The Microflora Danica atlas of Danish environmental microbiomes

Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans<sup>1</sup>, in the human gut<sup>2</sup> and on Earth<sup>3</sup>, with compilations encompassing thousands of public datasets<sup>4,5</sup>. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N<sub>2</sub>O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.

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Publication Details

Journal
Nature
Published
2025-12-03
DOI
https://doi.org/10.1038/s41586-025-09794-2
Citations
5
Primary Topic
Microbial Community Ecology and Physiology
Type
article
Field-Weighted Citation Impact
8.58
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article

The Microflora Danica atlas of Danish environmental microbiomes

Andreas Schramm, Nadieh de Jonge, Francesco Delogu, Emil A. Sørensen et al.
5 citations
Nature
Microbial Community Ecology and Physiology
8.58
article

The Microflora Danica atlas of Danish environmental microbiomes

Andreas Schramm, Nadieh de Jonge, Francesco Delogu, Emil A. Sørensen, Michael Wagner, Jes Vollertsen, Jannie Munk Kristensen, Thomas Bygh Nymann Jensen, Inge Søkilde Pedersen, Eva Egelyng Sigsgaard, Sebastian Mølvang Dall, Caitlin M. Singleton, Ditte Andreasen Søborg, Henning Thomsen, Kasper Urup Kjeldsen, Martin Johannesen Klepke, Daan R. Speth, Andrew T. Giguere, Signe Normand, Ben J. Woodcroft, Chenjing Jiang, Francesca Petriglieri, Morten Dencker Schostag, Rita Hørfarter, Kai Finster, Marlene Mark Jensen, Vibeke Rudkjøbing Jørgensen, Bent T. Christensen, Jeppe Lund Nielsen, Morten Simonsen Dueholm, Fan Liu, Mads Sønderkær, Mads Albertsen, Sanne Kjellerup, Rasmus Ejrnæs, Sven Knutsson, Thomas A. Davidson, Cecilie Hermansen, Ann‐Sofie Dam, Dan Bruhn, Philip Francis Thomsen, Erik Aude, Bjarke Madsen, Kåre Lehmann Nielsen, Camilla Lemming, Per Halkjær Nielsen, Tobias Guldberg Frøslev, Giulia Dottorini, Peter Roslev, Lone Gram, Anne‐Cathrine Storgaard Danielsen, Niels Iversen, Mantas Sereika, Lene Thomsen, Rasmus Hansen Kirkegaard, Lis Wollesen de Jonge, Torsten Nygaard Kristensen, Urs A. Treier, Marta Nierychlo, Mogens Humlekrog Greve, Samuel T. N. Aroney, S. M. Karst, Torben Lund Skovhus, Ian P. G. Marshall, Kasper Reitzel, Christina Karmisholt Overgaard, P. Svendsen, Kalinka Sand Knudsen, J. Pedersen, Yuhong Yang, Marie Vestergård
article en
5 citations

Abstract

Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans<sup>1</sup>, in the human gut<sup>2</sup> and on Earth<sup>3</sup>, with compilations encompassing thousands of public datasets<sup>4,5</sup>. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N<sub>2</sub>O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.

NatureVol. 649(8098)
Global Biodiversity Information Facility (DK), University of Copenhagen (DK), University of Vienna (AT), Translational Research Institute (AU), Queensland University of Technology (AU), University of Southern Denmark (DK), Aarhus University (DK), Aalborg University Hospital (DK), Nordic Institute of Asian Studies (DK), NIL Technology (Denmark) (DK), Knowledge Centre for Agriculture (DK), TDC (Denmark) (DK), VIA University College (DK), Aalborg University (DK), Technical University of Denmark (DK)
Openalex Percentile: Top 2%
Microbial Community Ecology and Physiology
8.58
DOIOpen Access PDFOpenAlex
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