First Nationwide Microbiome Atlas Reveals Hidden Nitrifiers Across Denmark

An international research team led by Aalborg University with contributions from the University of Vienna has systematically mapped the microbiome of an entire country for the first time. In the study "Microflora Danica," published in the renowned journal Nature, over 10,000 environmental samples from across Denmark were analyzed - on average at intervals of only around 4 square kilometers. The result is an atlas of Danish environmental microbiomes with unprecedented spatial resolution and functional depth. Michael Wagner, Daan Speth, and Andrew Giguere from the Center for Microbiology and Environmental Systems Science at the University of Vienna played a key role in the evaluation of nitrifiers, a key group in the global nitrogen cycle.

Focus on Nitrifiers: Major Players Still Uncharacterized

The nitrifiers in microbial soil microbiomes determine how long reactive nitrogen from fertilizers remains available to plants and when it transforms into environmentally harmful forms that enter the atmosphere or waterways. The current study shows the nationwide abundance distribution of these organisms for the first time and reveals something surprising: two particularly widespread lines – TA-21 within the ammonia-oxidizing archaea (AOA) and comammox-Nitrospira Clade B – have no cultivated representative to date. Therefore these nitrifiers cannot yet be studied directly in the laboratory, even though they dominate large areas of agricultural and natural soils, respectively. In addition, the researchers found strong evidence of widespread, previously unknown, and also not yet cultivated groups of nitrite-oxidizing bacteria.

Why It Matters: Fertilizers, Water Bodies, and Nitrous Oxide

Denmark is heavily agricultural (around two-thirds of its land is used for farming). The widespread use of nitrogen fertilizers means that large amounts of reactive nitrogen end up in the environment-with direct consequences for groundwater, coastal waters, and the climate. In agricultural soils, nitrifiers influence how much fertilizer nitrogen remains in the system – and how much enters water bodies as nitrate or escapes into the atmosphere as nitrous oxide (N₂O). Overfertilization of water bodies leads to algal blooms and dead zones in the oceans, and nitrous oxide is a powerful greenhouse gas that also contributes to ozone depletion. Different nitrifiers produce varying amounts of N₂O and react differently to nitrification inhibitors, which are added to fertilizers in many countries to limit losses.

"Understanding which nitrifiers are present and how abundant they are opens up major future potential for making agriculture more precise, efficient, and sustainable," the Vienna researchers emphasize.

Anthropogenic Influence Detectable in the Microbiome

The study also documents that the degree of habitat disturbance -such as intensive farming-is clearly reflected in microbial profiles. Disturbed habitats show high diversity locally, but are more homogenized nationwide. Natural habitats, on the other hand, preserve more overall diversity. These "microbial Fingerprints" could be used in the future to evaluate the success of renaturation projects from a microbial perspective.

Relevance for Austria

Our results show that microorganisms that are key drivers of biogeochemical processes are sensitive to land use and environmental changes. Microbiomes drive Planetary Health. "If we want to make agricultural systems more sustainable and take climate protection seriously, we must systematically consider the microbiome – both in research and in practice."

Michael Wagner, study author, University of Vienna, head of the FWF Cluster of Excellence

Austria faces similar challenges to Denmark: in both countries, agriculture, nutrient inputs, and water protection shape environmental policy. The Danish results are therefore a model case for comparable analyses in Austria-from optimizing fertilizer use to estimating greenhouse gas emissions from soils. "A national microbiome atlas opens up new ways of combining agriculture and nature conservation on a data-based basis," says the Viennese researcher.

About the Study

"Microflora Danica – the atlas of Danish environmental microbiomes" is based on 10,683 metagenomes and supplementary rRNA data sets and links sequences to a five-level habitat ontology. In addition to a country-wide assessment of microbial biodiversity, the focus is particularly on nitrifiers, a group of microbes that is crucial for climate and water quality.