Read the full interview with Torsten Struck below:
1. Can you introduce yourself and how you got involved with ERGA and the Sampling & Sample Processing (SSP) committee?
I'm Torsten Struck and I work at the Natural History Museum of the University of Oslo. I've been working my whole academic life with marine invertebrates and with genomic data for a long time already. I started this work early on in Germany, initially with transcriptomic data. And nowadays my focus has shifted to genomic data. I got involved with ERGA because I am also part of the community of the Norwegian Earth BioGenome Project (EBP-Nor). When I became an ERGA member, I was asked where I would like to contribute and I chose two topics which I find most interesting: sampling and sample processing and sequencing and assembly. I was interested in the sampling topic because we gathered some previous experience with other projects and knew how challenging it can be for the species we work with in my group. And that’s how I got more involved with the SSP.
2. What are the main activities of the ERGA SSP and why should someone consider joining the committee?
The first activities of the SSP committee were related with the ERGA pilot project, we worked a little bit with species selection for the project but mainly developing the Sampling Code of Conduct and from that we developed guidelines on how to collect all the necessary metadata associated with the samples. We were also involved in developing the sampling manifest in close cooperation with the Darwin Tree of Life project. At this stage, we also organised that all the countries in Europe learned about the (Pilot) project, especially the Nagoya focal points of each country. We reached out so they could learn about ERGA to hopefully make the permitting process easier.
Another important activity last year was the development of criteria of how to select species for genome sequencing. Since all projects are limited, somehow there needs to be a decision on how to select the species and usually this is a top down process - whoever “owns” a project decides about the selection procedure. But we made it bottom up and developed it as a committee. Everybody who was interested could join and could bring in what they thought was important. Based on this we developed the procedure and then the final decision was made by the ERGA council, but it was really a bottom up process. Right now we are working on standard operating procedures on how to sample different taxonomic groups to get data for genomic analysis and we are also working on a paper on what challenges one can face when sampling for genomics.
Video: Presention of the species selection procedure developed by the SSP.
I think this variety of activities is one of the main reasons why it might be really interesting to join the group. We are a quite diverse group and we address a broad portfolio of different topics related to sampling. And so members can really get into different topics, on what interests them even within the SSP. It’s not just one topic, but there are different possibilities of how to participate and bring in your expertise.
3. What are the most interesting and the most challenging aspects of chairing the SSP?
What I find most interesting about being part of the committee and now also as a chair is that I get to meet many people with different taxonomic expertise and I think that’s the beauty of the group. But we are not all taxonomists, we also have lab folk with different backgrounds in the committee. That makes the work with the SSP really interesting, because you learn a lot. Before joining the committee, I was aware of the challenges I face sampling and studying marine invertebrates, but there are many other challenges I didn’t know about. For example, with mammals it can be really challenging to be even allowed to sample and sometimes you are not allowed to provide the sampling locality, if the species is endangered - which I was not aware of. Or how to sample plants, fungi, or lichens - lichens are more “meta” organisms and are very hard to process. You really have to tweeze them apart. Also I learned a lot about all the different aspects one has to consider while sampling and what metadata are most important for the different taxonomic groups. I also learned much about the challenges that come with the permits, given the different countries we are in or with logistics. Here in Norway it’s relatively easy to get to ship material, but that’s not always the case.
There are also many aspects that we need to consider for the species selection process that I had never thought too much about before joining ERGA. Such as JEDI (Justice, Equality, Diversity and Inclusion) and important principles such as FAIR (Findable, Accessible, Interoperable and Reusable) and Open science data. Other people in our committee had much more experience with these topics, and it was quite interesting to also learn about that. All these different aspects are also reasons why I think it’s so interesting to join our committee. Because you learn a lot and start thinking about topics you haven’t thought about before.
The most challenging aspect I face as a chair is to coordinate all these many different tasks and to push them forward. Time is a challenge, since we only meet once a month. And it requires a lot of engagement by everybody and that can be challenging to keep up.
4. Sampling can be one of the most difficult steps in the reference genome generation pipeline, which can create critical bottlenecks in the effort to sequence all life on Earth. What do you see as the solutions to this in the European context?
I mean if we really think about it, sampling all life is difficult because we need to reach places like the deep sea or other remote areas, and many species are rare or can only be found through a certain time period. And I think the main reason sampling is so often seen as a challenge is because as of now we're doing very targeted sampling to sequence reference genomes. This is because there are really high standards of what kind of sample is needed to produce a reference genome and to fulfil them you need to collect at a very high standard: samples need to be flash frozen, for example. Generally, people will only follow these high standards when it's really necessary - when they know for sure that that specimen will be sequenced at the reference genome-level. Just doing it because maybe in the future the specimen might be sequenced takes a lot of time away.
But I think there are several solutions to this: First of all, we need to really invest in research and development to find ways to get reference genomes starting from lower-quality, not so well preserved specimens. This would also allow us to maybe use material that was collected in the past but not perfectly preserved. It might also ease the hurdle of logistics, as it's not always easy to ship these deep frozen samples across borders, even across European ones. So having the opportunity to work for example with ethanol preserved samples or dry material could be helpful. Maybe now with a growing body of reference genomes available that might be possible, if we can use them as “guides” to facilitate the assembly process.
The other thing is that we also need to engage more with other initiatives which are already out there doing fieldwork, such as ecological studies. In Norway for example there's the Artsdatabanken - they fund five to six projects each year which only go out to map different taxonomic groups across the Norwegian Coastline or the Norwegian landscape. The barcoding community hooked up really early with them. When people apply to obtain this funding, one of the requirements is that they agree to barcode all the species. With that, they managed to increase the number of barcodes for Norwegian species substantially. Maybe we could do something similar: that we hook up with these initiatives and ask that when they go to the field they should also collect samples that we can use to produce reference genomes. And we provide them not only with the knowledge but also the infrastructure by providing access to liquid nitrogen or at least dry ice, shipment and storage afterwards. So that’s another idea that I think might allow us to scale-up, besides being able to use lower quality samples/data, to hook up with this type of initiative.
5. What are the next steps for the ERGA SSP Committee?
We will continue working on the Standard Operating Procedures for sampling that I mentioned earlier. We need to develop them in more detail, and that means also taxonomically in more detail. At the moment we often work in very large groups of organisms. The other thing would be what I just mentioned about how we can overcome the bottleneck: that maybe the SSP could do some lobbying for this research and development topic of using lower quality material and maybe also more challenging taxa in general. On the other hand, the SSP can also act by building bridges. Since we have so many taxonomists in the group, they could be bridges to reach all these other initiatives which go sampling so that we can collaborate with them opportunistically. So that whatever they sample, they remember to sample also for genomics. And we as SSP maybe are the ones who can at least help building these bridges because we actually know what's going on at the national level.
And the other thing is what SSP needs to do is to keep up the engagement. It is still very good but on the other hand we need also to see that people get something concrete out of this work. If you invest a lot of time and you don't have papers or at least get a genome out of it in the end it's not very helpful for your career, especially for younger ones. We need to find ways to be able to do that. One way in which we do that is by writing papers together. We always try to work at least on a paper once in a while and everybody's free to join as they see fit.
So if you like to work on samples of different taxonomic groups and how to sample them feel free to join us. We are a very open community and we are happy about everybody who's keen on working with us!
Learn more about the work of Torsten and the "Comparative and Evolutionary Genomics” (CEG) Research Group on their blog: