Baltic Breakfast: Using microbes to track changes in the marine environment

Microscopic organisms such as bacteria and viruses, vastly outnumber most organisms in terms of abundance, biomass and diversity. They create habitable conditions for life on Earth and even help to regulate the climate. Despite their importance, most microbes have never been seen or grown in laboratories, but as new DNA-technologies emerge, the marine microbiome has recently gained more attention as a means of studying the state of the sea. During the Baltic Breakfast, scientists Emma Bell and Alexis Fonseca presented how we can understand the function of microbes in the Baltic Sea, using DNA sequencing approaches.

Revealing who is where and what they are doing

It all begins with the revelation of the genetic code, which is built on four DNA bases, adenine (A), cytosin (C), guanin (G) and thymine (T).

“A, T, C and G. Those four letters encode everything there is to know about an organism,” said Emma Bell, a microbiologist at SciLife Lab and Stockholm University Baltic Sea Centre.

By extracting DNA from seawater or sediment, it is possible to determine which microbes are present and the functions they provide in the environment. Two approaches are typically used. One is to sequence a single gene that all species of a microbial community share.

“This gives a fingerprint of the microbial community and reveals who is there,” Emma Bell explained.

The other approach analyses whole genomes, and investigate the highly diverse metabolic functions of microbes.

“In every environmental place that we find microbes, they have a metabolic niche,” Emma Bell stated.

Although DNA-methods are nothing new, rapid advances in technology and computing power over the past decades now allow for the routine and inexpensive analysis of thousands of microbial genomes from just a few samples. According to Bell, this greatly enhances our understanding of the marine microbiome – which is important for the marine ecosystem as a whole.

”Two-thirds of all life in the oceans is microbial, and these organisms form the foundation of marine ecosystems. Marine microbes perform photosynthesis on a scale comparable to plants on land, regulate greenhouse gases, recycle organic matter, and drive nutrient cycles. They form the base of the marine food web, supporting everything from zooplankton to fish and larger animals,” she said.

Bacteria predict the environmental conditions

The presence and function of microbial communities strongly depend on environmental factors. In the Baltic Sea, gradients in salinity, light, temperature and nutrients affect the conditions.

“Since the microbial communities are very tightly linked to these conditions we asked whether these microbes could be used to predict their environment,” Emma Bell explained.

In a project led by SciLifeLab, microbial DNA was collected from seawater samples alongside detailed environmental measurements from the Baltic Sea. Information on microbial abundance, as well as data on nutrients and salinity was then used to train a machine learning model to recognise the relationship between microbial communities and their surrounding environment.
Once trained, the model could analyse DNA from a new seawater sample and accurately predict the environmental conditions.

“So DNA can be used almost like a biosensor where the status of the environment is recorded in the microbial DNA,” Emma Bell concluded.

Microbial communities are shaped not only by physical and chemical conditions, but also by their interactions with other organisms. One key interaction involves viruses, that hijack the cellular machinery of a bacteria in order to replicate, burst out and kill their host. It is estimated that viral infections destroy 20 to 40 percent of microbial cells every day, which could alter the cycling of carbon and nutrients in the sea.

“The carbon that comes out of the microbial cell can become a food source for other organisms or it can form aggregates and sink to the bottom of the ocean and export carbon to the sea floor. And this doesn’t just happen on the scale of a single cell. It happens on the scale of the ecosystem,” Emma Bell said.

Tons of information in one litre of seawater

To understand which viruses infect which bacteria, researchers study the genetic regions that store fragments of viral DNA from past infections. These genetic records allow scientists to link specific viruses to their bacterial hosts.

These examples, according to Bell, are only a glimpse of what microbial DNA can reveal. She emphasised that DNA sequencing is a powerful tool and that microbes should be included in environmental monitoring.

“From just one litre of water we can learn so much information about the ecosystem. We can see the microbial communities that are there, status of the ecosystem and even predict how the ecosystem might change. We can also see who they interact with and how microbes drive ecosystem processes”.

Seafloor interactions influence nutrient cycling

Interactions between viruses and other organisms, that influence the geochemical cycles also occur in the sediments. Alexis Fonseca, a marine biologist at Stockholm University Baltic Sea Centre and the Department of Ecology, Environment and Plant Sciences presented new research on these previously overlooked interactions.

Viruses in the marine environments come in two types. RNA viruses are prone to infecting large organisms like fish, algae and mammals. DNA viruses, on the other hand, primarily infect bacteria. Bacteria have been fighting against viral infection for millions of years, which has forced them to develop sophisticated defence mechanisms. But an infection is not always negative, as viruses also can transfer useful genes that enhance bacterial functions.

“They can endow superpowers to the bacteria,” Alexis Fonseca presented.

In the Baltic Sea, bacteria that eat, or oxidise, methane could be provided with genes that makes their oxidisation even more efficient. That prevents this potent greenhouse in the sediment from reaching the water column and atmosphere.

“This bacteria receive a gift and they then become more efficient in oxidizing methane or sulphur. This impacts the geochemical cycles,” Alexis Fonseca stated.

Viruses should be considered in nutrient cycles

Fonseca means bacteria-infecting viruses, or phages, can have a considerable impact on the geochemical cycle budgets, a notion supported by recent research. It is already known that bioturbation, whereby sediment-dwelling animals, or infauna, such as worms, clams and crustaceans, mix and alter sediment conditions, affect bacterial communities. Less is known about how they affect viruses. Fonseca and colleagues tested sediments with different densities of animals and analysed DNA and RNA activity in the surface layer after ten days.

“We discovered that infauna significantly affect DNA-viruses – with more animals we have more viruses, they are more diverse and more active”.

Conversely, they could not detect any difference in RNA viruses which, according to Fonseca, is new knowledge. No previous research has investigated whether these very different layers of organisms in the food web – animals and viruses – can interact directly.

“My point is that we should integrate these phages into the budgets of geochemical cycles”.

Electricity-conducting bacteria provide new insights

The breakfast ended with the fascinating discovery of research into anoxic sediments along the Swedish west coast. The so-called 'cable bacteria' are quite different from your typical idea of a microbe. These multicellular bacteria can grow up to a centimetre.

“But this is not the main characteristic actually, the reason these cable bacteria are unique is because they can conduct electricity on a scale of centimetres," Alexis Fonseca presented.

They live across sediment layers, and use their deeper end to consume sulphur and their surface end to respire oxygen. During this process, electrons are transported along the internal “nanowires” of the cable bacteria, creating an electrical circuit. By doing this, the bacteria remove toxic sulphide from sediments and prevent it from entering the water column.

Their abilities have attracted interest due to their potential applications, ranging from biodegradable electronic materials to symbioses with plants, such as rice, that reduce methane emissions. However, recent fieldwork along the west coast revealed something even more unexpected.

“These bacteria are always found on top of the sediments in which oxygen and sulphur is present. But in Koljö fjord, a very anoxic place, we found these bacteria very deep, below 20 cm,” Alexis Fonseca explained.

He suggested that these findings indicate that cable bacteria can form some kind of a collaboration, or syntrophy, with other organisms that produce substances other than oxygen that bacteria can respire. This resembles primitive life on Earth which relied on inorganic energy sources in oxygen-free environments. Fonseca concluded by reaching out with these results to people that look for life beyond Earth.

“People expect to find little green men out there. I thought the same but I now changed my mind, I think we are probably going to find this kind of anoxic community that respire something different from oxygen and get energy from inorganic sources”.

Text: Isabell Stenson