Exploring the fascinating world of industrial microbiology, from career advice on how to break into the field to insights into how industry is using micro-organisms to solve global challenges.
MICROBIOLOGY TODAY 50:1 May 2023
Exploring the fascinating world of industrial microbiology, from career advice on how to break into the field to insights on how industry is using micro-organisms to solve global challenges.
Editor Chris Randall Deputy Editor Victoria Easton
Managing Editor Kimberley Ndungu Production Editor Raymond Antwi Editorial Board André Antunes, Raphael Galleh, Mel Lacey, Michael Macey, Arindam Mitra, Catrin Moore, Marta Filipa Simões, Michael Ukwuru, Ashish William Design Rob King, Debbie Webb, Ian Atherton (@corbiculadesign)
From the Editor
“Hello, and welcome to the May 2023 issue of Microbiology Today !”
A s I enter my third and final year as Editor of the Magazine, I can’t help but look back over my editorials (and all the wonderful articles!) from past issues and reminisce
In our first issue of 2023, we have a focus on the industrial side of microbiology. We start the issue with an article from Matt Streets at Rawwater. Matt shares with us a discussion on the role of micro-organisms in the ‘souring’ of oilfield reservoirs. This souring is a consequence of hydrogen sulfide produced by sulfate- reducing prokaryotes and leads to the formation of corrosive substances which cause significant damage to production facilities. In his article, Matt describes the processes by which souring occurs, and how this can be modelled and managed effectively. Our second article continues our industrial theme with Oliver Severn from Singer Instruments, who has provided us with an excellent guide on progressing in your career. Oliver reflects on his own transition from academia to industry and has distilled his careers advice into three key steps for people to follow, with lots of practical advice and personal insights. To finish our issue, we have two articles exploring a well-known application of industrial microbiology – the production of mycoprotein. First, Jose Munoz and Jonathon Woods explain the importance of understanding how the human gut microbiota interacts with mycoprotein, given the important role this microbiota plays in our overall health. Munoz and Woods focus their article on key components of mycoprotein – mannan-based glycoproteins (mannoprotein), β -glucan and chitin – and explore the mechanisms by which these components can support the growth of beneficial organisms within the gut microbiota. Continuing our mycoprotein focus, the issue ends with a comment by Angel Li from Enough foods. Angel gives an overview of the impact of the global food system (particularly meat and dairy production) on the climate crisis and how replacing this system with alternative proteins like mycoprotein can help mitigate this. Angel then discusses the growth of start-ups in this area and the obstacles they face to break into the wider food system.
about the fun I’ve had in this role. Despite starting in the middle of a pandemic, it’s been such a pleasure to talk to individuals so passionate about the work they do and to
help convey this passion to you, the reader, in the pages of this magazine. Before I share with you the contents of this issue, I’m delighted to announce that Dr Victoria (Vikki) Easton joins me this year as Deputy Editor of Microbiology Today . Vikki will be working with me before shedding the ‘Deputy’ part of her title and taking over as Editor in 2024.
Hello! I am thrilled to be the new Deputy Editor of Microbiology Today . As Chris said, my name is Vikki, and I am a virologist at the University of Leeds. I first became a member of the Microbiology Society as a PhD student in 2013. If you had told me then that 10 years later I would have a role within the Society, I would
have laughed. Little did I know then that I would attend Annual Conference (almost) every year, let alone that I would look forward to meeting new and old friends there. Since becoming a member, I have been continuously awed by the fantastic community of world-leading scientists within the Microbiology Society, and I see Microbiology Today as a huge part of that community. I am very glad that I have a year of ‘on the job’ training as Deputy Editor, as I feel like I have big shoes to fill by following Chris’ footsteps.
Victoria Easton v.easton@leeds.ac.uk @Vikkieeaston
Chris Randall c.p.randall@leeds.ac.uk @randall_uk
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Contents
Articles
16 Simulating the Sour Subsurface… and Beyond Matt Streets 20 Microbiology: How I Learned to Stop Worrying and Love the Job Oliver Severn
24 The Impact of Quorn Products on Human Gut Health: Exploring the Relationship Between Mycoprotein and the Microbiome Jonathon Woods and Jose Munoz 36 Comment: The Untapped Power of Fungi for Food Angel Li
Features
8
28 The Academia to Industry Journey Chris Cooper 30 Early career member Forum Update Jo Kite 35 Investing in the Microbiology Community Sheila Patrick 38 Champions Spotlight Azul Zorzoli 40 Sustainable and Resilient Global Food Security Michael Ukwuru 41 Coccus Pocus 2022 Georgios Efthimiou
Microbiology Editors Q&A Gavin Thomas and Tracy Palmer
9
Open Access success story
10 Member Q&A
Touseef Hussain 12 The Academia to Industry Journey Connor Bowen and Steven Dunn 14 Access Microbiology Editor Q&A Helina Marshall 15 Microbial Genomics Editor Q&A Lucy Weinert
Regulars
1 3 4 5
32 Annual Conference 2023 42 News 43 Grant Deadlines 44 Reviews
Editorial
Council 2023
From the President
From the Chief Executive
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Council 2023
Executive Officers
President
General Secretary
Treasurer
Professor Gurdyal Besra president@microbiologysociety.org
Dr Karen Robinson karen.robinson@nottingham.ac.uk
Professor Robin May r.c.may@bham.ac.uk
Co-Chairs and Chairs of Committees
Co-Chairs of Sustainability
Co-Chairs of Building Communities
Co-Chairs of Impact and Influence
Chair of Early Career
Microbiologists’ Forum Executive Committee
Professor Jose Bengoechea j.bengoechea@qub.ac.uk
Professor Paul Hoskisson paul.hoskisson@strath.ac.uk
Dr Catrin Moore camoore@sgul.ac.uk
Dr Jo Kite jk867@cam.ac.uk
Dr Sarah Maddocks smaddocks@cardiffmet.ac.uk
Professor Gill Elliot g.elliott@surrey.ac.uk
Associate Professor Tina Joshi tina.joshi@plymouth.ac.uk
Elected Members
Professor Laura Bowater laura.bowter@uea.ac.uk
Dr Sharon Brookes sharon.brookes@ apha.gov.uk
Professor Nigel Brown nigel.brown@ed.ac.uk
Dr David Clarke d.clarke@ucc.ie
Dr Andrew Edwards a.edwards@ imperial.ac.uk
Professor Kim Hardie kim.hardie@ nottingham.ac.uk
Professor Alan McNally a.mcnally.1@bham.ac.uk
From the President
“When we think of the Microbiology Society community, we think of one that is welcoming to everyone.”
