Unearthing the role of microbiology in shale gas extraction: a bioreactor approach

Lead Research Organisation: University of Manchester
Department Name: Earth Atmospheric and Env Sciences


More than 1300 trillion cubic feet of natural gas is estimated to reside in UK shale formations, kilometers below the surface. This resource has the potential to fuel the nation for decades, and bridge the energy gap between the UK's dependence on coal and oil towards the sustainable renewable energies of the future.
Natural gas is locked away in tight spaces within shale. To recover this gas for use as a fuel, these deep shale formations must be artifically fractured by a process called hydraulical fracturing. This process involves pumping millions of litres of water and chemicals into a horizontally-drilled well at high pressure, causing fractures to open through which natural gas can flow unimpeded.
Although the government supports the exploitation of the UK's natural gas reserves, there is deep public concern over the environmental risks of hydraulic fracturing, triggered by widely publicised reports of environmental damge from hydraulic fracturing in the US. Whilst a comprehensive independent report deemed the risks of extraction to be low when conducted properly, these concerns must be addressed in order for the full potential of UK economy to benefit from this resource to be met.
A number of chemicals that are added to injection water during hydrualic fracturing are known to stimulate microorganisms, and in particular microbial processes that negatively impact on natural gas and its extraction. These processes may lead, for example, to a depletion in additives in the input fluid (each of which serves a particular purpose in making shale gas extraction more efficient), as well as spoiling the natural gas, and causing corrosion of the well infrastructure. Collectively, these 'biofouling' processes lead to increased costs, reduced efficiency and a greater potential environmental impact.
The research I propose is designed to tackle these issues. In partnership with a UK oil and gas servicing company, Rawwater Engineering Company Limited, I will test an array of injection fluid chemicals (individually and mixed together) for their potential to stimulate biofouling processes. These experiments will be conducted using bespoke, high pressure bioreactors that are designed to mimic the conditions of UK shale formations. Throughout these experiments I will apply state-of-the-art techniques to monitor changes to the chemistry and microbiology, and in doing so unearth the role of microbiology in the efficiency of shale gas extraction.
The results of this research will shed light on the potential for injection fluid chemistry to stimulate biofouling, as well as the types of microorganisms that are responsible for these processes. In partnership with Rawwater and their links to the wider oil and gas industry, these results will allow me to develop diagnostic tools and control strategies that can be applied to field operations in order to maximise the efficiency and hence minise the environmental impact of shale gas extraction, to the benefit of the UK economy.


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Description Through this award, we have shown that the microbial communities in freshwater used to fracture shale for gas production are unable to withstand the high pressure and temperature conditions of the fractured shale environment. In other words, the microorganisms that are known to proliferate in the fractured shale environment are likely to come from other sources, such as the drilling mud and the subsurface.

We have also demonstrated that microorganisms in fractured shale environments are able to degrade the most common hydraulic fractured fluid additive, guar gum, but appear unable to use synthetic friction reducers (polyacrylamide). Guar gum degradation was coupled to the production of the toxic and corrosive by-product hydrogen sulfide, so our work has highlighted that using guar gum is likely to stimulate microbiological activity that could damange the gas extraction infrastructure.

Finally, with this award we have reported the presence, diversity and metabolic activity of microorganisms recovered from fractured shale environments in the UK. This is the first report of the fractured shale microbiome outside of North America and China.
Exploitation Route We have recovered a novel strain from the UK fractured shale environment I refocussed the project on, which will be used in future projects. Further, we have shared some of our data with existing collaborators in the US who will include our UK study site in a global metastudy of fractured shale microbiomes.

We also believe our findings on the relative degradability of guar gum will influence future hydraulic fracturing operations where alternative additives will be favoured instead. For instance, although guar gum is the cheapest polymer to use in hydraulic fracturing operations, the alternative synthetic polymer used in slickwater fracturing (polyacrylamide) is unlikely to stimulate damaging microbial activity in situ in the way that using guar gum is likely to.
Sectors Energy

Description Microbial carbon cycling under geological CO2 storage conditions: understanding the rules of life in the engineered subsurface
Amount £967,405 (GBP)
Funding ID BB/V00560X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 12/2026
Description Cuadrilla Resources 
Organisation Cuadrilla Resources
Country United Kingdom 
Sector Private 
PI Contribution I visited the head office to deliver a presentation to a small number of company staff relating to the microbiological implications of shale gas extraction
Collaborator Contribution Access to the drilling rig for sample acquisitioon, provision of flowback and produced water samples, permission to publish results
Impact This collaboraion has already underpinned two publications (Cliffe et al 2022 Microbiology Spectrum; Hernandez Becerra et al 2023 Environmental Microbiome) on which I am senior / final author. The samples acquired through this collaboration have underpinned two PhD studentship projects, including a NERC CASE project (Lisa Cliffe). There are a further 3 publications in preparation.
Start Year 2018
Description Scripps Institution of Oceanography 
Organisation University of California, San Diego (UCSD)
Department Scripps Institution of Oceanography
Country United States 
Sector Academic/University 
PI Contribution I visited the laboratory of Prof Douglas Bartlett for 3 weeks, partly funded through this award, in addition to a Deep Carbon Observatory Cultivation Interneship award ($3k). Whilst there, I gave a talk on my research, which facilitated a knowledge exchange from the trip.
Collaborator Contribution Access to laboratories, high pressure experimental facilities, analytical facilities, and input of intellectual contribution and technical expertise.
Impact A research paper, accepted in Access Microbiology, detailing our collaborative experimental work and findings. This work was also the turning point for the fellowship research plans since the outcome of these experiments was to prove the underlying assumption was incorrect.
Start Year 2018
Description Jodrell Bank Discovery Centre / NERC 'Meet the Expert' panel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact I gave a talk at a NERC 'Meet the Expert' event during the summer holidays of 2018, which took place at Jodrell Bank Discovery Centre. This talk was focused on my subsurface microbiology work (especially relating to shale gas extraction) and was followed by a Q&A session with the audience (>60 members of the public, mostly parents with their kids).
Year(s) Of Engagement Activity 2018
Description Pint of Science Manchester 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact I gave a talk on my subsurface microbiology research, much of which occurred as part of this grant
Year(s) Of Engagement Activity 2019