Wednesday, 05 July 2017 13:09

Fractured Shale Makes a Cozy Home for Sulfur-Cycling Microbes

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Published in mBiosphere

For about a decade, hydraulic fracturing, or the practice of injecting sand, water and chemicals at high pressure into shale formations deep below the ground surface, has boosted the oil and gas industry’s ability to recover more hydrocarbons from wells.

But for Mike Wilkins’ group at The Ohio State University in Columbus, it brought a unique way to look at ecosystem development among microbial communities living in one of the most unlikely environments on Earth.

mSphere report: Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

In 2016, his group was part of a team that published one of the first characterizations of the microbial community present in these hydraulically fractured, or “fracked” shale formations—a “pretty inhospitable” environment 2 kilometers underground of high pressure, high temperature and high salinity. It’s also pretty inaccessible.

So Wilkins’ group makes use of the well operator’s pump that draws the produced fluids, which contain the released hydrocarbons and any microbes flourishing down below, to the surface. “It continually pulls up fluids that have been sitting down there for months on end,” explains Wilkins, a biogeochemist. “It’s a way to get a chemical and biological look at what’s going on down there.”

While significant research has investigated the rock-water reactions in the subsurface during fracking, Wilkins’ group wants to get a better grasp of the microbiology. By combining temporal sampling with powerful genomics and proteomics tools, they track how the microbial community changes and behaves over time. They previously found several salt-tolerant microbial species persisted in the fracked shales over time.

“Humans are totally creating these ecosystems,” he says. In 2016, when his group sampled a pristine, un-fractured shale core from the US Department of Energy’s Marcellus Shale Energy and Environment Laboratory research site to see what might be living there before any human activity, they failed to find inhabitants. “Even with a whole series of molecular tools thrown at it, we couldn’t detect viable life, we couldn’t grow anything,” he recalls. That means the fracking process itself creates new, reactive surfaces to which microbes can attach and introduces chemicals these microbes might use.

In a study published this week in mSphere, Wilkins’ group further describes how one group of salt-loving microbes, Halanaerobium, is most likely using environmental thiosulfate to produce sulfide—a toxic and corrosive chemical that well operators would like to avoid. “Sulfide poses toxicity issues to people working on the well pad, but it also has to be stripped out of the hydrocarbon stream, which costs a huge amount of money,” Wilkins explains.

Sampling a well in southeastern Ohio above the Utica shale formation, the team used assembly-based, shotgun metagenomic sequencing in collaboration with Kelly Wrighton, an environmental microbiologist at Ohio State, to reconstruct the microbial genomes present in the produced fluids of the well. They showed that Halanaerobium grows like a weed, taking over the microbial community by 90 days post-fracking and dominating for at least the next 100 days. [image: banded mass sulfide, Wikimedia Commons]

When Wilkins’ group cultured one Halanaerobium isolated from the well in the lab, they showed that it could use thiosulfate, a natural product that can leach out of fractured shale, to produce sulfide. The team also measured the levels of thiosulfate, sulfide, and sulfur isotopes in the fluid samples from the well. While the sulfide levels were a bit erratic, going up and down over the 120-day sampling period, the thiosulfate levels dropped steadily over time, as did the levels of sulfur-32 compared to sulfur-34—an indication that microbes transformed the sulfur.

“Sulfide is very reactive, so the fact that we even measure it all the way at the surface means it’s probably an underestimate of what’s being produced by the microbes down below,” says Wilkins. The study’s data point to a trend for extensive sulfur cycling by Halanaerobium that results in sulfide production.

In addition to the problems of toxicity and well “souring”, sulfide precipitates or simply the biomass of Halanaerobium itself could easily clog up the fracture networks, which are literally held open by grains of sand, making extraction less efficient, notes Wilkins. Moreover, current industry tests for sulfide producers would not detect Halanaerobium.

Aside from the practical applications of discovering which microbes thrive in a fracked well and what they pump out that might be detrimental to oil and gas production, Wilkins marvels at the microbes’ ability to adapt to such a strange, human-made environment. Culturing Halanaerobium wasn’t all that difficult in the lab, he notes, as long as the media was salty enough.

“Salinity seems to be a master controller, a big constraint on life,” he says. “These guys preferred really salty media, saltier than the ocean and even the Great Salt Lake at about 15-20% salt.” Most cells introduced to such brine would immediately lose their water, shrivel up and die, but Halanaerobium have strategies for living in such a saline environment. They and other salt-tolerant microbes appear to prosper in fracked wells across the US. “Why do we see the same communities in Texas, West Virginia, and Pennsylvania?” asks Wilkins. “It’s an evolving idea, but perhaps because they all get to these same salinities.”

Last modified on Wednesday, 05 July 2017 15:08
Kendall Powell

Freelance science writer and editor, Kendall Powell covers the realm of biology, from molecules to maternity. She has written news stories, features and scientist profiles for a variety of publications including the Washington Post, Los Angeles Times, Nature, PLoS Biology, Journal of Cell Biology, Science Careers and the HHMI Bulletin. She is a contributor to The Science Writers’ Handbook: Everything You Need to Know to Pitch, Publish, and Prosper in the Digital Age (2013 Da Capo).