A s a community, the Microbiology Society is welcoming to any scientist interested in microbes, their effects and their practical uses. It’s wonderful to be able to hear more from our colleagues working in industrial settings and the impact their work is having on microbiology and wider society. This
authors and readers alike, please visit our website ( microb.io/2ULJOD3 ).
As members of our community from across the globe open this issue of Microbiology Today , I hope they feel connected to that worldwide community and consider how they can support it. The Microbiology Society is not for profit, and everything we offer our community happens thanks to the revenue generated by publishing. When you submit your manuscript to one of our titles, you are supporting your entire community: ensuring that we can continue to provide events, grants and professional development for microbiologists at all career stages in the UK and internationally. Find out more about how we publish for the community on our website ( microbiologysociety.org/publishing-for-the- community ).
issue highlights the yet-to-be harnessed power that microbes have in the modern world and the power of cross-disciplinary research from across the microbiology community. This year the Society embarked on a new five-year strategy in which the principal goal is to strengthen our culture of being a community-driven Society by amplifying our members’ voices, wherever they are in the world, and empowering them to embed the benefits of microbiology within wider society. The importance of our community is never more evident than at Annual Conference, and it was wonderful to meet so many of you there. I encountered a huge amount of enthusiasm about the Society, and it was inspiring to hear how many careers have been positively impacted by involvement with our activities. The Society exists only due to its members, and I’d encourage everyone to let their voices be heard and get involved. The opportunities are endless, and the impact you have is, from my own experience, incredibly rewarding. Visit the Get Involved page to find out about current opportunities ( microb.io/2ULJOD3 ). When we think of the Microbiology Society community, we think of one that is welcoming to everyone. Being a member of the community is not determined by where you live, and as we go forward into the coming years, it’s important that we are able to continue to amplify the voices of microbiologists from around the globe. The President’s West Africa Roadshow brought together microbiologists from across 33 different countries. As this issue goes live, the first in-person international Microbiology Society event, Candida and Candidiasis, will be taking place in Montreal, Canada. These examples showcase the Society’s ability to connect and empower communities globally. Moreover, our efforts towards open access are not limited to events only. The Society’s flagship journal, Microbiology , has successfully transitioned to a fully open access model, enabling unrestricted access to its research content for readers worldwide. To learn more about the significance of this move for
Gurdyal Besra president@microbiologysociety.org
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Our publishing portfolio
JOURNAL OF GENERAL VIROLOGY ACCESS MICROBIOLOGY an open research platform FULLY OPEN ACCESS
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We are not-for-profit – publish with us to benefit your community
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From the Chief Executive
“To continue its success as a welcoming home for all microbiologists, the Society has to adapt to the changing environment...”
W hen the first President, Sir Alexander Fleming, opened the very first meeting of the Microbiology Society, he stressed the founders’ desire to welcome any scientists who were interested in microbes, their
contributions from microbiologists doing exciting research in Ghana, Nigeria and Burkina Faso.
Another major change has been to the working lives of microbiologists in different sectors. Scientists in academic careers have less and less time to devote to anything that does not contribute rapidly and directly to their institutions’ requirements, while those in industry have to work harder to convince their employers of the value of getting involved in community activities with a society like the Microbiology Society. To continue its success as a welcoming home for all microbiologists, the Society has to adapt to the changing environment, focusing on how we sustain the things the community values and build on them. We need to look harder and harder at the financial sustainability of everything we do, how we make efficient use of the time of members of Council and Committees, Divisions and Editorial Boards, and how we communicate effectively both in terms of letting you know what the Society is doing for you and in listening to your voices about what you want from the organisation. So we are constantly reviewing our activities and always on the lookout for improvements in our ways of working. What is crucial is that where we make changes, they are aimed at preserving the core identity, values and purpose of the Microbiology Society – the same things that Alexander Fleming discussed at that inaugural meeting. And a real focus at the moment is ensuring that our journals and open research platform continue to thrive in a changing publishing landscape. As the President explains in his introduction on page 4, our ability to run conferences, give grants, foster collaborations, and communicate with microbiologists and on behalf of microbiologists depends on the income from our journals. So when you submit papers to the Microbiology Society’s titles, you are not just choosing a fantastic place to get your research noticed and to increase your reach, you are supporting your entire microbiological community.
