Enabling detection of ecological patterns in 10.000 samples representing the Danish soil microbiome

Soils are inhabited by immensely complex microbial communities, but detailed analysis is hampered by lack of reference genomes and 16S rRNA gene sequences in the databases. In this project, we generated near perfect full length 16S rRNA gene sequences from 1.000 environmental samples to increase the obtainable taxonomic resolution of 16S rRNA gene fragments from shallow shotgun metagenomes. By doing so we aim to enrich the interpretation of ecological patterns of the Danish microbiome (10.000 samples).
In the pilot phase of the project, 130 samples (from the project Biowide) representing major terrestrial habitats in Denmark, have been sequenced. The samples were collected in a stratified random design covering the major ecological gradients of succession, moisture, and soil fertility (including agriculture and silviculture) and represent sampling across all major regions of Denmark
Full length 16S rRNA gene sequences were generated utilizing unique molecular identifiers in Nanopore sequencing and produced 101770 unique sequences (99% clustered) with an error-rate >Q30 and chimera rate of