Why is subsurface microbiology so important for CCS monitoring, safety and risk assessment? (Sophie Nixon and Leanne Walker)

Professor Sophie Nixon and Dr Leanne Walker, at the University of Manchester, were awarded UKCCSRC Flexible Funding in 2023 for research into “Microbiological response to geological CO2 storage“.  This project has led to further collaborations with industry investigating microorganisms in the subsurface, trying to build a picture of baseline microbial communities across as many different CO₂ storage settings as possible in order to understand how they respond to CO₂ injection, and when that response might matter for storage.

What issue is your research trying to address?

Sophie: In the broader sense, our research comes from an acknowledgement that the deep biosphere is highly diverse and extensive, but still poorly understood.  There is a lot of life in the subsurface, and we know from decades of oil and gas exploration that this activity can have significant consequences. Microorganisms can contribute to reservoir souring, biofouling and corrosion.

Whenever we intervene in the subsurface, we perturb the conditions for native microorganisms already living there, as well as introducing new organisms and substrates from the surface. Yet this biological component of the subsurface is often overlooked when we think about emerging technologies, including carbon capture and storage (CCS).

We don’t yet know whether microbial activity in a CO₂ storage facility will pose a risk, or perhaps an opportunity, or simply be inconsequential under prevailing conditions. We want to understand which microorganisms are present in prospective storage formations and how they respond to CO₂ injection. Could their activity create problems over the very long timescales required for permanent CO₂ storage? Or could some microbial processes actually contribute to storage security, for example, by mediating or expediting the conversion of CO₂ into mineral forms?

Ultimately, we need to consider these storage environments as whole systems. A geological storage formation is a natural system in which microbiology interacts with geochemistry, geophysics and geology. Within this system, the goal of CCS is not to protect an asset (like in conventional and unconventional hydrocarbon recovery), but to ensure the secure storage of CO₂ deep in the subsurface over tens of thousands of years. So, although there are parallels with what has come before, we are dealing with a system that is fundamentally different in purpose, and that must remain stable over very long timescales.

Ideally, our work will help ensure that subsurface microbiology is considered appropriately in CCS monitoring, safety and risk assessment.  The aim is not to argue that microbiology will always be important, but to develop the evidence that is needed to understand when it matters, how much it matters, and what we should do about it.

Are people forgetting that there are other forms of life present in the storage facilities, e.g. the aquifers or the old oil fields, rather than them being empty vessels?

Sophie: Sometimes yes. People who aren’t directly involved in field operations can be quite far removed from the biogeochemical reality of the subsurface.

We’ve encountered assumptions that there is no water in these environments, or that they are effectively sterile. But microbial life is widespread in the subsurface. Our motivation is to make sure its potential influence on engineered systems isn’t ignored, whilst also avoiding the assumption that microbial activity is necessarily negative.

There may be opportunities as well as risks. If organisms from these environments have evolved unusual ways of using CO₂ or surviving under extreme conditions, understanding them could reveal useful processes that we can harness everywhere. In that sense, there is an element of bioprospecting to our work too: CCS gives us access to fascinating and underexplored communities of microorganisms who may hold biotechnological promise for a greener future.

What did you do with the Flexible Funding Award in 2023?

Leanne: We had some industrial collaborators who provided us with samples from various industrially relevant sites – lots of them were water samples from currently operating oil fields. From those samples, we were able to extract the DNA, so that we could then try and profile the microbial communities, and what they could possibly do in response to CO₂. We also had some culturing bottles – which is the paper we’ve currently got under review – and we were looking at how microbial communities respond to high concentrations of CO₂. One of the big conclusions from that work is that even in the presence of high concentrations of CO₂, we were able to see evidence of microbial processes persisting that are known to cause problems in conventional oil and gas. They can still carry out those processes even under saturated CO₂ conditions, although at a lower rate than we saw in the oil field simulations. That tells us that high CO₂ alone doesn’t necessarily eliminate this activity. If we can detect it over a six-month study, it highlights why we need to understand whether, and under what conditions, it could become significant over the much longer timescales of permanent CO₂ storage.

Field trip to Bergen, NO, with the Northern Lights CCS project onshore systems in the distance

Subsurface microbial activity can have big implications on asset integrity via corrosion and leak pathways. Once CO₂ injection wells become permanently sealed, site operation becomes an abandonment management strategy. Many CCS operator license agreements outline company liability for 20 years of asset maintenance after operation stops. After those 20 years the liability for well maintenance reverts to the government and becomes a taxpayer issue. So, understanding whether microbial activity presents a meaningful long-term risk – and under what conditions – is important not only for operators, but for ensuring that CCS remains safe and secure long after active site management has ended.

Are you able to make suggestions about how to mitigate, or do you present the situation to people and they then need to find mitigations?