effects and their practical uses, whatever the researchers’ specific interests and whatever their workplace. In
an attempt to describe the range and breadth of members whom he wanted to feel at home in the Society, he listed different taxonomic interests, speaking of bacteriologists, mycologists and protozoologists and introducing a short talk on the importance of studying viruses. He also spoke of particular scientific approaches – biochemistry, for example. He encompassed what he called “fundamental knowledge” and “practical problems” and different sectors of the economy including academic, medical, agricultural and industrial. This broad and general approach has always been one of the Society’s great strengths and it is part of the reason that our Annual Conference is always so vibrant. Last month’s conference in Birmingham was no exception. I always look forward to the event each year because it is so varied and because it allows microbiologists with different backgrounds and diverse primary interests to come together to share their experiences, learn from one another, and cross-fertilise each others’ ideas and research directions. Of course, the world has changed a great deal in the 78 years since Fleming was speaking. The challenges are different, both for the research community and for the Microbiology Society. We need to adapt to new circumstances in all sorts of ways. One of those is the globalised nature of microbiology – the Society has members all over the world, and not all of them can attend an in-person event in the UK. So we need to make sure that there are other ways for our global community to come together, and I really valued our online event for members in West Africa a few months ago, hosted by Phillippe Sessou and Victorien Dougnon in Benin and with
Peter Cotgreave p.cotgreave@microbiologysociety.org
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Microbiology Editors Q&A Gavin Thomas and Tracy Palmer
The Microbiology Society is proud to announce that our founding journal, Microbiology , has flipped to Open Access (OA) as of January 2023. This transformation of our most established journal demonstrates our dedication to Open Science and to sharing knowledge more widely and transparently for scholars everywhere.
A s a Society, inclusivity has always been one of our core missions, and we are bringing it to life with this flip: not only does OA allow wider access to research across the globe, but greater visibility for authors. Publishing OA with the Society can help you to: Expand your reach OA research can be read by anyone, anywhere in the world, with no restriction on reading, sharing or reusing. Increase your impact Articles published OA in Society titles get on average 3 times more citations and 4 times more usage than paywalled content, based on data from Web of Science. With Microbiology now being fully OA, what are your hopes for the journal’s impact? Microbiology has been operating as a hybrid journal for several years, with authors being given the option of making their work fully OA. Plan S, which is backed by all of the major science research funders including UKRI and Wellcome requires that hybrid journals should transfer to a full OA model in order to be compliant. It is exciting for us that Microbiology is the first hybrid journal in the Society’s stable to transition to full OA. In practice this means that publishing with us will satisfy all of the requirements of research funders, and authors can submit their work to us in full confidence that they are meeting the terms of their awards as well as supporting the discipline of microbiology. Transitioning to OA expands the journal’s readership; why is this beneficial to authors? As authors, we want our work to be read widely and cited by others. Articles published behind a paywall are by definition only accessible where an institution or individual has paid for a subscription. This limits their visibility and ultimately their utility to others. There is nothing more frustrating than reading an interesting article abstract only to find out that you cannot access the full text! Publishing your work OA expands the reach of your research to anyone who might be interested. This includes other scientists at institutions across the world, but also interested members of the public. What has been the most rewarding part of working on Microbiology ? It has been particularly rewarding to work for the journal as it celebrated its 75th year. Looking back at some of the seminal papers we have published over the years and seeing how they have influenced multiple different research fields has been a real highlight. How can members support or get involved with Microbiology ? Microbiology has broad scope, and we publish research across bacteria, archaea and eukaryotic microbes. Our wide remit means
Support your community Publishing with the Microbiology Society raises funds for grants, events and professional development for microbiologists across the world. With over 75 years of publishing advances across the field, Microbiology’s move to OA is a milestone in the Society’s Open Science future, empowering more international researchers to make an impact. We spoke with the Editor-in-Chief, Professor Gavin Thomas, and Deputy Editor-in-Chief, Professor Tracy Palmer, about this exciting transformation for the journal. that Microbiology would be a good home for research articles from many of our members, and the best way that members can support us is to publish in the journal. Members can also get involved by reviewing, for example by applying to be on the board of reviewers, or as editors. What excites you about the future of microbiology research? What most excites us about where microbiology is going is that we are now in a period when we are not afraid to study microbes in their natural complex communities, clearly helped through massive advances in genomics that give us insight into ‘who’s there’ and now enable us to ask the question ‘and what do they do’? Whether it be the gut, the skin, a plant root or an anaerobic digester, we are opening up all these black boxes which until now have been impregnable. It also forces us to consider vertical interactions in these communities from bacteriophage, bacteria, archaea and fungi to protists, and their multitude of positive and negative interactions, and makes us broader, more inclusive general microbiologists.
