New methods provide future environmental gains

Fast, reproducible and large-scale. The company eDNA Solutions AB develops technologies to analyse large amounts of environmental data. “It is exciting to contribute to the betterment of
society. We can now produce more reliable results about how climate change affects biodiversity, for example,” says researcher Mats Töpel.

the corridor a few flights up at the Department of Marine Sciences has pale, light brown walls that match the overcast grey December weather in the winter-weary Botanical Garden outside. Behind one of the plain doors in the hallway, a faint hum can be heard. But what transpires on the other side is anything but plain. Hidden here is a giant computer – or rather several interconnected computers – that analyse enormous amounts of biological data. When the door opens, the noise level rises several decibels and a wave of heat spills out of the room. The 350 processors in the room are revved up, analysing the approximately 100 terabytes of data that the system contains. “When I started working on a doctorate 13 years ago, I discovered the GNU/
Linux operating system. Being able to handle large amounts of data with this system seemed exciting to me. So I began assembling computers into a cluster and created my own computer lab,” says Mats Töpel, proudly patting the bench with the black computers.

today the computer lab is the hub of his own research. Mats Töpel began studying biology and marine geology and received his doctorate in systematic biology, species identification and speciation. But his interest in how computers can be used in biological research soon gained the upper hand. Today he conducts research on genomics and bioinformatics.  He sequences DNA and studies changes that occur in genes in connection with various environmental changes, and he is working to create new algorithms to analyse biological data.

in parallel with his research, Töpel runs eDNA Solutions AB along with colleagues Alexander Eiler and Thomas Larsson. The company specialises in environmental surveillance and assessment. They use DNA-based techniques to track individual species and assess biodiversity of macroorganisms and microorganisms. “Traditionally researchers have gone out in the field looking for a species, held it in their hands and identified the species. We take a water sample and see what DNA molecules are in it. All living organisms leave traces of DNA. In this way
we can see which species have been there,”Töpel explains.

DNA-based technology offers many advantages. Mats Töpel highlights three main aspects:

  • It is fast. A single water sample can contain large quantities of DNA, and you do not need to know exactly what species you are looking for.
  • It is reproducible. With this technology, it is easy to do comparative studies in exactly the same way.
  • It is large-scale. Tests are run against reference databases, and instead of comparing sequences manually, one by one, you can now parallel process hundreds of thousands of sequences simultaneously.

“This means that the analyses, results and conclusions are far more certain and more reliable,” Töpel adds. “It is a cost-effective way to perform inventories and environmental monitoring.”

with his dna-based technology, Töpel focuses on large companies that want to make environmental impact assessments of their own operations and on various environmental monitoring companies. The technology is not entirely new. England, France and Belgium lead the way in using eDNA, and they are now starting to use it in large, national environmental monitoring programmes. But in comparison with the rest of the world, Mats Töpel and his colleagues are at the forefront.

“It is exciting to be able to apply academic research to different social problems. One of the UN’s global goals for sustainable development is to preserve ecosystems and biodiversity. We can
help here by providing technology that monitors biodiversity and by observing how biodiversity is changing due to climate change.”

he cites his own ongoing research project on diatoms as an example. Along with two other research teams, Töpel and his research team are studying how diatoms living in the water outside a nuclear power plant in Lovisa, Finland, have been affected by climate change. Cooling water from the nuclear power plant has caused a rise in water temperature, making this an area for a “natural experiment”. Diatoms can go into dormancy and rest on the bottom for at least 100 years. The researchers are now taking samples of the sediment and waking up algae that have lived in the 1930s and later. “We can see what they looked like and how they have responded to the increase in water temperature. How have the algae adapted? Have certain variations of a gene disappeared? Has a positive selection for certain characteristics occurred?”

we have gone down a flight of stairs, and Töpel opens the door to another laboratory. Here it is much cooler, and it feels as if we are stepping into a gigantic, white fridge illuminated by a blinding chalk-white light. Crowded in trays on the shelves and benches are 600 small diatom samples. They provide Mats Töpel with data to process in the computer lab. However, these analyses tell us something about more than diatoms alone; the results can also apply to other organisms. “By studying changes in the genes of diatoms, we also gain information about how other organisms respond to changes,” says Töpel. “Are they malleable and able to adapt or will this mean a collapse? We expect a change in climate, of course. With this technology, we can get an idea of how organisms in our ecosystem will react to it.”

 

eDNA solutions

WHAT? eDNA Solutions AB. A company developing various technologies for analyzing environmental DNA (eDNA) – for various bioinformatic analytical methods, for example. These are used for studies of biodiversity, among other things.

WHEN? The technologies are used in specialised projects to make environmental impact assessments. They have been used to make inventories of salamanders, frogs and individual species, but soon they will also be able to track plankton and microorganisms in water and do pollen analysis.

WHY? Because it is a reliable and cost-effective method that provides more dependable results than traditional biological research. It is reproducible and can scale up to very large amounts

Mats Töpel

Age: 45
Occupation: Researcher in genomics and bioinformatics
Lives: In Vallda
Family: Yes, my wife Paula och children Malte and Märta My