The Microflora Danica atlas of Danish environmental microbiomes
Caitlin M. Singleton, Thomas Bygh Nymann Jensen, Francesco Delogu, Kalinka Sand Knudsen, Emil A. Sørensen, Vibeke Rudkjøbing Jørgensen, S. M. Karst, Yuhong Yang, Mantas Sereika, Francesca Petriglieri, Sven Knutsson, Sebastian Mølvang Dall, Rasmus Hansen Kirkegaard, Jannie Munk Kristensen, Christina Karmisholt Overgaard, Ben J. Woodcroft, Daan R. Speth, Samuel T. N. Aroney, Henning Thomsen, Bent T. Christensen, Lis Wollesen de Jonge, Anne‐Cathrine Storgaard Danielsen, Cecilie Hermansen, Mogens Humlekrog Greve, Rasmus Ejrnæs, Thomas A. Davidson, Signe Normand, Urs A. Treier, Bjarke Madsen, Andreas Schramm, Ian P. G. Marshall, Ann‐Sofie Dam, Kasper Urup Kjeldsen, Kai Finster, Philip Francis Thomsen, Eva Egelyng Sigsgaard, Martin Johannesen Klepke, Marie Vestergård, Erik Aude, Lene Thomsen, Camilla Lemming, Rita Hørfarter, Marlene Mark Jensen, Tobias Guldberg Frøslev, Lone Gram, P. Svendsen, Morten Dencker Schostag, Sanne Kjellerup, Torben Lund Skovhus, Ditte Andreasen Søborg, Kasper Reitzel, Jørgen F. Pedersen, Andrew T. Giguere, Inge Søkilde Pedersen, Mads Sønderkær, Jes Vollertsen, Fan Liu, Peter Roslev, Niels Iversen, Kåre Lehmann Nielsen, Nadieh de Jonge, Dan Bruhn, Jeppe Lund Nielsen, Torsten Nygaard Kristensen, Chenjing Jiang, Marta Nierychlo, Giulia Dottorini, Michael Wagner, Morten Simonsen Dueholm, Per Halkjær Nielsen, Mads Albertsen
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 oceans1, in the human gut2 and on Earth3, with compilations encompassing thousands of public datasets4,5. 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 N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function. Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.