Gavin Thomas Editor-in-Chief, Microbiology University of York, UK gavin.thomas@york.ac.uk @GavinHThomas
Tracy Palmer Deputy Editor-in-Chief, Microbiology Newcastle University, UK tracy.palmer@newcastle.ac.uk @proftracypalme
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Member Q&A Touseef Hussain
This is a regular column to introduce our members. In this issue, we’re pleased to introduce Touseef Hussain.
Where are you currently based and what is your role? I am an Early Career Microbiologist (ECM) from India and completed my PhD at Uttarakhand Technical University, India. What area of microbiology do you specialise in? Molecular environmental microbiology; antimicrobial resistance (AMR); molecular diagnostics and biosynthesis of new microbial metabolites. Tell us about your career journey to date, particularly why you decided to work in industry. I obtained my undergraduate and postgraduate degrees in General Biology/Biotechnology from Chaudhary Charan Singh University, India. Afterward, in 2009, I joined the ICAR-Central Potato Research Institute Campus in Modipuram, India, as a Senior Research Fellow. My main research project focused on molecular detection and quantification of late blight of potatoes caused by Phytophthora infestans from seed tubers and infested soil, which was also a part of my PhD thesis. I developed a new molecular marker for the early detection of Indian isolates of P. infestans . Coming from a poor family was not easy for me. I did not receive proper guidance as my family's earnings were not sufficient, but my parents' main focus was to provide me with a good education. During job interviews, people often say that I did not receive a good education from reputed colleges or universities. They often question why a minority like me would study for so long, but my passion to keep trying is the reason I never give up. I was awarded my first independent research project as the Principal Investigator at the Department of Botany, Aligarh Muslim University in India, from 2017 to 2019, by the Science and Engineering Research Board in India. During my research, I isolated a newly improved biosurfactant-based biocontrol agent that can manage soil-borne pathogens of potato tubers. However, I have often been rejected from academic interviews due to a lack of teaching experience. Nonetheless, the key skills that I learned and gained during my PhD program have always helped me, and I am now moving to a start-up company in Gujarat, India. When and why did you first become interested in microbiology? I am fascinated by nature, especially when the monsoon season rain drops fall on the soil; that amazing smell!
As an Early Career Microbiologist (ECM), what are some of the professional challenges you face and how do you overcome these? Right now, I am exploring my career options in academia, industry and agroclinic laboratory settings. I think my educational background and willingness to conduct teaching, research and lab work will help me to make a decision. It is very difficult for a Muslim minority to receive a good education in the current system in India.
You recently joined our Champions Scheme, what were your motivations for doing so?
I want to motivate young minds towards microbiology and to be part of future research activities happening around the world. Do you have any role models, if so, who? My family and all my teachers, supervisors and mentors that helped and supported me during my academic journey. What has been the highlight of your career so far? Learning the tools and techniques and interacting with people of multidisciplinary subjects. What do you hope to achieve in your career in the future? The world of life sciences is changing incredibly fast and it is sometimes challenging for an ECM to keep up with the science and technology. I hope to create balance, meaning and vitality between my work and personal life, collaborating in diverse subjects, in the future.
If you would like to be featured in this section or know someone who may, please get in touch via getinvolved@microbiologysociety.org.
Touseef Hussain Chief Scientist Sevama Agri Clinic and Laboratory at Bhavnagar Gujarat, India
hussaintouseef@yahoo.co.in @Hussaint789
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The Academia to Industry Journey Connor Bowen and Steven Dunn
For our industry edition, we caught up with two members who have made the move from academia to industry. Find out more about Connor Bowen and Steven Dunn’s journeys.
Hi Connor, where are you currently based and what is your role? I am currently working at Ingenza Ltd, UK, based at the Roslin Innovation Centre. I am a Senior Scientist in the Molecular Biology team. My role currently involves strain construction for production of proteins in the yeast Pichia pastoris ( Komgatella phaffi ). How did your journey from academia to industry begin? After I had made the decision to move on from academia, I was fortunate to have a good friend who had made the transition to industry a few years earlier so asked for his advice. He answered some of my questions about what to look for in a company and helped guide me on how to change my CV from being academically focussed to having a more industrial focus. I then started to look for companies in the area that had a scientific focus and made contact with these companies. Fortunately, at the time I was looking to move from academia, Ingenza was hiring, so I sent them my new industry focussed CV and was invited for an interview. What has been your biggest challenge so far? I think one of the biggest challenges initially was leaving my colleagues and projects behind after investing so much energy into them. Once I started at Ingenza it was bit of a learning curve working in a larger team on projects with lots of people performing different roles within a project. This means your work must fit into a much bigger machine and you need to all be working to the same standards and schedules to ensure everything is delivered on
time. This can be a challenge but also a motivation to ensure you keep everything moving for the team and the customers. What has been your best experience so far working in industry? I think, so far, it has been the team that I am part of. All the team at Ingenza are incredibly supportive and very positive. The variety of projects we work on is also very exciting as you never quite know what you may be involved in next or what the product may be used for in the future, whether that be towards addressing global challenges in human health or helping make our planet more sustainable. Finally Connor, do you have any advice for others considering a move from academia to industry? My major piece of advice would be to try it; the move may be right for you. I would also say that moving from academia you have many skills that you may not be aware of that industrial positions are looking for, so don’t sell yourself short. Non- academic positions come in different shapes and sizes, so there will be an industry role out there that will suit you and your skillset.
