Written by Catherine Jimenez-Quiros at the The University of Worcester. This is the report from a BSPP Junior Fellowship. Click here to read more/apply for one yourself.
Three and a half years ago I started what I called “My PhD adventure”. I got the good fortune, if it can be called that, to be accepted in a program, of which the main aim is to control a fungal pathogen in wheat. Being from a Latin-American country means that, you are more likely to be in contact with wheat. Contrary, in my country, rice is the stable food which is cultivated frequently, not the wheat. There was much to learn. However, my challenge was just about to start.
Previously, I used to work in a research group dedicated to the biological control of insect pests, therefore I was familiar with the main insect pest of coffee, H. hampei. This did not resemble the work I was about to begin in the biological control of the fungus, or the work with cereal crops. Luckily, the group shared facilities with another group dedicated to investigating rice.
Biological control is a subject that fascinates me. I believe that plant pathology can help to improve the lives of everyone without of use of many pesticides, that ultimately results in healthier food. Nonetheless, the world is facing a threat in the food supply due to climate change and due to population growth. So, how can this be balanced? One answer is the development of projects, like this one in my PhD, which not only looks into the use of beneficial bacterial strains in the control of plant pathogens, but also looks to understand the genomic background behind them.
I developed this project at the University of Worcester, a city that was catalogued, in the year that I started my PhD, as one of the safest and happiest places in the UK. What a wonderful description! Located between the city and open country side, Worcester is rich in tradition and history. Kings, pottery, archaeology and of course, the famous Worcestershire sauce. It was a great start to my PhD!
From the beginning, through the experimentation and analysis, the project found, not surprisingly, good results. The Bacillus strains demonstrated to be interesting candidates for the control of the F. graminearum and remarkably, they were able to improve the trade-off of plants affected by pathogens. This was an important outcome of the study, since wheat is a crop that is constantly under research to improve its productivity.
A second scope of my study was performed in genomics of the Bacillus strains. Fascinating data were found, mostly about the relationships between the bacterial strains. One strain, non-commercial, displayed promising results in in vitro assays and the genomic data supported this finding.
A third study, looked to obtain RNA from the interaction of the fungus with the Bacillus. The laboratory experiments were carried out, however, we needed bioinformatic support, then we looked to the John Innes Centre (JIC) as part of this project, for help.
We decided to apply for this fellowship to support a visit to the Paul Nicholson’s laboratory at JIC, to get bioinformatic support, training for RNA-seq analysis and to get some laboratory skills in the process. Well, the plan was to go by February this year (2020). However, 2020 has proven to be an unprecedented year.
The first two weeks meeting everyone inside JIC, was an amazing experience. The staff and students radiated a welcoming and good vibes atmosphere. Sadly, the COVID-19 pandemic started to appear around the country. Cases were not occurring in Worcestershire or Norwich yet, but this was about to change.
In the second week, the news about the first cases of COVID-19 appeared in both cities. This produced a whole change in my plans. JIC quickly steered towards to a total shut down, putting in place resources, allowing everybody to work from home.
I was well impressed with the arrangements that were made. Personally, I was concerned about the laboratory skills I had planned for this fellowship, would not happen now. But the most important thing was health and safety. The focus of the visit then became bioinformatics and RNA-seq analysis. The arrangements to work from home were set-up during my second week. At the same time, within the Nicholson’s lab, a rota was created for the continuation of the experiments. COVID-19 had arrived, but the plants aren’t going to wait! They had planned experiments that otherwise, would have been delayed for a whole year. The communication within the group was amazing.
Somehow, from this situation, I got more bioinformatic training, than I was planning for: RNA-seq, plotting with R and NGS analysis training. Zoom was the preferred tool for virtual meetings. I know that Teams is the norm for many institutions but, for these training purposes, Zoom worked well. The engagement of the trainers, as well as the participants, made this whole experience very valuable. Having the opportunity to hear about the ideas and troubles of others, within their experiments, made this training-time great.
I am grateful to the BSPP for providing this support and colleagues at JIC for their help. Without this support, I would not have been able to meet lovely people at JIC, get a great training in Bioinformatics, and update my knowledge in the field.
Crop genetics students and research staff’s office of Paul Nicholson’s group, JIC. About the time of lockdown started in UK.