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At the age of 16, all I wanted was a simple life – staying in my small Estonian village, taking on a simple job and having a family. However, things don’t always go to plan.

The initial plan did not include moving to the capital to study biotechnology or later to Denmark, the Netherlands, Oman and Switzerland. However, as life offered exciting opportunities, I had no option but to embrace them. Maybe a simple path wasn’t for me.

I had always enjoyed mathematics and biology at school. Once I realised that hunting novel microbes in Italian rice fields to find how much methane they consume is something one can earn a PhD with, I knew I hit a jackpot.

Plodding in the paddies

Paddy fields, flooded land used for growing crops such as rice, account for about 20% of human-related emissions of the greenhouse gas methane. My task during my PhD was to look into these “evil” emissions and figure out the role microbial populations play in the process. Could we possibly find enough methane-consuming microbes dwelling in those swamps to fight methane emissions?

Toiling under the blazing sun of Italian rice fields in Vercelli, I sampled rice plants and soil and brought them back to the lab. It was an excellent chance for me to combine field ecology, laboratory work and molecular biology. With novel methods based on DNA sequencing, we can unravel the composition of the whole microbial community and check how abundant these microbes are. In tightly sealed vessels supporting biologically active environments called bioreactors, we can create conditions that mimic the nature of rice fields and feed these microbial communities to make them grow. Some bacteria divide within hours, and we get a pure culture with days. However, the microbes I was seeking (called archaea) are agonisingly slow growers. To this date, there is still no pure culture available. It took me four years to reach an enrichment in which these archaea make up about 95% of the whole community. At the time, my muddy rice field soups became one of the highest archaea enrichments on the planet.

These fundamental findings show that archaea can be cultivated. Although currently we cannot apply them yet to mitigate methane emissions, the future may hold new opportunities.

Recently, I took on another challenge and another environmental hazard to fight, also with microorganisms: finding microbes that can eat plastic in the ocean.

From rice fields to Pacific islands

When a plastic bottle ends up in nature, it may take hundreds of years before it is degraded. We know that microbes can consume the most complex compounds. They degrade pollutants, wood and oil, so why not plastic? One catch is that little time has passed since we created plastic polymers, so could it be that microbes have not evolved enough to consume these as food? I was set to find out.

In the ocean, plastic accumulates in hot spots called “plastic islands”. One of the largest marine landfills is in the middle of the Pacific. On these islands, plastic is carried by currents in the ocean and broken down to a high concentration of small pieces that float there for a long time. A plastic hotspot like that would also be a hotspot for microbes with a possible taste for plastic. This gives me the chance to study the composition of the microbial community living on different plastic polymer types to see which microbes like to attach to which kind of plastic. I only had to get there.

We sailed on a research vessel in one of the most bizarre places you could imagine. The sea was the only thing I saw for weeks. I faced storms and 10m waves but I got my samples, many plastic pieces retrieved from the ocean.

Back in the lab, I inspected the micro-organisms living on these pieces, and I found the most bizarre creatures: marine bacteria and marine fungi, not champignons, not a chanterelle but tiny little fungi living on discarded water bottles and fishing gear lost at sea. We could identify a few species that actually participate in breaking down plastics that would otherwise persist hundreds of years in nature, but a lot is still unknown. Now I’m trying to understand the mechanisms microbes use to break down the plastic. Once we identify these enzymes we may be able to use them in future biotechnological applications.

That’s the beautiful thing about science, it takes one on a discovery journey. Despite it storms and high waves, to me it’s a journey I never want to come back from.

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