MicroFlora Danica:Searching for Nitrifiers across 10,683 Danish samples

Flora Danica, a comprehensive atlas documenting the native plant species of Denmark and surrounding regions, was developed over 122 years and includes 3,000 botanical engravings. Inspired by this effort, we introduce Microflora Danica, a microbial atlas for Denmark, based on 10,689 samples reflecting Denmark’s diverse habitats and primary land uses. From these samples, we generated 10,683 short-read metagenomes, near full-length 16S rRNA gene data from 412 samples, 16S and 18S rRNA operon data from 450 samples, and 19,253 metagenome-assembled genomes (MAGs). Agriculture, which covers two thirds of Denmark’s land, is the dominant land use. Given the importance of agriculture and the nitrogen cycle in these systems, we focused our explorations of the dataset on the distribution and diversity of nitrifiers. We developed and curated new HMM search models for the amoA and nxrA genes through an iterative approach using the MAGs recovered from the metagenomes. Our search models improved classification resolution, enabling us to distinguish better between characterised nitrifiers, homologous enzymes, and putative nitrifiers. The MAGs enabled exploration of nitrifier diversity through single copy marker gene searches (SingleM) and genome quantification (sylph), which we could use to confirm our gene-based observations. Linking our findings to high-quality MAGs recovered from deep long-read sequencing facilitated metabolic reconstruction, and further functional inferences based on gene synteny. Overall, we show how the Microflora Danica dataset provides a new window for the investigation of key functional microbial groups of interest from both gene- and genome-based perspectives.