Microbial ecology for engineering biology

In March 2022, the Royal Society hosted a Theo Murphy Meeting to discuss the development of ecology-based design of engineered biological systems as a solution to sustainable technologies. The discussion highlighted the importance of prioritising research culture as a catalyst for change. Interface Focus recently published an issue that came out of the meeting. We spoke to the organisers, Professor Thomas Curtis and Dr Jane Fowler, to find out more. 

What was the aim of the Theo Murphy Meeting that led to this issue?

The goal of the meeting was to bring together people from diverse disciplines including environmental biotechnology, theoretical ecology, mathematical biology, engineering, physics and other related fields. What we had in common was a shared interest in the engineered open microbial communities that are so important for society - systems like wastewater treatment and resource recovery, drinking water treatment and other biotechnologies that will help us to solve societal challenges. We believe that we can develop more effective microbial biotechnologies by designing these systems with the microbes in mind. The component microbial communities could also be effectively managed by better understanding their ecology. However, optimal design and management of microbial systems requires the input of diverse expertise that is distributed across disciplines, so we need to get all of these people with distinct skills and knowledge on the same page to make progress.

Can you comment on some particular highlights in the research presented?

We had diverse presentations by a wide range of people from established experts to postdoctoral fellows. The diversity of presentations brilliantly illustrated the important contributions that can be made by different fields. Presentation topics ranged from quantitative ecology, to the implications of physical interactions of individual cells, to the conversion of  genomic data into accurate metabolic models of communities. The structure of the meeting allowed for ample group discussion on topics from design, microbial community management, to the types of opportunities that we as researchers and practitioners can leverage to fund the advancement of engineered open microbial systems. This opened a dialogue across disciplines, and hopefully led to fruitful interactions that will lead to future new developments in the field. We were lucky to have members of the EPSRC/ UKRI in attendance. They were able to provide advice and insight into funding mechanisms, whilst also learning more about the research in this field and the outcomes that we believe are possible given sufficient funding opportunities and a research atmosphere that supports and values multi-disciplinary collaboration.

What are the current opportunities and challenges in your field?

Whilst we would not call climate change an opportunity, it certainly requires rapid change. We need to reengineer the way we provide many services in environmental biotechnology to make them more accessible and sustainable. We also need to develop new technologies, such as  energy capture from renewable resources, to the recovery of nutrients and rare earth metals which can form part of the circular bioeconomy and help to reduce greenhouse gas emissions. Most importantly, we need change in years, not decades, and technologies that work in every economy, not just wealthy ones. 

The opportunities are numerous, most notably there is an influx of a wide variety of people from different backgrounds and cultures into the field who will bring new and diverse thinking. Moreover, the tools available in computing, AI and genomics are very powerful in the right hands.

However, there are three major threats. Firstly, it will take time and effort to harness the new tools we have, and the old approach of ‘wait and see’ will not deliver solutions on the timescales humanity is currently faced with. Secondly, there is a perception by some that all engineering biology happens in a petri dish and that the messy complexity of real world open systems somehow means that engineering microbial communities is not engineering at all. Sadly, this is UK policy at present. The final threat is a contemporary culture that can discourage cross-disciplinary work and promote specific individuals above the overall aims of the research. This culture can unfortunately discourage and thus undermine our ability as a community to meet our shared goals. These barriers can be overcome, the field is full of passion and goodwill. 

How do you envision that a cultural change could help to move it forward?

At the final workshop of the session, we asked small groups to discuss how we could move the field forward faster. The overwhelming response that we heard from every group is that the culture of our research institutions does not support the types of research that are needed to develop the technologies that humanity needs. The funding mechanisms that support this kind of transformational work are similarly rare. Our inability to effectively leverage the diversity of skills, knowledge and experience across the research establishment is often due to systemic issues that promote and celebrate the work of a small number of individuals and that value individualism over collectivism.

The first step to changing our culture is to talk about it. The simple awareness that we are not where we want to be, or need to be, can precipitate change. This in turn can lead to change in our institutions and funding bodies. Many universities are now realising the importance of their research culture and is to be positively managed. Finally funding bodies can think about how they support researchers. For example, promoting the use of narrative CVs that emphasise service and collaboration over individual achievements [1]. Promoting mission-based collective approaches, which recognise everyone, regardless of seniority will help. 

[1] UK Reproducibility Network (UKRN) 2021. Available from: https://www.ukrn.org/2021/04/23/an-enhanced-narrative-cv-template-for-the-research-community/

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Image credit: Simulation of millions of elongated phytoplankton cells encountering each other in a turbulent flow. Reproduced from (Arguedas-Leiva J-A, Slomka J, Lalescu CC, Stocker R, Wilczek M. PNAS, 2022). https://www.pnas.org/doi/10.1073/pnas.2203191119 (https://doi.org/10.1098/rsfs.2022.0059).