Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New bacteria groups, and stunning diversity, discovered underground

24.10.2016

Berkeley Lab research also provides new clues about the roles of subsurface microbes in globally important cycles

One of the most detailed genomic studies of any ecosystem to date has revealed an underground world of stunning microbial diversity, and added dozens of new branches to the tree of life.


All the known major bacterial groups are represented by wedges in this circular 'tree of life.' The bigger wedges are more diverse groups. Green wedges are groups that have not been genomically sampled at the Rifle site --everything else has. Black wedges are previously identified bacteria groups that have also been found at Rifle. Purple wedges are groups discovered at Rifle and announced last year. Red wedges are new groups discovered in this study. Colored dots represent important metabolic processes the new groups help mediate.

Credit: Banfield Group

The bacterial bonanza comes from scientists who reconstructed the genomes of more than 2,500 microbes from sediment and groundwater samples collected at an aquifer in Colorado. The effort was led by researchers from the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley. DNA sequencing was performed at the Joint Genome Institute, a DOE Office of Science User Facility.

As reported online October 24 in the journal Nature Communications, the scientists netted genomes from 80 percent of all known bacterial phyla, a remarkable degree of biological diversity at one location. They also discovered 47 new phylum-level bacterial groups, naming many of them after influential microbiologists and other scientists. And they learned new insights about how microbial communities work together to drive processes that are critical to the planet's climate and life everywhere, such as the carbon and nitrogen cycles.

... more about:
»DNA »bacteria »microbes »nitrate »nitrogen

These findings shed light on one of Earth's most important and least understood realms of life. The subterranean world hosts up to one-fifth of all biomass, but it remains a mystery.

"We didn't expect to find this incredible microbial diversity. But then again, we know little about the roles of subsurface microbes in biogeochemical processes, and more broadly, we don't really know what's down there," says Jill Banfield, a Senior Faculty Scientist in Berkeley Lab's Climate & Ecosystem Sciences Division and a UC Berkeley professor in the departments of Earth and Planetary Science, and Environmental Science, Policy, and Management.

UC Berkeley's Karthik Anantharaman, the first author of the paper, adds, "To better understand what subsurface microbes are up to, our approach is to access their entire genomes. This enabled us to discover a greater interdependency among microbes than we've seen before."

The research is part of a Berkeley Lab-led project called Sustainable Systems Scientific Focus Area 2.0, which is developing a predictive understanding of terrestrial environments from the genome to the watershed scale. The project's field research takes place at a research site near the town of Rifle, Colorado, where for the past several years scientists have conducted experiments designed to stimulate populations of subterranean microbes that are naturally present in very low numbers.

The scientists sent soil and water samples from these experiments to the Joint Genome Institute for terabase-scale metagenomic sequencing. This high-throughput method isolates and purifies DNA from environmental samples, and then sequences one trillion base pairs of DNA at a time. Next, the scientists used bioinformatics tools developed in Banfield's lab to analyze the data.

Their approach has redrawn the tree of life. Between the 47 new bacterial groups reported in this work, and 35 new groups published last year (also found at the Rifle site), Banfield's team has doubled the number of known bacterial groups.

With discovery comes naming rights. The scientists named many of the new bacteria groups after Berkeley Lab and UC Berkeley researchers. For example, there's Candidatus Andersenbacteria, after phylochip inventor Gary Andersen, and there's Candidatus Doudnabacteria, after CRISPR genome-editing pioneer Jennifer Doudna. "Berkeley now dominates the tree of life as it does the periodic table," Banfield says, in a nod to the sixteen elements discovered at Berkeley Lab and UC Berkeley.

Another big outcome is a deeper understanding of the roles subsurface microbes play in globally important carbon, hydrogen, nitrogen, and sulfur cycles. This information will help to better represent these cycles in predictive models such as climate simulations.

The scientists conducted metabolic analyses of 36 percent of the organisms detected in the aquifer system. They focused on a phenomenon called metabolic handoff, which essentially means one microbe's waste is another microbe's food. It's known from lab studies that handoffs are needed in certain reactions, but these interconnected networks are widespread and vastly more complex in the real world.

To understand why it's important to represent metabolic handoffs as accurately as possible in models, consider nitrate, a groundwater contaminant from fertilizers. Subsurface microbes are the primary driver in reducing nitrate to harmless nitrogen gas. There are four steps in this denitrification process, and the third step creates nitrous oxide--one of the most potent greenhouse gases. The process breaks down if microbes that carry out the fourth step are inactive when a pulse of nitrate enters the system.

"If microbes aren't there to accept the nitrous oxide handoff, then the greenhouse gas escapes into the atmosphere," says Anantharaman.

The scientists found the carbon, hydrogen, nitrogen, and sulfur cycles are all driven by metabolic handoffs that require an unexpectedly high degree of interdependence among microbes. The vast majority of microorganisms can't fully reduce a compound on their own. It takes a team. There are also backup microbes ready to perform a handoff if first-string microbes are unavailable.

"The combination of high microbial diversity and interconnections through metabolic handoffs likely results in high ecosystem resilience," says Banfield.

###

Other co-authors of the paper include Berkeley Lab's Eoin Brodie, Susan Hubbard, Ulas Karaoz, and Kenneth Williams; and UC Berkeley's Chris Brown, Cindy Castelle, Laura Hug, Alexander Probst, Itai Sharon, Andrea Singh, and Brian Thomas. The research is supported by the Department of Energy's Office of Science.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy's Office of Science. For more, visit http://www.lbl.gov.

DOE's Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Media Contact

Dan Krotz
dakrotz@lbl.gov
510-486-4019

 @BerkeleyLab

http://www.lbl.gov 

Dan Krotz | EurekAlert!

Further reports about: DNA bacteria microbes nitrate nitrogen

More articles from Life Sciences:

nachricht NYSCF researchers develop novel bioengineering technique for personalized bone grafts
18.07.2018 | New York Stem Cell Foundation

nachricht Pollen taxi for bacteria
18.07.2018 | Technische Universität München

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: First evidence on the source of extragalactic particles

For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.

To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...

Im Focus: Magnetic vortices: Two independent magnetic skyrmion phases discovered in a single material

For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.

Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...

Im Focus: Breaking the bond: To take part or not?

Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.

A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...

Im Focus: New 2D Spectroscopy Methods

Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.

"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....

Im Focus: Chemical reactions in the light of ultrashort X-ray pulses from free-electron lasers

Ultra-short, high-intensity X-ray flashes open the door to the foundations of chemical reactions. Free-electron lasers generate these kinds of pulses, but there is a catch: the pulses vary in duration and energy. An international research team has now presented a solution: Using a ring of 16 detectors and a circularly polarized laser beam, they can determine both factors with attosecond accuracy.

Free-electron lasers (FELs) generate extremely short and intense X-ray flashes. Researchers can use these flashes to resolve structures with diameters on the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Leading experts in Diabetes, Metabolism and Biomedical Engineering discuss Precision Medicine

13.07.2018 | Event News

Conference on Laser Polishing – LaP: Fine Tuning for Surfaces

12.07.2018 | Event News

11th European Wood-based Panel Symposium 2018: Meeting point for the wood-based materials industry

03.07.2018 | Event News

 
Latest News

NYSCF researchers develop novel bioengineering technique for personalized bone grafts

18.07.2018 | Life Sciences

Machine-learning predicted a superhard and high-energy-density tungsten nitride

18.07.2018 | Materials Sciences

Why might reading make myopic?

18.07.2018 | Health and Medicine

VideoLinks
Science & Research
Overview of more VideoLinks >>>