Hydraulic fracturing, or fracking, is a key method for harvesting the fossil fuels that power much of the world. To frack means to increase the permeability of subsurface rocks deep in the Earth to extract oil and gas trapped inside. Microbes—which populate fracking fluids, subsurface reservoirs, operation products and equipment—complicate this process by decreasing oil and gas quality and corroding equipment. Learning more about the form and function of these microbial communities is necessary for minimizing the economic, environmental and health risks of fracking as we transition toward a more sustainable future. 

What is Fracking?

Fracking frees oil and natural gas ensconced in the tiny pores of shale, a fine-grained sedimentary rock layered miles below the earth’s surface. The fracking process involves drilling a wellbore several miles into the Earth to bisect oily or gassy shale formations (known as “shale plays”), then drilling horizontally for a couple more miles to cover as much (under)ground as possible. Fluid shot through holes along the wellbore creates fissures in the rock. This “frack fluid” contains water, chemical additives and particles (e.g., sand or ceramic pellets), which prevent the rock fractures from closing during extraction. 

Following a shut-in period, the fluid eventually returns to the surface, along with the extracted oil or gas. The composition of this fluid varies depending on time from post-shut-in. Flowback—the first fluid to return from the Earth’s depths—is similar in composition to the initial frack fluid, whereas produced water, which is generated over the course of the well’s lifetime, is saltier and contains extracted hydrocarbons (i.e., oil and gas) along with other naturally occurring compounds (e.g., metals). Both flowback and produced water are collected before being treated and recycled or disposed of, often by pumping them far underground. 

The Microbiology of Fracking

Some of the challenges associated with fracking are linked to microbes. For example, bacteria can produce corrosive compounds that weaken the integrity of fracking infrastructure and equipment—thus increasing chances of equipment failure and/or leaks—as well as release hydrogen sulfide that “sours” extracted hydrocarbons. As such, “if we understand the microbiology of these [fracking] systems, we can have smarter, more targeted biocontrol treatments,” said Djuna Gulliver, Ph.D., an environmental engineering researcher at the National Energy Technology Laboratory. “In addition, the microbiology in these systems can signal different types of subsurface and infrastructure behavior that we otherwise wouldn’t understand.” 

But where exactly do shale-dwelling microbes come from? Subsurface shale environments aren’t necessarily conducive to microbial habitation, due to factors like low permeability and nanometer-sized pores (in which microbial cells, most of which fall in the micrometer range, can’t fit). While the answer is still unclear, it is generally thought that microbes present in fracking inputs (e.g., frack fluid) may seed fissures formed during the fracking process and proliferate within the new spatial niches, leeching nutrients from fracking fluids to support their growth.  

To that end, microbial communities associated with fracking typically include methanogens (methane-producing organisms), bacteria with fermentative metabolisms and those that produce hydrogen sulfide from sulfate or thiosulfate (abundant environmental salts). Sulfide-producing organisms—including species of Halanaerobium, a bacterial genus with thiosulfate-reducing capabilities—are particularly problematic for fracking operations due to sulfide’s ability to corrode metal equipment and present operational hazards. Gulliver’s research suggests that frack fluid can leach sulfate from shale, especially as it travels to other wells in a shale play; this may provide further metabolic fuel for sulfide-reducing organisms and subsequently lead to more sulfide production, thus triggering a vicious cycle.

However, while there are commonalities, not all shale environments are the same and, thus, neither are the microbial communities associated with them. For example, Halanaerobium is abundant in the Marcellus Shale, which spans New York, Pennsylvania and West Virginia, and the Permian Basin in Texas and New Mexico, but is absent in plays in Oklahoma and the U.K., likely because these areas have lower salinity than salt-rich basins where Halanaerobium thrives. 

“Since there are so many different shale plays, and there is so much heterogeneity amongst the shale plays, the microbial ecology is still not completely understood across all these different environments,” Gulliver noted. Factors like salinity, temperature and even the presence of bacteriophages (viruses that infect bacteria) influence the composition and function of microbial communities recovered from produced fluid. Moreover, biocides are routinely added to fracking fluid to minimize growth of biofilms and may also shape community structure by selecting for biocide-resistant bacteria, which can obviate the efficacy of the biocide and may create “hotspots” of resistant organisms.  

