Art & Maths in Modelling Plankton

Claudia Traboni, MixITiN’s ESR9, reports on her secondment at Swansea University

June 2019

Short but sWEeT

I feel very happy to have tasted a small bite of the Welsh life in Swansea. While I was there for my secondment I had the chance to enjoy the city, small enough to recognize familiar places and streets but international at the same time. The Swansea University campus is spacious and looks very welcoming. I met students from a range of different countries and I managed to spend time socialising with them. These moments were stimulating and mind opening especially as I was invited to take part in their university life. During the weekends I explored the surrounding beautiful landscapes of Wales and I tasted a traditional Welsh breakfast cooked by local people. Laverbread and cockles are the must-have ingredients making up the early morning marine food-web in Welsh kitchens!

One of the most amazing places I have been to was the Gower Peninsula. It reveals stunning panoramic views teeming with rocky shores, tidal pools, surrounded by vibrant green life both on land and along the seaside. Algae covering rocks looked like the hair of a goddess. Cliffs were enveloped in a grass blanket smelling like rain and wind. Sheep and cows accompanied me sometimes during my walks along the coast path and gentle ladies on their horses passed by making me feel in a different time.

One day ESR6 Andreas Norlin took me to explore the coast path in the Gower towards Three Cliffs Bay. We walked along the beach and sometimes we climbed on rocks to take shortcuts on our way. At the end we were rewarded with a slice of cake and a cup of coffee!

Before leaving Swansea, (my bosses) Dr Mitra and Prof Flynn took me to a place called “Worm’s head” in Rhossili Bay. We spent a really nice afternoon having picnic and taking pictures of the gorgeous landscape. I particularly enjoyed it because that was the hottest and probably sunniest day I have experienced in Swansea! I felt home for a couple of hours!

However “All that glitters is not gold“! For the first one month and a half, rain has been quite annoying for the Mediterranean me. Even a simple walk along the beach turned into a muddy experience where I understood how it feels to retain 99% humidity in the bones! Yet, the Welsh landscape comes from this constant water supply, therefore I would have never appreciated beautiful grasslands and canopies otherwise.  I have definitely been suffering from sun-sickness but a new exciting opportunity was there for me to catch it: untying the knots of a marine food-web.

Who eats who in a drop of seawater?

If you hear the phrase “Marine Food-web” what do you think of? I visualise lots of moving creatures living in the sea in the act of feeding. Contrary to the un-realistic terminology “food chain”, food-webs are networks with multiple performers. So in a food-web the same organism can act as prey and predator and also helps in recycling of material. Also, different predators can have a preference for the same prey type while a predator may pick and choose different prey items at a time.

During my secondment at Swansea, I have been learning about how to deal with marine planktonic food webs in virtual platforms. But to really do so, we need to envision our food-web first. Since I am passionate about drawing, I used this to visualise my food-web where unicellular phototrophs and mixoplankton are being grazed by copepods as their zooplankton predators. In my food-web artwork I also included fish and jellyfish as predators of copepods and the catching-escaping drama at this level.

Artistic illustration of a marine planktonic food-web, © Claudia Traboni

Subsequently, I converted the artwork into a mindmap to help me visualise all the possible relationships within my food-web. As you see, my beautiful copepods and microplankton have now been reduced to boring squares connected by arrows. So now I have a conceptual model! It is conceptual because it shows the actors playing on stage, but it does not show how the movie develops and ends. In creating artwork or conceptual models, I can give shape to organisms and display their relationships to other organisms, with a touch of creativity and colour. Yet, what organisms actually do in the environment is an overarching question in marine ecology where art and concepts are only the starting point.

Conceptual model of my experimental food-web showing all my planktonic performers and their connections

What if?

When we do change our diet in the long term profound changes do happen. So what if suddenly copepods are offered a different-quality snack? This is the core question around which my research is based on. I’m studying the effects of a mixotrophic diet on copepods’ physiology and fitness versus strict photo- or heterotrophic meals.  In fact, mixoplankton can be among the favourite food for zooplankton, but sometimes they can compete with copepods for food or even harm and kill their predators by releasing toxins. Did you expect a tiny cell could collapse an entire ecosystem? Yes, they actually can. But how do we know that beforehand? How can we predict in due time before irreversible damage takes over?  How do we account for cascading effects at food-web level in a test tube? To really understand how a food-web works, flasks are good tools to re-construct interactions governing the complex network of organisms in accurate fashion. However, I have to bear in mind that for each process taking place there will be hundreds of feedback responses going on. So I need to add more boxes and more and more arrows to my scheme to eventually simulate every important process down to the smallest detail. Through the software Powersim Studio I can connect the boxes with arrows and obtain something similar to what happens in nature. The huge amount of flows and dependent relationships between the plankton communities makes the system extremely interlinked and astonishingly complex to predict.

Multi-trophic conceptual model developed through the software Powersim Studio. How do you feel looking at it?!

Of course, I cannot make predictions that complex in a flask. And this is where maths come to help us! Over the last century marine scientists have attempted to integrate marine ecology with numerical computations to finely simulate various micro-interactions among planktonic organisms. Through defined sets of differential equations, each component or process (square or circle in the diagram) is described and changes are predicted over time as the simulation proceeds. Thanks to simulation models, we can conduct in silico experiments without any live sample. Certainly, we should know the basic features of the system we are going to simulate but accept that we would need to make a certain degree of assumptions. It is like we have some spoilers from a movie and we are trying to figure out how the story develops using mathematics! Sounds pretty exciting, right?!

I had never had any experience with models before joining Team MixITiN. In fact, I have always been quite scared by the huge amount of intrinsic mathematic notions behind their functioning. However, with a little patience and passion, anything can be obtained. I learnt about models during my first two MixITiN workshops, where I had limited time to play with them. Now, in my second year of training, I am configuring a food-web model with my actors – the species that I am going to use for wet laboratory experimentation at Consejo Superior de Investigaciones Científicas – Instituto de Ciencias del Mar in Barcelona.

These are my pets. Two marine calanoid copepods of the species Paracartia grani that I spotted under the microscope (left: young male, right: female). Females are usually bigger and feed more than males

Throughout the duration of my PhD, I will test my research hypotheses both in vivo and in silico, reproducing the conditions of the simulation set-up (some of them!!) in real incubation experiments whose results will serve eventually for validating my in silico experimental set up.

Needless to say that the most exciting part of a simulation set-up is the use of, what I call, the “What if” buttons. I can literally switch “things” on and off required by my experimental question. And, in doing so I can remove or add the contribution of specific organisms or processes to my system.

Examples of “What if buttons” created using the software Powersim Studio. I can decide when it is time to feed!

In practical terms, this would probably imply entire nights spent in the laboratory to effectively turning the light on and off at the desired time or feeding the organism whenever the experiment requires it. In a nutshell, the capability of models for temporal prediction gives us the opportunity to understand what could happen if we had the time to monitor ourselves. This is why I love models!