An interview with Dr Sophie Nixon

March 2020

Dr Sophie Nixon is a Natural Environment Research Council (NERC) Research Fellow in the Department of Earth and Environmental Sciences, University of Manchester. She is also a member of the Microbiology Society and in this interview, tells us more about her research into the role of microbiology in shale gas extraction and the potential for microbial life on Mars.

© Sophie Nixon

Tell us about your research.

I study microbial life in the deep terrestrial subsurface. The subterranean world harbours a rich diversity of microbial life and a substantial fraction of the planet’s biomass. Over the coming decades humankind will increasingly rely on the subsurface for resource recovery, gas storage and waste disposal; it is therefore essential to understand what role micro-organisms play in these engineering ventures. In the process, we can gain valuable insights into the limits of life on Earth and the potential for life elsewhere.

My current research, funded by the Natural Environment Research Council (NERC), focuses on the role of microbiology in shale gas extraction. Despite their extreme conditions, fractured shale environments harbour active and persistent microbial communities. The goal of my research is to better understand the microbial processes that can negatively impact on shale gas extraction, such as sulfide production and biocide resistance, as well as developing tools to diagnose and control these problems in industry. These issues also increase the risk of environmental damage, so a better understanding of the drivers of these processes paves the way to effective control. I use a combination of high-pressure subsurface simulation, anaerobic culturing, geochemical analysis and metagenomic approaches in my research. 

You have previously studied microbial survival in extraterrestrial environments. How did you go about this research and what were the key outcomes?

My PhD research focused on the feasibility of microbial life on Mars. Since Mars is so iron-rich, I focused on microbial iron reduction, which I argued is a compelling metabolism to support life on the red planet. To address this, I followed two approaches. First, I looked for iron-reducing microbes in extreme environments on Earth that in some way resemble Mars, for instance Iceland, the Rio Tinto river in Spain and subglacial environments. The second approach was to assess the different sources of chemical energy available for the metabolism. For this, I focused on the types of organic compounds present in meteorites that should have accumulated on Mars throughout its history, including unusual amino acids.

Key findings from this research showed that iron-reducing micro-organisms are widespread and cold-adapted in sediments beneath glaciers and that unusual amino acids, common to meteorites but rare on Earth, can support the metabolism, although they can be toxic.

I continue to research life in extreme environments on Earth and the potential for life elsewhere through external collaborations and through student projects. My current research in these areas draws more on understanding the diversity and function of life in extreme environments, using metagenomic and metatranscriptomic tools.

What qualifications did you obtain before starting this role?

I studied Geography at the University of Bristol for my undergraduate degree. It may sound like an unusual starting point for a microbiologist, but in fact the MSci course provided a solid foundation in environmental sciences, which built nicely on my Chemistry, Biology and Geography A levels, and introduced me to microbiology – the two dissertations I carried out addressed microbial life in glacial environments. This sparked my interest in life in extreme environments and led me to a PhD in Astrobiology, during which I became a fully-fledged environmental microbiologist. Since then, I have continued to study life in extremes but with a more practical outlook, undertaking several postdoc projects on the role of microbial life in high pH nuclear waste disposal scenarios and during shale gas extraction.

What are the professional challenges that present themselves and how do you try to overcome them?

Perhaps the biggest challenge I face is juggling the academic and industry-facing sides of my research. At the heart of my research interests are fundamental questions about the rules of life, such as how microbial communities degrade organic carbon and via which pathways. These insights feed into the development of practical solutions in addressing industry problems, such as which genes to target for biofouling assays.

Working in an academic institution where fundamental science dominates, it can be challenging to maintain both goals simultaneously. I have found the best approach is to maintain regular contact with my industry partners and present at industry-focused conferences. This contact with industry is invaluable to ensure the meaningful impact of the work I carry out; but it can also mean prioritising industry events over academic conferences – I am learning to live with the fear of missing out that results!

What is a typical working day for you?

My day tends to revolve around writing projects (papers, book chapters, proposals) and bioinformatics data analyses. I work increasingly with metagenomic data, and find myself chipping away at these for hours on end – it’s very addictive! My brain is sharper in the afternoons so I tend to spend the mornings working on data and concentrate on writing after lunch. Much of my experimental work is done off-site with my industrial partner, but I am known to venture to the labs from time to time. I also co-supervise masters and PhD projects, so my days are often punctuated with progress meetings and chats in the lab.

Tell us about your biggest professional achievement(s) so far

Being awarded the NERC Industrial Innovation Fellowship. I worked hard to nurture my industrial relationships over the past few years, even when working on unrelated projects and I am proud to cement this collaboration with a significant grant. It takes us a big step closer to translating fundamental science into practical applications. It has also been an invaluable stepping-stone to an independent career, enabling me to pursue new collaborations and visit other labs.

You are an active member of the Microbiology Society – tell us more about your involvement.

I have enjoyed presenting and hearing about other microbiology research at Annual Conference and have attended several Focused Meetings too. I really enjoy the breadth of subjects covered by the Society at these events, especially since the genomic approaches I use transcend the various subdisciplines, and there is a huge amount to be gained from stepping outside disciplinary silos from time to time.

Why is it important to be a member of an organisation like the Microbiology Society?

Societies such as the Microbiology Society are invaluable for networking and presenting at Annual Conference and Focused Meetings. They are also a source of support for travel grants to conferences and other research laboratories.

I was awarded a travel grant from the Microbiology Society to visit a research lab at the Scripps Institution of Oceanography in 2018. During this visit, I was able to learn high pressure culturing techniques and conduct experiments to simulate hydraulic fracturing conditions, which has led to a manuscript with an internationally-renowned research group and enhanced my fellowship research in the process. These types of awards are so valuable to early career researchers and are an excellent way of forging new collaborations and learning new skills.

Where did your interest in microbiology come from?

My interests stem from my undergraduate training, where the modules about microbial life in glacial environments quickly became my favourite. I started to appreciate that the natural world is teaming with microbial life and these micro-organisms play essential roles in biogeochemical cycling. To learn that even the most extreme environments on Earth host dynamic microbial consortia fascinated me and understanding life in extremes has remained at the heart of my research career to date; be it in the context of life elsewhere, or in the engineered subterranea of our own planet.

Why does understanding life on other planets matter to microbiology matter?

Whether we are alone in the universe is a fundamental question of profound importance to all of humankind. But it is especially important to microbiology, since the search for life beyond Earth is focused primarily on microbial life. We have a sample size of one, so we must find the limits for life on Earth in order to define habitability elsewhere and in doing so, we learn more about the microbial life on our own planet than we otherwise would. There are practical applications to this knowledge too: extremophiles represent reservoirs of enzymatic tools that can be harnessed in biotechnology – perhaps the best example is Taq polymerase, an enzyme from the thermophile Thermus aquaticus, integral to the polymerase chain reaction that underpins so much microbiology research.

Astrobiologists are increasingly looking at life in salty environments, since a number of environments beyond Earth are expected to be salty (think subsurface brines on Mars or subterranean oceans of icy moons Enceladus and Europa). Insights from this research will extend far beyond astrobiology and will doubtlessly lead to the discovery of useful novel enzymes that can operate optimally under salty conditions. Microbiology will play central roles in both the search for life elsewhere and the development of novel biotech solutions. It’s an exciting time to be a microbiologist!

If you are a member of the Society and would like to find out more about how you can get involved with Society activities and/or showcase your research, please email us at [email protected].