 | Materials Sciences

Unique communication strategy discovered in stem cell pathway controlling plant growth

23.03.2018 | Agricultural and Forestry Science

Sharpening the X-ray view of the nanocosm

23.03.2018 | Physics and Astronomy

Science & Research
Overview of more VideoLinks >>>