Invisible inhabitants of the sea – unknown microbes with huge impact
Out at sea, at the classic environmental monitoring measuring station B1 near Askö in the Trosa archipelago, the very first samples of a new long series are collected. These samples will reveal the activities of the sea’s smallest inhabitants.
What lives in the water? We can see some of it with our own eyes, such as aquatic plants, macroalgae, fish and small animals. Even the phytoplankton and zooplankton in the Baltic Sea, which are microscopic, are fairly well understood thanks to scientists and their microscopes. However, the smaller the organisms, the less we tend to know about them. Every litre of seawater also contains billions of bacteria, but few people know much about them or what they do.
Vital processes
Vital processes take place in the sea, on which the entire ecosystem, including humans, depends completely. Nutrients are metabolised and oxygen is produced and consumed, as are carbon dioxide, methane and other greenhouse gases. pH levels change and various substances (including pollutants released by humans) are bound in sediments. Other substances are broken down and built up, resulting in a variety of effects. These processes affect food webs, water quality and the climate. The smallest inhabitants of the sea – bacteria, archaea and viruses – play key roles in all these processes.
New molecular biology technologies, known as ‘omics’, have revolutionised our ability to study marine organisms that are invisible to us, and the activities they engage in.
A newly launched research project, in which the Baltic Sea Centre is collaborating with the Environmental Genomics group at SciLifeLab, is using combined expertise in biogeochemistry, ecology and ’omics’ to explore marine microbes. This project is called SeaLab. The main focus is on bacteria, archaea and viruses, but a lot of information will also be gained about small eukaryotic plankton.
Preparing for filtration
In the filtration laboratory at Askö Field Station, microbiologist Emma Bell is assembling the components of the peristaltic pump that will transport the water samples through filters designed to capture the organisms to be studied. The pores in the filters are 0.2 micrometres in size – one-fifth of a thousandth of a millimetre. Such fine filters trap most of the bacteria in the sea. Many viruses also get trapped, as they are often attached to or inside bacteria.
Of course, even bigger things get stuck.
”We don't want to do any pre-filtration anyway, because we would end up filtering out some of the bacteria we are interested in,” explains Emma Bell. ”Especially during blooms, many bacteria form aggregates, i.e. clumps of individual cells, and some cyanobacteria form long filaments. We would miss these in our samples.
Sampling at B1
Eighteen litres of water need to be collected. Emma Bell and Eva Lindell, station manager at the Askö Laboratory who will now regularly go out to collect water samples for SeaLab, step into the small workboat Sprattus with the water sampler and containers. Eva drives out to the classic measuring station B1 in Yttre Hållsfjärden, which is located just outside the Askö Laboratory. As part of the national marine environmental monitoring programme, samples are taken there 25 times a year. This provides valuable marine environmental data with which to compare the microbial samples.
The samples can also be compared with the 15 years of microbial sampling that has been taking place at the LMO station east of Öland by Professor Jaronne Pinhassi's group at Linnaeus University, who shared their methodology
B1 is marked with a yellow buoy. There is a smaller red buoy located next to it, to allow for boats to attach to it. Emma Bell pulls it in with the boat hook.
The water sampler is rinsed with seawater from the site before being lowered for the very first sample of the SeaLab research project. The water is collected two metres below the surface – shallow enough to include bacteria that depend on sunlight for their life cycle, such as photosynthetic cyanobacteria.
The water looks perfectly clear, as if it were completely devoid of life.
”It's amazing to know that it contains all these microorganisms,” says Emma Bell.
Eva measures the salinity and temperature and Emma takes notes: 6.5 per mille; 8.5 degrees Celsius.
Different stabilities
Back on Askö, it's time for the most time-consuming part of sampling: filtration. Four hoses simultaneously pump water from the containers to each filter. In omics it is possible to study genes, RNA (‘messenger’ molecules that carry information between genes and protein factories in cells), proteins and metabolites (substances formed or transformed in the metabolism of organisms).
RNA degrades rapidly, so it is urgent to filter and freeze the RNA samples. Within an hour of collecting seawater, the first filters are ready. Emma swiftly injects a stabilisation solution into the filters, which are then sealed with parafilm and placed in the freezer. She then moves on with the DNA samples, which are more stable and therefore less time-sensitive.
Eventually, samples to be analysed for proteins will also be collected. This requires a liquid nitrogen freezer, which enables the samples to be stored at minus 80 degrees.
Once about twenty samples are ready, they will be transported to SciLifeLab in Solna for analysis.
”I’m excited to get the DNA out and see what’s in there!” says Emma.
”Everything I work with is always transparent: clear water, clear DNA. You cannot see anything. But then you get out some really cool data!”
New long series
Exploration of the smallest inhabitants of the marine ecosystem has now begun, at a site with one of the world's longest series of marine environmental data.
”It's great that we are now starting a new long series of samples,” says Eva Lindell. ”It’s also great that we can do the initial filtering here on site while the samples are fresh.”
When the samples are analysed, the researchers will obtain a huge amount of data. Then comes the hard work of processing it all and making sense of it.
”We want to see what the microbial communities look like and how they interact with each other. All the microbes in the water rely on each other. Each one produces and consumes something. It will be exciting to see who’s there, how they can be linked to the geochemical conditions in the water, and start figuring out what they are doing,” says Emma Bell.
Ecosystem and climate
In the long term, samples can reveal how microbial ecosystems change over time, between seasons and from year to year. This can be due to factors such as nutrient availability, oxygen levels and climate change.
”The great thing about omics analyses is that you can always discover something new and interesting in the data. The technology is also developing rapidly, making it possible to investigate new things all the time,” says Emma Bell.
SeaLab will also take samples at the recently installed floating platform at the Askö Laboratory, where aerosols, volatile organic compounds and greenhouse gases are observed in order to study air-sea interactions and their effect on the climate. Microbes play a key role in these processes, too, which is why the researchers intend to link the platform’s measurements to studies of microbial communities in the water.
With SeaLab, a long-term, systematic investigation into the very smallest inhabitants of the coastal Baltic Sea ecosystem is being initiated. While different omic methods (collectively referred to as ’meta-omics’) have greatly expanded our knowledge of marine microbes and their roles in the ecosystem, they have also shown us that much remains to be explored.
Text: Michaela Lundell
SeaLab is led by Christoph Humborg at the Baltic Sea Centre and Anders Andersson at the Environmental Genomics Group at SciLifeLab. You can read more about the project here.
Last updated: June 10, 2025
Source: Baltic Sea Centre