New genus of bacteria found living inside hydraulic fracturing wells

'Frackibacter' one of dozens of microbes forming sustainable ecosystems there, study finds

OHIO STATE UNIVERSITY

Ohio State University researchers and their colleagues have identified a new genus of bacteria living inside hydraulic fracturing wells. These jars contain samples of "produced water fluids" -- the fluid that is collected at the surface of a hydraulic fracturing well after fracturing -- from wells in Marcellus and Utica shale formations. The fluids are orange because they contain large amounts of iron that oxidizes when the fluids are brought to the surface. By analyzing the genomes of microbes in the water, the researchers are piecing together the existence of microbial communities inside the wells. 

CREDIT: Photo by Rebecca Daly, courtesy of The Ohio State University.

COLUMBUS, Ohio--Researchers analyzing the genomes of microorganisms living in shale oil and gas wells have found evidence of sustainable ecosystems taking hold there--populated in part by a never-before-seen genus of bacteria they have dubbed "Frackibacter."

The new genus is one of the 31 microbial members found living inside two separate fracturing wells, Ohio State University researchers and their colleagues report in the Sept. 5 online edition of the journal Nature Microbiology.

Even though the wells were hundreds of miles apart and drilled in different kinds of shale formations, the microbial communities inside them were nearly identical, the researchers discovered.

Almost all the microbes they found had been seen elsewhere before, and many likely came from the surface ponds that energy companies draw on to fill the wells. But that's not the case with the newly identified Candidatus Frackibacter, which may be unique to hydraulic fracturing sites, said Kelly Wrighton, assistant professor of microbiology and biophysics at Ohio State.

In biological nomenclature, "Candidatus" indicates that a new organism is being studied for the first time using a genomic approach, not an isolated organism in a lab culture. The researchers chose to name the genus "Frackibacter" as a play on the word "fracking," shorthand for "hydraulic fracturing."

Candidatus Frackibacter prospered alongside the microbes that came from the surface, forming communities in both wells which so far have lasted for nearly a year.

"We think that the microbes in each well may form a self-sustaining ecosystem where they provide their own food sources," Wrighton explained. "Drilling the well and pumping in fracturing fluid creates the ecosystem, but the microbes adapt to their new environment in a way to sustain the system over long periods."

By sampling fluids taken from the two wells over 328 days, the researchers reconstructed the genomes of bacteria and archaea living in the shale. To the researchers' surprise, both wells--one drilled in Utica shale and the other drilled in Marcellus shale--developed nearly identical microbial communities.

In addition, the two wells are each owned by different energy companies that utilized different fracturing techniques. The two types of shale exist more than a mile and a half below ground, were formed millions of years apart, and contained different forms of fossil fuel. Yet one bacterium, Halanaerobium, emerged to dominate communities in both wells.

"We thought we might get some of the same types of bacteria, but the level of similarity was so high it was striking. That suggests that whatever's happening in these ecosystems is more influenced by the fracturing than the inherent differences in the shale," Wrighton said.

Wrighton and her team are still not 100 percent sure of the microbes' origins. Some almost undoubtedly came from the ponds that provide water to the wells, she said. But other bacteria and archaea could have been living in the rock before drilling began, Candidatus Frackibacter among them.

Shale energy companies typically formulate their own proprietary recipes for the fluid they pump into wells to break up the rock and release oil or gas, explained Rebecca Daly, research associate in microbiology at Ohio State and lead author of the Nature Microbiology paper. They all start with water and add other chemicals. Once the fluid is inside a well, salt within the shale leaches into it, making it briny.

The microorganisms living in the shale must tolerate high temperature, pressure and salinity, but this study suggests that salinity is likely the most important stressor on the microbes' survival. Salinity forces the microbes to synthesize organic compounds called osmoprotectants to keep themselves from bursting. When the cells die, the osmoprotectants are released into the water, where other microbes can use them for protection themselves or eat them as food. In that way, salinity forced the microbes to generate a sustainable food source.

In addition to the physical constraints in the environment, the microbes also must protect themselves from viruses. The researchers reconstructed the genomes of viruses living inside the wells, and found genetic evidence that some bacteria were indeed falling prey to viruses, dying, and releasing osmoprotectants into the water.