Connor Bowen Senior Scientist Ingenza Ltd, UK
connor.bowen@ingenza.com @ConnorB_micro @IngenzaLtd
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Hi Steven, where are you currently based and what is your role? I work at a microbial genome sequencing company called MicrobesNG. I’m in charge of new service development (I take a service idea and help to develop it into something we can sell). How did your journey from academia to industry begin? I started a consultancy business as a side hustle, and I really enjoyed the nature of working with industrial clients; you often saw an immediate impact from your work, and it contributed to something very tangible like a service or a resource. In contrast to academia, where one of our papers was in review for almost a year, it was a welcomed change of pace. I started looking around at industrial posts, but I was still having a great time in academia, and I couldn’t find a job that topped what I already had. It wasn’t until a friend who worked for MicrobesNG contacted me with essentially my ideal job role, better pay and a permanent position that I really saw industry as a truly attractive prospect. What has been your biggest challenge so far? My experience with academia is that it’s relatively relaxed; you have the scope to make your own destiny, and in very general terms the quality of your career depends (largely, but not exclusively) on the quality of your output. In industry, just by the nature of needing to make money, you have a different set of priorities, drives and performance indicators. Your immediate output needs to be accessible across multiple departments, skillsets and knowledge bases, so it requires a much more structured and accountable form of working practice.
What has been your best experience so far working in industry? The people and the general buzz! I can’t speak for every company, but in a small or medium-sized enterprise like MicrobesNG it feels like you and your lab group decided to start a business – you still get an abundance of science and technical data to scratch that itch, but you also get an opportunity to contribute to a wide range of business needs, and there’s always something to get involved in. Finally Steven, do you have any advice for others considering a move from academia to industry? Network! Speak to vendors at conferences, let people know you’ld be interested in any jobs coming up, or just ask people for advice. In my experience, people are more willing to help than you might think. Many of us have been in your position, and we know exactly what it’s like. I’d also say that other than the people, I don’t miss academia – everything I enjoyed about life as a postdoc is present in industry, and I’m glad I moved! If in doubt, reach out to a scientific recruiter – see what’s out there and what’s possible.
Steven Dunn New Services Bioinformatician MicrobesNG, UK
mail@stevendunn.co.uk @StevenJDunn
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Access Microbiology Editor Q&A Helina Marshall
The Access Microbiology Open Research Platform relaunched with a commitment to transparent research and supporting the microbiology community.
Helina Marshall, Editor-in-Chief of Access Microbiology , discusses the importance of publishing negative or null findings, the benefits of submitting work to the platform, and her hopes for the future of scientific publishing.
sure other researchers don’t waste time in repeating “failed” experiments. If the research is sound, there should be a way for this to be published and shared with the community. What advice would you give to someone thinking about submitting to the journal? Access Microbiology is a great place to submit work that was maybe part of a larger story initially, but for various reasons didn’t work out or ended up being less relevant to the final project. If the science is sound but doesn’t seem to fit in your other work, it fits in Access Microbiology !
Please introduce yourself I completed my PhD at University College London before going on to carry out postdoctoral work at Queen’s University Belfast and University College Dublin. Currently, I am a new Chancellor’s Fellow at the University of Strathclyde, working on host-pathogen interactions and immune evasion mechanisms, primarily focusing on clinically relevant but rare serotypes of Salmonella , as well as Streptococcus pneumoniae . What has been the most enjoyable part of working on Access Microbiology ? The Access Microbiology Open Research Platform is committed to promoting open research and serves as a platform for publishing all sound science within the Microbiology Society’s portfolio. It offers a unique model that includes preprints, transparent peer review, and a record of the article’s history from original submission to final version. The platform’s broad scope results in submissions covering a wide range of subject areas, providing an opportunity for our early career researcher Editors to handle papers they would not typically encounter. Furthermore, our Editor Mentors are readily available to assist Mentees with any questions that may arise. Having such a communicative and supportive Editorial Board is a great asset. What does publish for the community mean to you? Our publishing portfolio supports and invests in the work of the Microbiology Society, publishing for the community and reinvesting the profits in supporting microbiology and microbiologists. With commercial for-profit publishers expanding their reach so much in recent years, there has never been a more important time to publish with and for our community. Why is it important for negative or null findings to still be published? The ability to combat data waste is so important, both in ensuring an accurate scientific record and pragmatically to make
What are your hopes for the future of science publishing?
The future of scientific publishing matters to everyone – the publication of data and ideas that arise from research is fundamental to how science advances. I hope that, with the move to Open Access and open science, we place more emphasis on sound, reproducible research. We’re no longer publishing in a print medium, we don’t need to limit ourselves to only publishing the most novel results. Digital publishing means more seats at the table.