Leanne: It depends whereabouts in the world you are, because that’ll have a big impact on legislation, on what chemicals can go into the ground, etc. For example, if it’s in the North Sea, there are only two biocides which are legislated for use in the subsurface – THPS and glutaraldehyde. However, chemical selection will also depend on logistical feasibility, for example, if treatment is needed, how frequently the chemical would need to be applied compared with the logistics of how often the chemical can be dosed in the field. Chemical vendors can recommend what the best chemical will be – operationally, economically, logistically, etc. – but the difficulty with all of that is that it’s largely untested.

Sophie: There are, broadly speaking, three target formation types: saline aquifers, depleted oil and gas reservoirs, and mafic/ultramafic formations. Depleted oil and gas reservoirs have the most information available in the literature, mainly due to historical CO₂ injection for enhanced oil recovery. We understand saline aquifers less well because there isn’t the same legacy of exploring them – historically, there hasn’t been much reason to do that unless you want to put something in them. That is changing, but there’s likely to be huge variability from site to site, and we’re still not really sure how that translates into the microbiology. We know even less about mafic and ultramafic formations might behave as storage formations. Each formation type is likely to have a different biogeochemical baseline, and we currently have very little information about how native communities in these formations might respond to injected CO₂ or to any microbial control treatments that might be used.

Iceland basalt deposits, and subsurface Icelandic basalts are target formations for CO2 storage

In my view, recommending specific remediation strategies is outside the scope of our research. Our role is to provide the microbiological evidence needed to understand whether intervention is warranted and to inform further investigation where it is.

Our research is still very exploratory, and we’re also interested in broader questions about the deep biosphere – what lives there, and how does life adapt and evolve in these extreme environments? Those questions are interesting in their own right, beyond the industrial implications for subsurface engineering operations.

Leanne: One thing we see a lot in our discussions with different companies involved in CO₂ storage, is that, realistically, it’s always going to be a race to be second. No one wants to be the first to implement something that costs them more money when there’s little evidence at this stage that they need to be doing it. There’s a sense that there isn’t enough data to be proactive about, and that’s where we’re trying to fill the data gap: providing evidence to understand when microbial activity needs to be taken into account, as well as data demonstrating where microbial activity could enhance CO₂ sequestration in the subsurface.

Sophie: We’re working closely with Equinor now, and hopefully they’ll be the first, then others will queue up to be second.

We’ve been looking at some analogue systems that have such a high salinity that life is already very restricted, and is further inhibited by exposure to CO₂. So, it’s also about understanding the conditions in which we don’t need to not worry about microbial activity. We need to build up a picture of when microbiology matters, when it doesn’t, and what it might do, so that we can make better-informed decisions about CO₂ storage.

What other funding have you had since that Flexible Funding project, and what work have you built on top of that award?

Sophie: I have a large fellowship, which comes to an end this year, focused on CO₂ storage microbiology, so the Flexible Funding Project fitted within that wider programme and allowed us to extend the work in new directions. It enabled us to develop ideas with Equinor and others, which has led to a directly funded project with Equinor. Through that we’ve gained access to a large number of samples from relevant oil fields, storage formations and active CCS sites. Accessing representative subsurface fluids was one of the first objectives of my fellowship when it began in 2021, but building the relationships needed to access these samples has taken time. So, developing that project with Equinor has been a major outcome.

We’re also developing new research looking at some of the less well-understood environments relevant to CO₂ storage. That will allow us to broaden the range of geological settings we study, while exploring both the potential risks and opportunities associated with subsurface microbial activity.

Leanne: We also have a project at the moment with a service company, who are providing us with various North Sea samples. And we have a collaboration with ExxonMobil, which was part of this project originally, and it’s continued beyond that.

What do you hope to achieve with all the work you’re doing right now?

Sophie: We’re trying to build a picture of baseline microbial communities across as many different CO₂ storage settings as possible. That’s not the end goal in itself; it’s the foundation we need to understand how microbial communities respond to CO₂ injection, and when that response might matter for storage.

There are two sides to that. The applied question is how microbial activity might affect what we’re trying to achieve with CCS. But there’s also a fundamental discovery aspect, which is the reason I’m interested in the deep subsurface in the first place. It’s a window into a vast difficult-to-access reservoir of microbial life that we still know remarkably little about. These organisms survive in extreme environments, often far removed from sunlight and surface hydrology, and understanding how they’ve adapted to those conditions can teach us a great deal about microbial life more broadly.

For us, those two perspectives are complementary. We want to understand these communities and how they function but also ask how that knowledge can be useful. Being both discovery- and application-focused is much more powerful than either in isolation: the fundamental microbial ecology gives us the evidence base to understand where microbiology matters for CCS, while the application gives us a reason – and an opportunity – to explore these fascinating systems.

We haven’t got an agenda, it’s important to us that we approach this honestly. If we find that microbial communities don’t respond significantly to CO₂ injection under particular conditions, that’s a positive result and removes uncertainty. Equally, where microbial activity does matter, we need to understand how and why.

For me, the bigger point is that CCS needs to be approached as a system-level science. Microbiology isn’t an additional consideration to bolt on afterwards, it’s an integral part of an interconnected system alongside the geology, geochemistry, physics and engineering.