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.

###

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

First almost fully-formed human brain grown in lab, researchers claim

Research team say tiny brain could be used to test drugs and study diseases, but scientific peers urge caution as data on breakthrough kept under wraps

The tiny brain, which resembles that of
a five-week-old foetus, is not conscious.
Photograph: Ohio State University

An almost fully-formed human brain has been grown in a lab for the first time, claim scientists from Ohio State University. The team behind the feat hope the brain could transform our understanding of neurological disease.

Though not conscious the miniature brain, which resembles that of a five-week-old foetus, could potentially be useful for scientists who want to study the progression of developmental diseases. It could also be used to test drugs for conditions such as Alzheimer’s and Parkinson’s, since the regions they affect are in place during an early stage of brain development.

The brain, which is about the size of a pencil eraser, is engineered from adult human skin cells and is the most complete human brain model yet developed, claimed Rene Anand of Ohio State University, Columbus, who presented the work today at the Military Health System Research Symposium in Fort Lauderdale, Florida.

Scientists create lab-grown spinal cords. Read more

Previous attempts at growing whole brains have at best achieved mini-organs that resemble those of nine-week-old foetuses, although these “cerebral organoids” were not complete and only contained certain aspects of the brain. “We have grown the entire brain from the get-go,” said Anand.

Anand and his colleagues claim to have reproduced 99% of the brain’s diverse cell types and genes. They say their brain also contains a spinal cord, signalling circuitry and even a retina.

The ethical concerns were non-existent, said Anand. “We don’t have any sensory stimuli entering the brain. This brain is not thinking in any way.”

Anand claims to have created the brain by converting adult skin cells into pluripotent cells: stem cells that can be programmed to become any tissue in the body. These were then grown in a specialised environment that persuaded the stem cells to grow into all the different components of the brain and central nervous system.

According to Anand, it takes about 12 weeks to create a brain that resembles the maturity of a five-week-old foetus. To go further would require a network of blood vessels that the team cannot yet produce. “We’d need an artificial heart to help the brain grow further in development,” said Anand.

Several researchers contacted by the Guardian said it was hard to judge the quality of the work without access to more data, which Anand is keeping under wraps due to a pending patent on the technique. Many were uncomfortable that the team had released information to the press without the science having gone through peer review.

Zameel Cader, a consultant neurologist at the John Radcliffe Hospital, Oxford, said that while the work sounds very exciting, it’s not yet possible to judge its impact. “When someone makes such an extraordinary claim as this, you have to be cautious until they are willing to reveal their data.”

3D-printed brain tissue. Read more

If the team’s claims prove true, the technique could revolutionise personalised medicine. “If you have an inherited disease, for example, you could give us a sample of skin cells, we could make a brain and then ask what’s going on,” said Anand.

You could also test the effect of different environmental toxins on the growing brain, he added. “We can look at the expression of every gene in the human genome at every step of the development process and see how they change with different toxins. Maybe then we’ll be able to say ‘holy cow, this one isn’t good for you.’”

For now, the team say they are focusing on using the brain for military research, to understand the effect of post traumatic stress disorder and traumatic brain injuries.

ORIGINAL: The Guardian

Helen Thomson

Tuesday 18 August 2015 

Polar insects help scientists make gene expression discovery

ORIGINAL: RD Mag

03/13/2013

Although they live in similarly extreme ecosystems at opposite ends of the world, Antarctic insects appear to employ entirely different methods at the genetic level to cope with extremely dry conditions than their counterparts that live north of the Arctic Circle, according to National Science Foundation- (NSF) funded researchers.

Writing in the Proceedings of the National Academy of Sciences, the researchers concluded, "Polar arthropods have developed distinct... mechanisms to cope with similar desiccating conditions."

The researchers noted that aside from the significance of the specific discovery about the genetics of how creatures cope in polar environments, the new finding is important because it shows how relatively new and developing scientific techniques, including genomics, are opening new scientific vistas in the Polar Regions, which were once thought to be relatively uniform and, relatively speaking, scientifically sterile environments.

"It's great to have an Antarctic animal that has entered the genomic era," said David Denlinger, a distinguished professor of entomology at Ohio State University and a co-author of the paper. "This paper, which analyzed the expression of thousands of genes in response to the desiccating environment of Antarctica, is just one example of the power that the genomic revolution offers for advancing polar science. "

The collaborative research—which included contributions from scientists at Ohio State University, the Centre National de la Recherche Scientifique (National Center for Scientific Research) in France, Catholic University of Louvain in Belgium, Stanford University, and Miami University in Ohio—was supported in part by the Division of Polar Programs in NSF's Geosciences Directorate.

Polar Programs manages the U.S. Antarctic Program, through which it coordinates all U.S. research on the southernmost continent and aboard ships in the Southern Ocean as well as providing the necessary logistical support.

The finding also adds to the developing picture of the Polar Regions as having similarities and yet subtle and perhaps very important differences, previously undetected by science. NSF-funded scientists late last year, for example, published research indicating that differing contributions of freshwater from glaciers and streams to the Arctic and Southern oceans may be responsible for the fact that the majority of microbial communities that thrive near the surface of the Polar oceans share few common members.

Although Antarctica's surrounding oceans and coastal margins are home to a variety of large creatures such as seals, penguins and whales, insect life is rare, except on the Antarctic Peninsula.

There, the Antarctic midge, Belgica antarctica, occupies its unique ecological niche.

The research team that produced the new findings collected specimens for their research from offshore islands near NSF's Palmer Station on Anvers Island in the Peninsula region.

Surrounded by an ocean, the Antarctic continent is a polar desert where creatures have adapted to life with infrequent access to liquid water. The researchers note that Antarctic midge larvae, for example, "are remarkably tolerant of dehydration, surviving losses of up to 70% of their body water."

The larvae of Belgica antarctica, a flightless midge and Antarctica's only indigenous insect. Credit: Photograph by Richard E. Lee, Jr., NSF

Among Antarctic insects, the ability to tolerate dehydration is an important evolutionary development, allowing the creatures to successful survive the cold and dry southern winter.

"The loss of water enhances acute freezing tolerance," they write. "In addition, overwintering midge larvae are capable of undergoing another distinct form of dehydration, known as cryoprotective dehydration.

Cryoprotective dehydration is a mechanism in which a gradual decrease in temperature in the presence of environmental ice "creates a vapor pressure gradient that draws water out of the body, thereby depressing the body fluid melting point and allowing larvae to remain unfrozen at subzero temperatures". They also note that, in general, "insects, in particular, are at high risk of dehydration because of their small body size and consequent high surface-area-to-volume ratio."

The researchers compared the midge's strategy to those of other terrestrial arthropods that cope with prolonged periods when water is lacking, including the Arctic springtail, Megaphorura arctica and Folsomia candida, which are more widely distributed across the globe; both species are members of a group of arthropods, which are closely related to insects, known as Collembola.

The differences, they concluded, lie in the way that various genes express themselves.

After a detailed analysis of gene expression in the various species, the researchers concluded that "although B. antarctica and M. arctica are adapted to similar environments, our analysis indicated very little overlap in expression profiles between these two arthropods."

They add that "these differences in expression patterns may reflect different strategies for combating dehydration; whereas B. antarctica shuts down metabolic activity and waits for favorable conditions to return, F. candida [instead] relies on active water-vapor absorption to restore water balance during prolonged periods of desiccation."

They further add that because of the taxonomic difference between the Antarctic midge and the collembolan species with which gene expression was compared, more work is needed "to better understand the evolutionary physiology of dehydration tolerance in this taxonomic family."

Source: National Science Foundation