Helina Marshall Editor-in-Chief, Access Microbiology University of Strathclyde, UK
helina.marshall@strath.ac.uk
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Microbial Genomics Editor Q&A Lucy Weinert
Lucy Weinert is Editor of Microbial Genomics . Her fellowship centres around the study of evolutionary genomics, specifically as it relates to bacteria.
While completing her undergraduate degree at Bristol, Lucy became fascinated with the evolution of sex and decided to pursue a PhD focused on sex-ratio distorting bacteria. Through this experience, she developed a deep interest in bacteria more broadly, as well as the emerging field of genomics, especially as high-throughput sequencing technology began to advance. She currently also serves as a lecturer at the University of Cambridge, UK, teaching undergraduate students about the intricacies of the evolution of sex.
What motivated you to get involved with Microbial Genomics ? The journal is my area of expertise and so it allows me to keep up with a nice variety of research, and find out what others in the field are doing and whether I’m going to get scooped anytime soon. The chance to support a non-profit journal is brilliant, and the team are so friendly and helpful. Why are Society journals so important to the microbiology community? Publishing is an essential but expensive part of science, and lots of private companies make huge profits from it. Society journals allow this money to be invested back into the community. My students and I have directly benefited from this extra support – thanks very much Microbiology Society. Why should members working within industry engage with Microbial Genomics ? It’s the perfect route to networking and knowledge exchange with public health and academia. What do you think the future holds for microbiology? Wow, that’s a broad question! Microbes pose a significant threat to humanity and will continue to do so, thanks to evolution,
despite the development of new vaccines and treatments. In short, the study of microbial evolution is clearly a crucial field. For my future research interests, I am particularly intrigued by the factors that influence bacterial mutation rates. While mutation rates tend to correlate well with genome size over the long term, there is substantial variation among pathogens over the short term. I am eager to explore new technologies that allow for quick and accurate measurement of mutation rates, as I have previously overseen 200 consecutive days of 300 single-colony streaks to obtain four highly precise estimates. In the future, people will likely laugh at our current efforts, much as I once laughed at those who spent their entire PhD sequencing a single PCR product, who in turn laughed at their predecessors, and so on.
Lucy Weinert Editor, Microbial Genomics University of Cambridge, UK
lw461@cam.ac.uk
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Simulating the Sour Subsurface… and Beyond Matt Streets
S ince the earliest days of hydrocarbon extraction (circa 1920), sulfate-reducing prokaryotes (SRP) have been observed in production fluid samples. These microbes reduce sulfate to hydrogen sulfide (H 2 S) – an extremely corrosive and toxic compound known to ‘eat away’ at the metallurgy in production facilities. The production of sour (i.e. sulfide-containing) fluid is considered to carry huge economic costs within the Energy sector. For example, in the United States upstream Oil and Gas (O&G) industry alone, it is estimated that corrosion costs around $1.4B each year, with a significant proportion of this being attributed to material exposure to H 2 S. However, only in the past 30 years has the activity of SRP in water-flooded assets been recognised as the main cause of oilfield reservoir souring. Even today, laboratory research and computer modelling continue to investigate these complex microbial interactions in the sour subsurface to better understand and predict the appearance of this phenomenon. Rooted in biology In the late 1980s, a joint industry project (JIP) was launched in the UK to evaluate and determine why some historically ‘sweet’ (i.e., non-sulfide-containing) North Sea oilfield reservoirs had begun to produce sour fluids. The programme of work, consisting of ten industrial sponsors, was led by a corrosion engineer, Dr Bob Eden (founder of Rawwater). Based on the findings of what was a two-and-a-half-year project, it was concluded that souring commencing from a sweet starting point was linked to water injection and subsurface biological sulfide generation. The JIP was the first research programme in the world to categorically identify the critical role which microbiology plays in oilfield reservoir souring. Further, the outputs of this work included a Nature paper, an HSE-sponsored HMSO report, and the origins for the world’s first oilfield reservoir souring forecasting tool, the DynamicTVS© model.
Surviving the subsurface During the initial production of hydrocarbon from an oilfield, the reservoir pressure is sufficiently high to drive fluids from the reservoir to the wellbore of a production well, for production at the topsides facility. This is termed ‘primary recovery’. As the pressure of the reservoir decreases over time, additional downhole pressure is required to maintain successful oil production. This is typically achieved through the injection of water into the formation and is termed ‘secondary recovery’. However, this process of ‘water-flooding’ will introduce SRP and other bacteria into the subsurface environment, typically contaminating the near wellbore of the injection well. Depending on the source of the injection water, significant sulfate concentrations are also introduced. For example, seawater typically contains around 2,700 mg sulfate l –1 (28 mM). Despite the relatively high pressures and temperatures which initially exist in oilfield reservoirs when compared with physical conditions at sea level, the act of injecting large volumes of cold, sulfate-containing water into the formation significantly reduces the temperature of the environment close to the base of the injector. During the initial production of hydrocarbon from an oilfield, the reservoir pressure is sufficiently high to drive fluids from the reservoir to the wellbore of a production well, for production at the topsides facility.
