A team of researchers has mapped the microscopic organisms that live in Danish soil and water, creating a national reference point for understanding how climate and land use are reshaping nature — much as Flora Danica once did for plants.
A team of researchers has mapped the microscopic organisms that live in Danish soil and water, creating a national foundation for understanding how climate and land use are reshaping nature — much as Flora Danica once did for plants.
We have a very good grasp of Danish animals and plants. That is largely thanks to Flora Danica from the 18th century, which named and described the kingdom’s plants and turned visible nature into shared knowledge.
But we have never had a comprehensive overview of the largest part of nature’s life. Microbes in soil and water cannot be pressed like plants or drawn in a book, and for decades it has therefore only been possible to guess how many species exist — from a few thousand to as many as billions.
Now, for the first time, there is a concrete estimate of how many bacterial species are actually hidden in Danish nature — based on the world’s first systematic, nationwide mapping of environmental microbiomes across an entire country.
The lead authors behind the mapping are affiliated with Aalborg University, but to collect samples from across the country they joined forces with the Microflora Danica consortium. The consortium brings together around 50 researchers and private organisations that work closely with the microbiome on a daily basis.
Samples from the consortium formed the basis for advanced DNA analyses, enabling the researchers to narrow down the number of widespread bacteria to around 100,000 species, defined on the basis of genetic relationships in their DNA.
This replaces a wide range of guesses with a figure that can be used for further calculations and as a shared yardstick. At the same time, the analyses show that a large proportion of the species have never been described before — even though they have been hidden in the soil beneath our feet all along.
The project is led by Professors Per H. Nielsen and Mads Albertsen, both from the Center for Microbial Communities at Aalborg University. Per H. Nielsen coordinated the nationwide sample collection across the project’s many collaborators, while Mads Albertsen serves as coordinator of the Microflora Danica consortium. For them, the atlas is about elevating microbes to the same level as visible nature and giving them a place in the national picture of nature.
“With Microflora Danica, we are carrying out the first systematic, nationwide mapping of microbes in an entire country. For the first time, this gives us an overall picture of which microorganisms are actually out there in the landscape,” says Mads Albertsen.
From soil samples to DNA: how the microbes were mapped
Microflora Danica began with a logistical feat. The core group of researchers at Aalborg University behind the project activated their established network and distributed the work across the country. SEGES was responsible for samples from fields and other cultivated areas, researchers in the Microflora Danica consortium covered forests, coastal dunes, heaths, meadows and lake shores, and nature consultants with responsibility for particularly vulnerable habitats collected samples in the most sensitive areas.
In this way, samples were gathered from all over Denmark, covering both cultivated and relatively untouched natural habitats, and each sample was accompanied by a detailed description of the area from which it originated.
The samples were taken in roughly the same simple way everywhere. Researchers and their collaborators used a soil probe, pushed it into the top layer of soil, twisted it to loosen the earth and scraped up a small portion.
The soil was placed in a plastic cup — the kind you might recognise from a doctor’s waiting room — the lid was screwed on, and the cup labelled with location and time. It was then placed in a cool box with the other samples before moving on to the next field, the next forest, the next bog. The routine was repeated thousands of times from north to south and from coast to coast, always following the same procedure, so that differences in the data would later reflect nature rather than sampling method.
When samples become maps: reading the traces of microbes
Back in the laboratory, the scene changed. The cups were opened, the soil treated, and DNA extracted from all the life hidden in the samples. The genetic traces were translated into long strings of letters that computers could read and sort.
For each sample, the researchers could see which microorganisms had been present and how often the same species appeared across the more than ten thousand samples — in practice, an overview of which bacteria are common and which are found only in a few places.
When patterns from all the samples were laid over one another, they formed a map of Denmark marked by microbial footprints, revealing which species were widespread and where nature was particularly diverse.
The contrast with the historic Flora Danica project was striking. Back then, botanists went out with baskets and boxes, collected plants one by one, carried them home, pressed and dried them, and then sat down at their desks to draw each species by hand. Everything took time, and each illustration provided knowledge about only one plant at a time, even though the work often stretched over days or weeks.
“It was a huge, manual task to map even a small part of the visible natural world. You ended up with beautiful drawings and a magnificent work, but you could only go as far as manual labour would take you,” says Mads Albertsen.
In Microflora Danica, the soil probe and DNA produced a completely different result from the same effort. Each time a sample was taken, traces of thousands of microbes came back at once, extracted from the same handful of soil. Where Flora Danica slowly built knowledge species by species, modern methods made it possible to reveal an entire microbial community in a single step.
“What used to take decades and still only gave a glimpse of the whole picture, we can now do in a few years with far greater detail,” says Mads Albertsen.
Three new insights: species, landscape and nitrogen
The study provides a comprehensive and well-grounded estimate of the scale of the microbiome in Denmark and has also led to three specific main findings: new species that now have names, a clearer picture of differences between habitat types, and a revised understanding of the bacteria that control the nitrogen cycle.
The first insight concerns the new species, which have now been named and included in the atlas for the first time. A large proportion of the bacteria identified by Microflora Danica were previously unknown to science. They have been present in the soil all along, but without an identity — and therefore without the possibility of being recognised in other studies.
