Back to the future: A time travel in scientific literature to understand protist interactions

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Nov 04, 2019
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Doc’s mad idea


It was summer 2014, and the PI of the future team was attending a conference on protists in an amazing scenery: The Rocky Mountains (more precisely, Banff, Canada). Nice views, relaxed atmosphere, and protists, of course, the perfect combination for good (or crazy) ideas to emerge. Conference sessions were focusing on diverse topics, from evolution, to taxonomy of specific protist groups (so specific that it had session names such as “Excavata”). Moving around sessions and topics, it was obvious that protists were participating in all sort of ecological interactions: from tiny grazers that could eat a culture of bacteria in hours, to aggressive parasites and hippie mutualistic symbionts. This myriad of ecological interactions is something we can associate to protists, and that differs from bacteria (and archaea), which have received much more attention by microbiologists and the general public. While bacteria and archaea evolved several types of metabolisms, protists explored cell morphology and architecture, and with that, they opened the Pandora’s box of physical interactions: larger cells could host symbionts, engulf other cells (and be parasitized too). In this “protistan” mindset, a question popped up “Did anyone compile all the observations on protist interactions that are available in the literature?”. The conference finished and the idea was stocked together with several other ideas, perhaps waiting for chance. 

Nobody calls me chicken! Getting serious (materializing the idea)


Louis Pasteur once said “dans les champs de l’observation le hasard ne favorise que les esprits préparés” which is often translated into English as “chance favors the prepared mind”. We could say that grant calls (chance?) favor meditated ideas. In one of these calls, we were fortunate enough to have this idea (among others) funded. Now we were going for real and the next step was putting together a team that could pursue this idea, and what’s better than a mix of Nordics and Mediterraneans to push forward a project on protists? So, the team was set up and, in the era of omics and bioinformatics, we decided to do something different: survey all the available literature on protist interactions back to the 1800s, reading all the papers and registering the interactions that other scientist observed through one and a half centuries using diverse tools and methods. This was a tremendous exercise that took us back in time, from near the origins of microbiology, through the naturalistic era, to the era of the newer microscopes, and finally to our present era of molecular tools, omics and high-precision microscopy. This time travel would not have been possible without the two heroes in our team that gave almost everything for the cause: together they searched manually (yes, manually!) for about one year all the available literature, reading the papers and compiling the observations with the patience and discipline of a yogi. Thousands of hours and coffees later, by the year 2017, we already had a good database of interactions that we called Protist Interaction DAtabase (PIDA). PIDA includes ~2500 ecological interactions from ~500 publications, spanning the last 150 years.

Networks summarising ~150 years of research on protist interactions

I know you just sent me back to the future, but I’m back -  I’m back from the future: Exploring PIDA and making sense of the compiled data


We were excited to have this new resource with us, and we started to explore it to see what the data could tell us about symbiosis, parasitism and predation. It turned out it could tell us quite a few interesting things (and you could have a look to the paper if you want to know more ). Donald Rumsfeld mentioned “there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns—the ones we don't know we don't know”. PIDA told us what we know, and gave us an idea of what we don’t know. Even though we compiled a lot of data, 150 years of research seem to have only scratched the surface of the myriad of ecological interactions aquatic protists are involved in, which help to keep the natural machine (or ecosystem) running. PIDA cannot say much about the unknown unknowns, but it points to vast unexplored areas in which exploration may bring new and unexpected knowledge.




https://github.com/ramalok/PIDA



Marit F. Markussen Bjorbækmo, Andreas Evenstad, Line Lieblein Røsæg, Anders K. Krabberød, Ramiro Logares

Go to the profile of Ramiro Logares

Ramiro Logares

Researcher, ICM-CSIC

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