16 Microbiology Today May 2023 | microbiologysociety.org
Various models and simulators offer insight into the likely souring potential of global oilfield assets. However, more recent research has demonstrated the necessity of high-quality, laboratory-based data to correctly calibrate the biological activity coefficients in the souring model. Extreme environment testing is essential to simulate downhole field conditions under controlled laboratory conditions. High-pressure, flowing bioreactors are best placed to mimic the hydrostatic pressure and thermal conditions which the microbial communities are exposed to under water-flooding conditions. The world’s largest souring database from extreme environment testing is considered to be held by Rawwater, standing at over 600 years’ of data at the time of writing and generated in the organisation’s world-leading high-pressure bioreactor suite. Managing the microbes Despite the systemic nature of SRP in the O&G industry, there are just a few tried-and-tested methods which have shown to be beneficial in mitigating and/or controlling the production of sour fluid topsides. Supplementing injection water with competitive exclusion chemicals such nitrate has been shown to reduce sour gas production. The presence of nitrate in the downhole formation stimulates the proliferation of nitrate-reducing bacteria (NRB) as the biological reduction of nitrate is more energetically favourable when compared with sulfate reduction. Complete nitrate reduction to inert nitrogen is clearly beneficial to operators as opposed to the production of sulfide from sulfate reduction. A further benefit of nitrate injection is that, under certain environmental conditions, incomplete nitrate reduction occurs, resulting in the production of nitrite. These nitrite compounds block the enzymatic reduction of sulfite to sulfide; therefore, blocking sulfate respiration.
During prolonged periods of water-flooding, this volume of cooled rock can extend into the reservoir, often supporting the growth of SRP along fracture faces of the downhole matrix. Supporting the SRP Outside of the standard requirements for anaerobic, sessile microbial life to flourish [water, anoxic conditions, chemical compounds for reduction and oxidation (redox) reactions, physical surfaces for attachment], the rate and extent of subsurface sulfide generation is often dictated by other physical and chemical conditions in the formation. Physical parameters such as pressure and temperature can either restrict or facilitate survival and growth of the SRP, whereas chemical parameters such as salinity and pH often determine the degree of microbiological sulfide generation. Generally speaking, SRP can be active at pH ranges from 4.0 to 10.0, and are most productive at temperatures up to 80 °C and at hydrostatic pressures below 10,000 psig (69 MPa). Modelling the microbes In order to inform material selection and field development, oilfield reservoir souring forecasting models are used to predict the future souring propensity of assets around the world. Using operational, planning and survey data from the field (namely outputs from reservoir simulators), good souring models describe (i) the reservoir cooling as a result of water injection, (ii) the growth of SRP and generation of H 2 S in the subsurface, and (iii) the transit of H 2 S through the formation to the production facility. Further calculations are often conducted to partition the mass of sulfide produced at predetermined pressure, volume and temperature (PVT) and pH conditions (e.g. at the first stage separator) to generate gas phase H 2 S ppmv concentration profiles.
17 Microbiology Today May 2023 | microbiologysociety.org
18 Microbiology Today May 2023 | microbiologysociety.org
Biocides are commonly used in upstream O&G extraction and are predominantly introduced to control unwanted biofouling in injection and production systems. Semi-regular, high-concentration batch injection of biocide products into oilfield reservoirs is not uncommon and has been shown to reduce microbial activity around the near wellbore of the injector. Some studies and pilot field trials have also demonstrated reduced souring rates under low concentration, continuous biocide injection. Key challenges to successful biocide application in the contaminated subsurface include ensuring significantly high biocidal concentrations at the required contact times, when in the presence of SRP, and biocide stability under downhole conditions. Sulfate removal from the injection water is both the most reliable and the most expensive option in reducing souring propensity. Traditionally used to reduce the formation of inorganic scale, sulfate removal uses nanofiltration membrane technology to reduce the overall sulfate concentration to between 10 and 30 mg l –1 . This significant decrease in concentration limits the overall capacity of microbial sulfate reduction. Some studies have also demonstrated that low- salinity water injection into oilfields may have an enhanced oil recovery (EOR) effect. Beyond souring As the Energy sector transitions to ‘cleaner’ initiatives, many issues associated with deleterious microbiology are likely to remain. However, using our existing understanding of oilfield microbiology can guide the exploitation of both new and existing subsurface environments. For example, depleted oilfield reservoirs or saline aquifers, used for the long-term storage of gases such as carbon dioxide (CO 2 ) or hydrogen (H 2 ), could prove susceptible to microbial fouling, significantly reducing the success of operations. However, through further development of microbial modelling and laboratory-based simulation studies, linked with the latest microbial community analysis techniques, we can determine which assets are most suitable for processes such as carbon capture and storage (CCS) and ultimately de-risk the future of carbon sequestration for decades to come. Biography Matt has worked at Rawwater since 2010, specialising in understanding and managing problems associated with microbial biofouling in the Energy industry. His main expertise lies in souring forecasting modelling and extreme environment testing. Alongside his industrial role, Matt is the Industry Liaison Officer for the Geomicrobiology Network and is undertaking a part-time PhD in Environmental Geochemistry and Geomicrobiology at the University of Manchester.
