Lead Research Organisation: Newcastle University
Department Name: Sch of Engineering


There has never been a more exciting time to be at the interface of biological engineering and petroleum geosciences. Recent discoveries in geomicrobiology and methodological breakthroughs in DNA sequencing place us on the brink of an unprecedented understanding of the role of microorganisms in globally significant processes in subsurface petroleum reservoirs. Qualified estimates reveal that the vast majority of microorganisms on Earth inhabit the subsurface. Most newly discovered taxa in this 'deep biosphere' have no representatives in laboratory cultures, thus knowledge about their role in economically relevant biogeochemical cycles is unknown. Fossil fuel reservoirs are microbial habitats of great scientific interest and even greater societal importance. Microbes native to subsurface petroleum reservoirs can cause significant damage and economic loss. However, understanding and harnessing this 'petroleum microbiome' has great potential for engineering interventions for more sustainable petroleum production and novel exploration strategies.The next generation of engineers faces the unavoidable challenge of reducing global greenhouse gas emissions. The oil and gas industry is at the epicentre of this challenge. Currently fossil fuels account for greater than 80% of global primary energy supply, yet even under optimistic projections of rapid innovation and modest population growth fossil fuels will still supply 70% of our energy in 2030 (International Energy Agency, 2010). It is clear that the transition towards more sustainable energy will require several decades, that fossil fuels will continue to be essential, and that innovation is needed in all areas of the energy sector. It is critical therefore to develop new engineering interventions and novel technologies focusing directly on the oil indsutry so that existing resources are exploited as responsibly as possible.It has long been recognized that microorganisms are important constituents of petroleum reservoirs and oil production systems, with the presence of sulfate-reducing bacteria (SRB) being reported almost a century ago (Bastin, 1926, Science 63:21). SRB are well known in the oil industry because they cause reservoir souring - the production of toxic hydrogen sulfide (H2S). Souring costs the oil industry billions of pounds annually due to production problems related to H2S (e.g., corrosion) and the lower value of high-sulfur petroleum. Nitrate-reducing bacteria (NRB) can be stimulated to control souring in an environmentally friendly way, and while nitrate injection is a strategy beginning to be practised offshore, it remains poorly understood. The first major objective of DEEPBIOENGINEERING is to develop a new understanding of souring and nitrate-driven souring control by applying a combination of geochemistry, microbiology and high throughput nucleic acid sequencing to reservoir production waters and experimental cultures inoculated with them. This research will deliver an unprecedented understanding of the petroleum microbiome, which will underpin prediction-based bioengineering interventions for souring control.The second major objective of DEEPBIOENGINEERING is to exploit the knowledge of the deep petroleum microbiome to track the distribution of formerly indigenous reservoir bacteria. This will lead to a totally new tool for offshore oil and gas exploration. This idea is based on the observation of oil reservoir-like bacteria (thermophilic SRB) in cold ocean sediments (Hubert et al 2009, Science 325:1541) and the hypothesis that petroleum fluids leaking from reservoirs at natural seafloor hydrocarbon seeps is a mechanism for microbe dispersal that can be quantitatively measured. This will lead to predictive models and concepts that will be use bioindicators to map the seafloor and predict or locate seabed hydrocarbon seeps. This environmentally friendly tool will assist offshore exploration for needed petroleum energy resources.

Planned Impact

Our high living standards in the UK are inextricably linked to fossil fuel energy. Currently fossil fuels account for greater than 80% of global primary energy supply. It is widely acknowledged that this must drop, and in the future new technologies for renewable energy will be required to replace fossil fuels. But when will this future arrive? Even under optimistic projections of rapid innovation and modest global population growth, fossil fuels will still supply 70% of our energy in 2030 (International Energy Agency, 2010). It is clear that our transition towards more sustainable energy sources will require several decades and that fossil fuels will continue to be essential. It is therefore critical to UK society and the UK economy that development of new energy technology includes a focus on the fossil fuels sector so that existing resources are exploited as responsibly and sustainably as possible during this slow transition. This is also strategic, since the UK hosts a major offshore oil industry that contributes significantly to national employment and economic prosperity.The DEEPBIOENGINEERING project promises concrete societal and economic impacts by focusing on innovative and more environmentally sustainable ways to produce petroleum and discover new petroleum reserves. The research proposed here represents a whole systems approach to energy by incorporating engineering with biology and geosciences. The work conducted will have broad impact touching on at least the following four domains:1. Souring control for more sustainable petroleum resource productionSouring (H2S production in oil reservoirs) costs the oil industry billions of pounds annually and is hazardous to offshore workers. Souring mitigation has traditionally used aggressive biocides that are carcinogenic and harmful to marine life. Nitrate injection therefore represents an environmentally friendly alternative, and is poised for widespread use if its efficacy can be understood through enhanced knowledge of the underlying microbiology and geochemistry. Our data will feed into predictive models (see letters from UK industrial partners Chevron and Rawwater Engineering) to allow oil companies to confidently deploy nitrate technology in their day to day operations, thus producing essential petroleum resources more cleanly and efficiently.2. Development of novel bioindicators for environmentally benign offshore oil and gas explorationSignificant fossil fuel resources exist in remote regions of the world including beneath deep water or in remote polar seas (Gautier et al 2009, Science 324:1175). New low cost technologies that feature environmentally benign sampling procedures will be highly attractive as existing energy reserves dwindle and new sources are sought. The use of seismic testing in offshore exploration is coming under increasing scrutiny and regulation, given our growing understanding of the effects of acoustic pollution on marine mammals. More sustainable tools and concepts for geoenergy resource mapping will also be useful for policy makers and environmental regulators in coastal states like the UK, where delineating marine protected areas within exclusive economic zones is a priority. In deep water and polar regions, companies and governments will be able to use the data generated for developing policies on offshore exploration in high risk and sensitive areas.3. Bioremediation of spilled oilIncreased understanding of the biogeochemistry of oil degradation by microorganisms will be of direct societal and economic benefit in relation to dealing with oil spills. As such this research will be relevant to environmental regulators such as the UK Environment Agency and similar agencies worldwide.4. Public outreachEnergy is on the public's mind. The public is less familiar with life in the deep biosphere. Outreach related to the 'petroleum microbiome' will stimulate awareness about where our energy comes from.


