Lead Research Organisation: Newcastle University
Department Name: Civil Engineering and Geosciences


Microorganisms are the most abundant life forms on Earth. It is estimated that there are around 10 thousand, billion, billion, billion individual organisms belonging to two main microbial groups (the bacteria and archaea). This is 1 million times more than the estimated number of stars in the known Universe. It is believed that most of this vast population is found in deep sediments far below the ground and the sea floor. It is easy to think that this huge repository of buried biological (microbial) diversity is irrelevant to mankind, but nothing could be further from the truth.

This intra-terrestrial microbiota has been coined the 'deep biosphere' and it is central to the cycling of matter over geological timescales. Of more immediate concern is the role that certain deep biosphere organisms have played in modifying oil in situ in petroleum reservoirs. Most of the world's oil (e.g. the giant tar sand deposits in Western Canada) has been degraded by microbes in situ long before humans recovered the first drop of crude oil. Research from our group has uncovered the microbial processes responsible for crude oil biodegradation in petroleum reservoirs and identified biological and geological factors that promote biodegradation. One of these factors is temperature. The temperature of the Earth's crust increases with depth by approximately 2-3 C every 100 meters and petroleum reservoirs at temperatures above 90 C are not subject to biodegradation. However cooler, shallower reservoirs are not always biodegraded. These non-degraded, cool shallow reservoirs once resided at greater depths but have been moved by geological uplift to shallower depths. It appears that they are not re-colonized by oil-degrading bacteria and the oil in these reservoirs remains intact. This process of transient heating of a petroleum reservoir which kills the resident oil-degrading microbiota has been termed palaeopasteurization.

Research in the Arctic has provided a window into the petroleum reservoir deep biosphere. Cold Arctic sediments harbour bacteria that have optimal activity at around 50 C and may have come from leaky warm petroleum reservoirs because their closest relatives were previously identified in hot oil wells. These organisms form spores which are highly resistant to environmental extremes and act as survival capsules that protect the bacteria on their journey from deep within the Earth. These bacteria thrive without oxygen (anaerobes) and the spores resist exposure to oxygen. Sediments in the UK harbour spore-forming bacteria that degrade crude oil without oxygen, providing another link between bacteria and petroleum reservoirs. This project aims to determine if spore-forming oil-degrading and Arctic bacteria ultimately derive from petroleum reservoirs and if the process of palaeopasteurization kills them and prevents them seeding surface sediments.

The project focuses on fundamental science at the interface between biology and geology and has practical implications. A supply of hydrocarbon degrading anaerobes from the deep biosphere has implications for microbial diversity in surface sediments where these bacteria may play a role in oil clean up in oxygen depleted sediments (i.e., in coastal sediments but also the deep Gulf of Mexico seafloor near the Macondo wellhead). Related bacteria also cause problems in the oil industry by producing the toxic gas hydrogen sulphide in a process known as reservoir souring. This reduces the value of oil and poses a hazard to workers. The UK hosts a major offshore oil industry that contributes significantly to employment and economic prosperity. During the transition between a fossil carbon energy economy and a renewable energy economy, the need remains for innovative operational practices to reduce the environmental impact of oil production and exploration; much of this is underpinned by an understanding of microorganisms associated with oil production and oil degradation in the environment.

Planned Impact

Fossil fuels currently meet 80 to 90% of global energy demand. While it is essential that fossil fuel use is superseded by renewable energy sources, in the face of growing global population and large scale economic development in countries such as China, India and Brazil, it is unlikely that fossil fuel reliance will be eliminated in the short to medium term. The UK hosts a major offshore oil industry that contributes significantly to national employment and economic prosperity. It is essential that we continue to improve our understanding of the processes and organisms that dictate the fate of fossil fuels in the environment. Furthermore during the transition between a fossil carbon energy economy and a renewable energy economy, the need remains for innovative operational practices to reduce the environmental impact of oil production and exploration and also for discovery of new resources. The research proposed here is relevant to all of these issues and we have identified four domains where the work conducted will have impact, elaborated in the Pathways to Impact document.

1. Fate of spilled oil
2. Controls on the formation of biodegraded petroleum deposits
3. Petroleum reservoir souring
4. Offshore oil exploration

The areas on which the research impinges are wide-ranging. As a consequence OILSPORE will be relevant to environmental regulators such as the UK Environment Agency and Marine Management Organization (MMO), and similar agencies worldwide. It will also be of interest to the oil industry from the perspective of environmental management and in relation to exploration and production.