By examining the genomes of the different microbes, the researchers found that the osmoprotectants were being eaten by Halanaerobium and Candidatus Frackibacter. In turn, these bacteria provided food for other microbes called methanogens, which ultimately produced methane.

To validate their findings from the field, the researchers grew the same microbes in the lab under similar conditions. The lab-grown microbes also produced osmoprotectants that were converted into methane--a confirmation that the researchers are on the right track to understanding what's happening inside the wells.

One implication of the study is that methane produced by microbes living in shale wells could possibly supplement the wells' energy output.

Wrighton and Daly described the amount of methane produced by the microbes as likely minuscule compared to the amount of oil and gas harvested from the shale even a year after initial fracturing. But, they point out, there is a precedent in a related industry, that of coal-bed methane, to use microbes to greater advantage.

"In coal-bed systems they've shown that they can facilitate microbial life and increase methane yields," Wrighton said. "As the system shifts over time to being less productive, the contribution of biogenic methane could become significantly higher in shale wells. We haven't gotten to that point yet, but it's a possibility."

In the meantime, research led by co-author Michael Wilkins, assistant professor of earth sciences and microbiology, has used genomics information to grow Candidatus Frackibacter in the lab and is further testing its ability to handle high pressure and salinity.

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This work is funded by the National Science Foundation's Dimensions of Biodiversity program, the Department of Energy and the Deep Carbon Observatory.

Among the study's co-authors from Ohio State is Paula Mouser, principal investigator on the Dimensions of Biodiversity grant. Other co-principal investigators and co-authors include Wrighton; Michael Wilkins, assistant professor of earth sciences and microbiology; and David Cole, professor of earth sciences and Ohio Research Scholar. Co-author David Hoyt of the Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory analyzed the compounds in the fluids that provided evidence of microbial metabolism.

Contact: Kelly Wrighton, 614-688-2189; Wrighton.1@osu.edu

Written by Pam Frost Gorder, 614-292-9475; Gorder.1@osu.edu

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

ORIGINAL: EurekAlert
by Pam Frost Gorder
 5-SEP-2016

The War Over Genome Editing Just Got A Lot More Interesting

The cutting circle GETTY IMAGES

IF YOU WANT to drop some real DNA editing knowledge—like, I don’t know, at a party!—here’s a tip. Instead of calling the much hyped precise genome-editing tool CRISPR, call it CRISPR/Cas9. CRISPR, you see, just refers to stretches of repeating DNA that sit near the gene for Cas9, the actual protein that does the DNA editing.

Well, at least for now. Today, gene-editing scientists dropped some curious news: They’ve found a CRISPR system involving a different protein that also edits human DNA, and, in some cases, it may work even better than Cas9.

The discovery comes at a time when CRISPR/Cas9 is sweeping through biology labs. So revolutionary is this new genome editing technique that rival groups, who each claim to have been first to the tech, are bitterly fighting over the CRISPR/Cas9 patent. This new gene-editing protein called Cpf1—and maybe even others yet to be discovered—means that one patent may not be so powerful after all.

And there’s good reason to think more useful CRISPR proteins are out there. CRISPR sequences are a part of primordial immune systems, found in some 40 percent of bacteria and 90 percent of archaea. In a study published today in Cell, Feng Zhang (no relation to this writer) and colleagues trawled through bacterial genomes looking for different versions of Cpf1. They found two, from Acidominococcus and Lachnospiraceae, that can snip DNA when scientists insert them into human cells.

“There are definitely many more defense systems out there, and maybe some of them might even have spectacular applications like with the Cas9 system,” says John van der Oost, a microbiologist at Wageningen University who is a co-author on the paper. “We have the feeling it’s just the tip of the iceberg.”

Zhang and van der Oost’s search was deliberate, but the initial discovery of CRISPR/Cas9 as a gene-editing tool was not. Back in the 1980s, microbiologists saw strange repeating sequences in the DNA of bacteria. Those clustered regularly interspaced short palindromic repeats became CRISPR, and scientists realized they were evidence of an immune system bacteria used to defend against viruses. The spacers between the repeats are in fact snippets of viral genomes, which CRISPR-associated proteins called Cas use as “mug shots” to recognize viruses and shred their DNA.