Matt Streets Head of Division and Senior Research Scientist Rawwater Engineering Company Limited, Culcheth Enterprise Centre, Withington Avenue,
Culcheth, Warrington, Cheshire WA3 4JE, UK
matt.streets@rawwater.com matt-streets-9911a315a
19 Microbiology Today May 2023 | microbiologysociety.org
Microbiology: How I Learned to Stop Worrying and Love the Job Oliver Severn
C areers. Finding what you want to do can be a daunting challenge. It’s a journey that never really stops. Constant re-evaluation of what you like, and don’t like, is tiring. I aim in this article to give you three easy to apply tools to help guide your career journey. I don’t wear ties. That being said, there are a few exceptions: • As a joke. • When impersonating someone else. • Funerals… That is where that line gets drawn. Bowties are great, but not the dangly kind. This in some small way has shaped the journey I am on. I like being myself, and want to perform research on my own terms. You’ve probably now reached the stage where you are thinking; “Gosh… Microbiology Today is really clutching at straws to get this guy writing an article”. Stick with me. I hope to highlight three steps in this article that will help guide your career journey from start to finish.
Step one: experiment in increments, and keep moving the goalposts Currently, I sit as the head of Research & Development at Singer Instruments. A role I love. A radical departure for someone who was never moving to industry. I wanted to lecture, lost to the valley of tweed forever. What does that mean? I oversee three departments of engineers, software developers and scientists. I coordinate them and create our strategic direction. I have the absolute pleasure of working alongside brilliant people. I’m a microbiologist, not a developer, so they tolerate my eccentrism. In return, I hope their days are a little brighter. Thinking about our scientific direction means I work with the strategic team, a group of senior managers looking after all of Singer Instruments. Including Harry Singer, current owner of the whole gig – I’d recommend meeting him. I also serve on our Advisory Board; executives who challenge how we do business, adding experience and insight to our own.
20 Microbiology Today May 2023 | microbiologysociety.org
The flow diagram method: for those of us who like to work in logical steps. • Create a diagram, and draw a box on the far right side with your current dream role written in it. • To the left of your dream role: create boxes with skills required; don’t ignore soft skills like networking, or presenting. These are things you can demonstrate on a CV! • On the left side of the diagram: create boxes with where you are with these skills. Then start linking them with arrows. Your current skills and where you need to jump; create another box that gets you some of the way there. • Follow the traffic light system. Anything that isn’t current, colour in red. If you are working on it, make it orange. If it’s been done, make it green! Once you have a vague roadmap, start experimenting. You can refer back to your roadmap; having it in your mind will help complete its components. You may decide to change your mind; feel free to edit the roadmap as this happens! Step two: be built by others, and build others up The often overlooked or ignored section of anyone’s career is other people. My career only exists due to the people I met, and the time investment they made. Hard work, good luck and societal factors all play major and minor roles. Yet, there are no ‘self-made’ individuals. Networking is a word so overused that it may as well be nonsense. Social media can make it hard to know who you can rely on in a pinch and who is an obligatory contact. Of the people you do rely on, it can sometimes be hard to know who has a genuine interest in building you up. Also, who of them, often for completely non-malicious reasons, would quite like you to stay where you are… There is no ‘one size fits all’ here, and any literature and guidance I have found on it leaves me feeling lacklustre. I have known draconian, and miserable, research leaders who have been instrumental in jettisoning colleagues to new heights. I’ve also known incredibly caring, compassionate and likeable leaders whose teams feel somewhat stagnant. There are some signs to look out for, and cultivating mentors and peers to help you on your journey is essential. In addition, finding your own way to give back and build others up is a duty – and not an option. The often overlooked or ignored section of anyone’s career is other people. My career only exists due to the people I met, and the time investment they made.
We like to think we have arrived here via a linear series of actions. A timeline. But, we change our minds, make mistakes and grab hold of opportunities as we go. A career goal is great, it shouldn’t stop you challenging yourself in new ways, and changing your mind. I never set out to work as Head of R&D. I didn’t know jobs like this existed. Most of the skills I needed were gained from being challenged by something else. Overcoming problems and solving them. By doing it, I found out how much I wanted to do it. These incremental experiments work better with structure. You are going to go ‘off piste’. This is good! But it helps to know how and when. Set a vague ‘roadmap’ for where you want to go. People think differently, but I find two major tools help here. Choose one, try not to overthink it: The presentation method: for those of us who think abstractly, this can be helpful. • Start a presentation, or get 5 pieces of paper if you like arts and crafts. • Write the next 5 years on each of them (2023, 2024, 2025, etc.). • On each of them, do a mind map of what ‘success’ would look like. You may want to start at the end and work backwards, or start on this year! • Once you have an idea of what success looks like, start mapping what skills, experiences, and other thoughts will help you achieve this vision of success (you will use this later).
To get started on this:
Pick a mentor – pick being the optimum word Outside of your direct line manager, or PI. They should be vaguely aligned to where you want your career to be and ideally not too far removed from where you are. • You may have dreams of being a CEO of a pharmaceutical company, but unless you are on a board already, a pharmaceutical line manager may be more enlightened to your cause! Also, they will likely be flattered if you ask. Go in with notes, and come out with notes. • This is really how you start to ‘feel out’ your mentor. Go in with questions and ask them. See how they respond. These questions should be future focused; anything that’s affecting your day to day is likely better with a peer.
21 Microbiology Today May 2023 | microbiologysociety.org
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