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Callbeck CM (2013) Improving PCR efficiency for accurate quantification of 16S rRNA genes. in Journal of microbiological methods

Description Different endospores of different Desulfotomaculum species have different heat resistance. This has been useful for developing a new model for understanding the onset of reservoir souring in hot deep biosphere oil reservoirs, and ExxonMobil has funded follow up research on the topic in our lab. New experiments have further determined the survival limits of thermophilic endospores.

New genomic and bioinformatic methods for assessing the diversity of thermophilic spores in a biogeographic context in order to ascertain likely source environments causing dispersal of endospores from hot to cold habitats.

The degree of existing crude oil biodegradation in situ determines the further ability of subsurface microbial communities to bioconvert residual oil into valuable products such as methane. Bituminous sands in Canada were investigated and it has been determined that they are highly unreactive, leading to detectable but low levels of biogas production. This work provides a useful end member for fossil fuel based conversions to cleaner energy vectors like methane or oil-to-electricity.

Reservoir souring collaboration with Rawwater Engineering is going well and as originally planned, with the company benefiting from additional genomics information that the EPSRC efforts are providing.
Exploitation Route end-user workshop with colleagues from Shell in March 2013
interest and new funding from ExxonMobil in 2013 and 2014
Sectors Energy,Environment,Other

Description ExxonMobil is considering changing the way they inject seawater into offshore oil reservoirs for oil production, based on research that they sponsored in our lab, linked to this EPSRC fellowship project. ExxonMobil collaborators are presenting these findings at scientific meetings and a manuscript for submission has been approved by ExxonMobil management.
First Year Of Impact 2014
Sector Energy,Environment
Impact Types Economic

Description Genome Canada biocorrosion project in Calgary AB Canada led by Lisa Gieg with Sven Lahme and Casey Hubert as co-applicants
Amount $4,000,000 (CAD)
Organisation Genome Canada 
Sector Charity/Non Profit
Country Canada
Start 10/2016 
End 09/2020
Description Genome Canada grant for understanding offshore oil spills in the Arctic; PI Casey Hubert University of Calgary
Amount $5,000,000 (CAD)
Organisation Genome Canada 
Sector Charity/Non Profit
Country Canada
Start 10/2016 
End 09/2020
Description ExxonMobil KB 
Organisation ExxonMobil
Country United States 
Sector Private 
PI Contribution Research experiments performed in Newcastle
Collaborator Contribution Funding and some sequencing and bioinformatics performed by ExxonMobil colleagues
Impact Presentation at 9th International Symposium on Subsurface Microbiology that included ExxonMobil scientists as co-authors (i.e., ppt slides were approved in advance by the company management)
Start Year 2013
Description Rawwater Engineering 
Organisation Rawwater Engineering Company Ltd.
Country United Kingdom 
Sector Private 
PI Contribution We provide genomics analysis to the company to help them understand the microbiota in reservoir simulation high pressure bioreactors that they operate for their clients in the oil and gas industry
Collaborator Contribution staff time in kind
Impact co-authored presentations at conferences, sometimes by Newcastle University staff and sometimes by Rawwater staff
Start Year 2014
Description Biogeography and the deep biosphere: deep-to-shallow dispersal routes revealed by thermophilic endospores in cold marine sediments. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact invited speaker at the 14th International Symposium on Microbial Ecology (ISME) meeting in Copenhagen in August 2012, and at the 15th ISME meeting in Seoul South Korea in August 2014. Also session chair for the 2014 meeting.

After my talk in 2012 the leading scientist in microbial biogeography, from UC Irvine, informed one of her PhD students about our research. Once the PhD student graduated, she applied for an EPSRC post doc position, was top ranked out of ~100 applications, was hired, and moved from California to Newcastle for a post doc opportunity.
Year(s) Of Engagement Activity 2012,2014