Many different proteins are associated with CRISPR. But in the early 2010s, Emmanuelle Charpentier, who was studying the flesh-eating bacteria Streptococcus pyogenes, stumbled onto one with special powers. Her bacteria happen to carry Cas9 proteins, which have the remarkable ability to precisely cut DNA based on a RNA guide sequence. In 2012, Charpentier and UC Berkeley biologist Jennifer Doudna published a paper describing the CRISPR/Cas9 system and speculated about its genome editing capabilities. And they filed a patent application. Much more on that patent later.

The Obscure Protein

While Cas9 has driven thousands of lab experiments and millions of dollars in funding for startups trying to capitalize on the technology, Cpf1 has remained relatively obscure. This study drags Cpf1 into the limelight. “It’s a very comparable to Cas9 and it has a few different features which could be quite useful,” says Dana Carroll, a biochemist at the University of Utah.

That’s because Cas9 isn’t perfect, despite its hype as a laser-precise genome editing tool. Cpf1 offers some slight advantages. For example, when it cuts double-stranded DNA, it snips the two strands in slightly different locations, resulting in overhang that molecular biologists call “sticky ends.” Sticky ends can make it easier to insert a snippet of new DNA—say, a different version of a gene—though the Cell paper does not actually show data directly comparing Cas9 and Cpf1 when inserting DNA.

Cpf1 is also physically a smaller protein, so it may be easier to put into human cells. It requires only one RNA molecule instead of two, with Cas9. But it’s not a rival so much as a complementary tool: The two proteins favor binding to different locations in the genome, so together, they might allow more flexibility in where scientist want to cut.

But Cpf1 has implications reaching far outside the lab.

Patent Wars

Not long after Doudna and UC Berkeley filed a patent, the Broad Institute and MIT filed their own patent on behalf of Zhang for the CRISPR/Cas9 system. Zhang had been working on actually showing that CRISPR/Cas9 can edit mammalian genomes in mammalian cells, an application he published in 2013 and says he came up with independently. The Broad’s and MIT’s attorney paid a fee to accelerate their application. Ultimately, the US Patent and Trademark Office awarded the patent to Zhang, MIT, and the Broad Institute. The University of California, obviously unhappy with the decision, filed an application for an interference proceeding to get the USPTO to reconsider. That process is ongoing.

But biotech companies have raced ahead to develop therapeutics and techniques with the system. Feng and Doudna have since licensed their technology to rival companies, Editas and Caribou. Charpentier also cofounded Crispr Therapeutics in Switzerland. Whoever wins the patent dispute will have a monopoly on CRISPR/Cas9 technology, the hottest new thing in biotech.

But with Cfp1, the stakes of that specific patent dispute go down. A lab or company could use Cfp1 without infringing on the CRISPR/Cas9 patent. “It takes power away from whoever the winner is going to be,” says Jacob Sherkow, a professor at New York Law School1 (Zhang has indicated the rights to Cpf1 may not necessarily go to the company he cofounded, Editas.) Whether a CRISPR/Cfp1 system is patentable as a separate invention—Sherkow says it probably is—perhaps isn’t even relevant because its very existence means Cas9 is no longer the only game in town.

And if biologists keep trawling through bacterial genomes, they might find even more proteins to join Cfp1 and Cas9. Who knows what else is hiding in the genomes of microbes?

ORIGINAL: Wired

By SARAH ZHANG

09.25.15

The Concrete Of The Future Is Here, And It Repairs Its Own Cracks

Henk Jonkers, a microbiologist at Netherlands Delft University of Technology, has been working on perfecting a bioconcrete since 2006.

Source: cnn.com

The "healing agent" contains bacteria that can produce limestone, and it's mixed into regular concrete.

Source: cnn.com

When the concrete cracks and water gets in, the bacteria are activated. Here is a test piece of the concrete on day one.

Source: cnn.com

After two months, the improvement in the large crack is significant.

Source: cnn.com

Concrete is the world's most popular building material and this small change can help extend the life of future structures.

Source: cnn.com

For all the details about this amazing "living concrete," visit CNN. 

ORIGINAL: Distractify