Prize Lecture Q&A - Professor Jill Banfield

11 April 2018

Our Prizes recognise excellence and are awarded to those making significant contributions in the field of microbiology, based on nominations received from the membership. They are awarded at our Annual Conference, where the winners also present their lectures. Ahead of the Prize Medal Lecture, Daniel Morse, from our membership, interviewed Professor Jill Banfield to find out what inspires her, more about her work and how it feels to win a Microbiology Society prize.

The 2018 Microbiology Society Prize Medal will be awarded to Professor Jill Banfield from the University of California, Berkeley. Jill investigates the diverse range of microbial communities living in different environments and she has made huge contributions to the disciplines of microbiology, earth sciences and phylogeny. For example, her identification of a new phylum of archaea has led to a new view of the tree of life, and her research group was the first to detect CRISPR sequences in natural microbial populations. Her other work has made significant impacts on the fields of remediation and nanotechnology. Jill has a vast publication record of well over 300 papers and has held Professorships at the University of Wisconsin–Madison and the University of Tokyo.

Could you provide a few sentences to give an overview of your current work?

We are currently studying microbial communities across a variety of environments with the goal of understanding the factors that shape community membership, organismal activity, interdependencies among organisms and ecosystem outcomes. Of great interest to us are symbioses, especially those that involve bacterial and archaeal hosts. Specifically, we are exploring the biosynthetic capacities of putative symbionts and how capacities vary across two major groups, one in Domain Bacteria and the other in Domain Archaea (CPR and DPANN). We are also involved in human gut microbiome work including infant gut colonization, and on phage and the adult gut in collaboration with Jo Santini.

What do you consider to be your biggest personal and/or academic/professional achievements?

My lab has trained almost 100 graduate students, almost half of which have already gone on to academic (almost all faculty) positions and independent and highly successful scientific careers.

What would you say is responsible for sparking your interest in the sciences, and particularly microbiology?

My initial interest in science was in natural history, specifically earth history (geoscience), but migrated to microbiology when I became aware of the amazing roles micro-organisms can play in bioremediation processes. I became fascinated by genomes around 1999, and then by the largely untested potential for genomics to uncover new organisms, pathways and organism interactions when applied to the natural environment. 

What were your early career aspirations, and how did they change as you progressed through your studies?

My earliest career aspiration was to be a field geologist and in fact I worked in exploration geology for a year. However, my passion was for research and so I returned to do masters and doctoral degrees and these experiences cemented my desire for a research-based academic career. In detail, my aspiration with regards to the field of expertise pivoted when, as an Assistant Professor, I transitioned from studying mineral structure, microstructure and reaction mechanisms to studying micro-organisms and their impacts on the environment.

With your interest in geomicrobiology, and interactions between environment and micro-organisms, as micro-organisms tend to behave in certain ways under specific conditions, and with the ever increasing evidence for climate change, how is this impacting your current and future academic interests?

For some years my lab has worked on soil, arguably the most complex and difficult microbial ecosystems and perhaps also the most important from the perspective of climate change. We continue to seek to understand how soil microbiomes vary with water inputs and how shifts in microbial communities will impact carbon turnover processes and trace gas emissions.

Is it possible to model this change and subsequent effects within your studies?

We do not attempt to conduct the sophisticated types of modeling required to interface with climate change research, but we are working to provide information that will be useful to collaborators who are seeking to develop such models.

How has the improvement in technologies within the past 20 years facilitated your research?

My research has been completely transformed by the availability of huge amounts of DNA and RNA sequence information, linked proteomic data and bioinformatics tools development. This has allowed us to scale up our studies from low complexity systems to investigate the microbiomes of aquifers, sediments and soils.

Do you foresee any further improvements or novel technologies that you could use in your studies? Or do you know of any technologies that would be of interest that are currently used elsewhere that would have a role in the general field?

My lab is currently working with collaborators to combine stable isotope probing methods with genome-resolved metagenomics so that carbon and water can be tracked during experiments. In other collaborations we are beginning to develop methods that will enable modern genome editing to be applied within the context of microbial communities to probe genes and pathways involved in inter-organism interactions, and to uncover the roles of hypothetical proteins in uncultivated organisms.

What would you say are the biggest challenges related to your research field, and how do you see them being overcome in the immediate or longer-term future?

One of the biggest challenges that comes to mind is the huge number of proteins that we identify in genomes for which we have no functional prediction. This greatly limits the inferences we can make about organism roles. I hope that genome editing methods will provide at least some insights. I’m also concerned about gaps and errors in genomes reconstructed from metagenomes as these limit the accuracy of metabolic reconstructions. I hope to see this second problem addressed via the integration of long read and other technologies into genome resolved metagenomics and through the automation of manual curation methods.

What are your research plans for the short and long term?

I plan to transition my lab’s research back into the laboratory to some extent, with a focus on co-cultivation of organisms that are unable (or difficult) to grow in pure cultures. I’m planning to increasingly work with geneticists and biochemists to explore interesting genes and pathways, especially those related to microbial interactions. I’m planning to work on microbial communities that contain eukaryotes with essentially the same high-resolution methods that we have used to study bacteria and archaea in microbiomes.

Congratulations once again on receiving the prize, can you tell us a bit about what it means to you?

Thank you! The prize is a remarkable honor but of course it largely recognises the fantastic work of students, postdocs and staff that I have had the honor of working with. It means a great deal to me that the broader microbiology community finds value in the genome-resolved metagenomic research we have been doing over the last almost two decades.

This lecture takes place today at the Microbiology Society Annual Conference at 09:00 in Hall 1.

Inspired by our outstanding Prize winners? Nominations for 2019 Prize Lectures and the 2020 Prize Medal are now open.

Visit microbiologysociety.org/prizelectures for more information.


Image: Roy Kaltschmidt.