For that reason, the researchers devoted a substantial part of their work to naming them systematically. Mads Albertsen explains that without a name, there is neither a clear reference point to which knowledge can be attached nor a shared language for talking about a species.
He also describes how he and his colleagues approached the naming process. The work was presented in a separate publication in Nature Microbiology and was named Danish Research Result of the Year by Ingeniøren. More than a thousand of the new species have been given names with roots in Denmark, making it possible to hear from the name where in the country they were first found.
Wherever possible, the bacteria are named after the towns or local areas close to their first known habitat. In connection with the naming, the research group published an interactive map of Denmark on the research unit’s website, where you can check whether a species is named after your city.
New species get names – and a place on the tree of life
One of the most striking examples is Oederibacterium danicum, named after botanist Georg Christian Oeder from the original Flora Danica project. This bacterium appeared in only seven locations out of more than ten thousand samples and represents a completely new branch on the tree of life. Scientists do not yet know what role it plays, but it illustrates how much hidden diversity has now become visible and can be investigated further.
The second insight concerns how bacteria are distributed across the landscape. In forests, bogs, meadows and other relatively untouched areas, the samples showed that microbial communities changed significantly from place to place. Each type of nature had its own combination of species, and even two forests could have distinctly different microbial “fingerprints”, just as two areas can host different plant and animal communities, even though they may appear similar at first glance.
In cultivated agricultural land, the pattern was more uniform. Here, the same bacterial species appeared across large areas, and the variation was much smaller. The atlas thus makes it possible to see how our use of land affects the invisible part of biodiversity and creates uniformity right down to the microbial level.
The third key insight points directly to the nitrogen cycle, which is crucial for both nature and agriculture. In Microflora Danica, researchers focused in particular on the bacteria responsible for the many small steps that make nitrogen available to plants — from the forms found in soil and air to the form plants can actually use — and later pass it on through the system.
Here, entirely new groups of bacteria emerged that had not previously been linked to the nitrogen cycle, but which turned out to be both widespread and frequent in Danish nature. At the same time, some species long considered central to these processes were so rare in the samples that their role in models of nitrogen turnover needs to be reconsidered.
“We are discovering new groups of bacteria that no one knew about before and that are clearly deeply involved in the nitrogen cycle. Conversely, we can see that some of those that were thought to be key players are almost absent in nature. This changes the way we model these processes and points to some completely new species that we need to understand much better in the future,” says Mads Albertsen.
Knowledge about nitrogen can make fertilisation more precise and less damaging
Knowledge about the bacteria that drive the nitrogen cycle can be used to change the way soil is cultivated, according to Mads Albertsen.
The mapping makes it possible to see which microbial communities bind nitrogen effectively in the soil and which allow more to escape into the aquatic environment. This information can be used to adjust models for fertiliser use — for example, how much fertiliser is actually needed on a field — so that yields are maintained or improved while the pressure on nature is reduced.
This could open the door to more targeted strategies in which both the amount of fertiliser and the conditions that give the most desirable microbial communities favourable conditions are regulated, he says.
At the same time, Microflora Danica provides Denmark with a microbial baseline that makes it possible to track how bacterial communities change as the climate warms, new farming methods are adopted, or political agreements such as the green tripartite agreement convert land to more wild nature.
“We can return to the same areas in a few years, take new samples and compare them directly with the conditions we see now, and then see which groups are advancing or declining,” says Mads Albertsen.
The microbial part of biodiversity often reacts quickly to change and can therefore serve as an early indicator of whether developments are moving in the desired direction. In this way, the atlas becomes both a status assessment and a practical tool for planning and adjusting future efforts in both agriculture and environmental management, he says.
Researchers are now mapping fungi — and searching for new enzymes
Microflora Danica is far from finished. It is one thing to know which bacteria exist and where they occur. It is quite another to understand how active they are, how they interact, and how their composition changes over time. DNA data tells us that a species has been present and how widespread it is, but not whether it is active or merely ‘on standby’ — or what causes it to decline.
Researchers involved in Microflora Danica are therefore already working along several lines. One is the sister project MicroFungi, which aims to map fungi in Denmark with the same thoroughness with which bacteria have now been mapped.
Another is Microflora Danica Unique, which focuses on particularly distinctive sites, including the bubbling reefs near the Hirsholm Islands and sand samples from Råbjerg Mile, as well as other unique habitats, to explore their distinctive microbial communities.
In addition, the researchers have carried out a mass experiment involving around 30,000 schoolchildren, who collected samples near their schools and in doing so helped to expand the map.
The first round of Microflora Danica serves as a fixed point of reference: a detailed picture of what microbial communities look like in Denmark right now, collected using uniform protocols that allow direct comparisons over time.
If researchers later have the opportunity to map the same areas again, they will be able to measure what has actually changed — for example as a result of the green tripartite agreement, the conversion of land to more wild nature, or other shifts in how the landscape is used.
At the same time, other research groups and companies, including Novonesis, continue to use the many DNA sequences as a resource in their own right — for example in the search for new enzymes that may prove useful in industry.
“With Microflora Danica, we now have a common reference point for microbial biodiversity in Denmark — a detailed snapshot that makes it possible to measure where and how the composition changes as climate, land use and nature management change over time,” says Mads Albertsen.