We have a strong track record of collaboration with major international oil companies and our biogeochemical research on crude oil biodegradation has been funded from UK research councils (e.g. NE/E01657X/1), the EU (BACTOIL and MICROBEOIL Marie Curie Fellowships, the last of these held by C. Hubert), and an industrial consortium of oil companies (Bacchus). Bacchus is a joint venture in collaboration with colleagues at the University of Calgary and is now in its third phase (see http://www.ceg.ncl.ac.uk/geoscience/research/projects/bacchus.htm).

Past projects have had demonstrable impact with the award of the Geochemical Society's prize for the best paper in organic geochemistry for 2009. The judges of this award included a senior oil industry scientist who noted that "The work has had a dramatic effect on current thinking about in-reservoir biodegradation, and the concepts in [the] paper are already in wide use within the academic and industrial geochemical communities. Indeed, in many respects it has revolutionized our thinking with regard to microbial degradation as a component of petroleum systems."

We will continue to work closely with the excellent network of industrial and academic collaborators with whom we currently engage. In addition, OILSPORE will establish new academic and industrial links (see letters of support), which we will develop by hosting a workshop that brings together stakeholders from industry, academia and government. An important element of our engagement activities for this project will be to extend our current network of engagement to include the Environment Agency and the MMO (recently relocated in Newcastle) to provide advice, criticism and new perspectives on our research in the context of environmental risk assessment and management.

Newcastle University's engagement strategy is focused on societal challenges with 2011 being designated the "Year of Sustainability". We will organize public lectures on the impacts of oil in the environment and the biological and physical processes responsible for dissipation of oil in the environment. Our lectures will communicate the importance of microbiological processes in purifying the environment and in sustaining the planet through the natural processes that recycle the elements in biogeochemical cycles.


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Daghio M (2016) Anodes Stimulate Anaerobic Toluene Degradation via Sulfur Cycling in Marine Sediments. in Applied and environmental microbiology

Description Full complement of staff only recruited in project by February 2013 and project therefore in very early stages.

We are currently analysing samples to determine the identity of putative spore-forning oil-degrading sulfate reducers in samples that we have archived.

We identified candidate spore forming hydrocarbon-degrading bacteria and discovered that these are probably hydrocarbon fermenting bacteria that likely work in consort with syntrophic sulphate-reducing bacteria.

We are constructing genome assemblies from metagenomes to further establish the metabolic capabilities of the spore-forming hydrocarbon degrading sulphate-reducing consortia

We have initiated collaborations with a group in Ghent on the role of sulphate-reducing bacteria in hydrocarbon degradation in bioelectrochemical systems.
Exploitation Route Project only recently inititiated, however we held a workshop on 26-27 March with representatives from an international oil company as part of our pathways to impact plans.
Sectors Energy,Environment

Description Collaboration on reservoir souring with Rawwater Engineering 
Organisation Rawwater Engineering Company Ltd.
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Analysis of microbial communities in high pressure system exhibiting souring
Collaborator Contribution Operation of high pressure reactors, provision of samples, staff time
Impact Platform presentation: 21st Reservoir Microbiology Forum. November 2015. London. Pressurised, sand-packed bioreactors to demonstrate the impact of downhole pressure on the sulphate-reducing microbial community
Start Year 2015
Description Microbial ecology of petroleum reservoirs with Shell 
Organisation Shell Global Solutions UK
Country Netherlands, Kingdom of the 
Sector Private 
PI Contribution Postdoctoral Researcher seconded to sponsors labs in Houston, conducting metagenomic analysis and microbial community analysis on a range of petroleum-releated samples
Collaborator Contribution Funding, Provision of samples, bioinformatics support
Impact Vigneron A, Alsop EB, Chambers B, Lomans BP, Head IM, Tsesmetzis N. (2016). Complementary microorganisms in highly corrosive biofilms from an offshore oil production facility. Appl. Environ. Microbiol. doi:10.1128/AEM.03842. Platform presentation:5th International Symposium on Applied Microbiology and Molecular Biology in Oil Systems. June 2015. Stavanger Microbial profiling insights from an offshore oil field in South East Asia Platform presentation: 21st Reservoir Microbiology Forum. November 2015. London Linking subsurface geochemistry to microbes and MIC through metagenomics and multivariate analyses
Start Year 2014
Description Joint Oil Company-OILSPORE workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Project only recently inititiated, however we held a workshop on 26-27 March with representatives from an international oil company as part of our pathways to impact plans

Representative from our research group and oil company personnel presented areas of research of potential mutual interest. This was conducted in an open forum to allow participation of research students and research associates and was followed by a small
Year(s) Of Engagement Activity 2013
Description Visit to Rawwater Engineering 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Meeting with potential industrial partner to discuss potential research collaboration.
Year(s) Of Engagement Activity 2015