New Tools for Analyzing Shale Microbiomes

The microbial variability between shale plays means that tactics for managing microbes associated with fracking systems may also change on a play-by-play basis. “There’s not just going to be 1 single microorganism that dominates every well that’s drilled,” said Kaela Amundson, a graduate student studying subsurface shale microbiomes at Colorado State University. For this reason, she noted, it’s important to be able to profile shale microbiomes, including delineating the identities and functions of subsurface shale microbes.

With that in mind, Amundson and her peers are developing a database and toolkit, called MAP-FRAC (Microbes Affecting Production in FRACturing systems), that allows researchers to examine the community composition and functional potential of shale microbial communities. In addition to taxonomic classification, MAP-FRAC summarizes the metabolic functions of metagenome-assembled genomes (MAGS) from shale samples. Amundson explained that analyzing these types of data is normally a complex, computationally expensive process that comes with a steep learning curve.The goal of MAP-FRAC is to make it easier and more efficient for scientists to disentangle the structure and metabolic processes of microbes in fracking wells, and potentially other engineered systems. 

For example, using MAP-FRAC, Amundson and her colleagues analyzed 978 MAGS from samples collected from 36 shale wells across 11 basins in the U.S., Canada, China and the U.K., representing a range of microbes from shales in diverse geographic regions. They found that no bacterial phyla were shared across all 11 basins, underscoring the microbial variability between shale environments.

Yet, despite the unique community compositions, there were 3 microbial metabolisms (i.e., fermentation, sulfate reduction and methanogenesis) that cropped up across basins, albeit with some slight variations in relative frequency. The findings indicate that while the organisms may differ from 1 shale basin to the next, there are common metabolic processes used by the organisms to survive in those environments. “It’s very useful to have a dedicated tool to analyze this large amount of data to be able to easily see how [these microbial communities] differ and how they’re similar,” Amundson said, noting that the next step is determining how to use information gleaned from these analyses in the field.

Gulliver and her team are also working to develop an easily searchable microbial DNA database that is specific to produced water. She highlighted that the database could be useful for determining how to manage produced water with microbial processes in mind. Coupled with computational analyses, the database could also be used to “identify microbes that have an outweighed impact on the microbial community,” associated with fracking systems, Gulliver said. Ultimately, identifying and targeting these so-called “keystone species” could guide more targeted biocide mitigation strategies as opposed to wiping out every microbe that might be present.  

Moving Toward a Sustainable Future

Fracking feeds the supplies of oil and gas that have contributed to climate change. So, why study the microbial underpinnings of fracking at all? Shouldn’t scientists turn their attention to renewable energy systems?  

The reality is that fracking underlies a large fraction of energy produced in the U.S.—in 2022, an estimated 80% of total dry natural gas production and 66% of total crude oil production in the U.S. were tied to fracking. And, according to Amundson, fracking “is projected to continue to be an important aspect of the U.S. energy portfolio in the coming decades.” Of course, she stated, the transition to renewable energy is critical—but this transition is not quick, and it varies on a state-by-state basis. As such, fracking is sometimes framed as a “steppingstone” or “gateway” to renewables. In a 2016 study, scientists reported that, over a 30-year period, energy from fracked natural gas could be used to build a wind, water and solar system capable of providing 83% of U.S. electricity demand. The use of natural gas extracted via fracking has also reduced how much coal the U.S. burns, which, while still a fossil fuel, has significantly larger CO2 emissions.

By studying microbes associated with fracking, researchers can ensure the systems work as efficiently as possible amid the development and deployment of sustainable energy options. In addition, Gulliver highlighted that “understanding the microorganisms of these systems helps...[us] understand how to monitor [fracking wells] and what processes might be happening as we decide to retire them.” If not plugged up and managed properly, retired wells can leak methane, an atmosphere-warming gas, and other pollutants into the environment. There’s also potential to use existing fracking infrastructure for new purposes, such as for storing hydrogen in the event the U.S. moves away from a carbon energy economy (fossil fuels) toward a hydrogen fuel economy. Knowing which microbes are present, or may emerge, in fracking wells is useful for determining if and how the wells can be repurposed.

Despite their negative effects in fracking systems, microbes are also being explored for their potential to clean up some of fracking’s byproducts, such as removing harmful compounds and organic matter from produced water. “I think microbes are amazing. I think that microbes can do anything.” Amundson said. “And so, if we can figure out how to leverage microbes [associated with fracking], that would be really powerful.” 

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Research in this article was presented at ASM Microbe, the annual meeting of the American Society for Microbiology, held June 15-19, 2023, in Houston.

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