Short read Whole genome shotgun sequencing of 276 wild A. thaliana rosettes from south west Germany.

Microorganisms from all three domains of life establish associations with plants. Although some harm the plant as pathogens, others antagonize pathogens or help the plant though priming of the plant immune system, nutrient acquisition, tuning plant hormone levels, and more. Most culture-independent plant microbiome research has focused on amplicon sequencing of 16S rRNA and/or the internal transcribed spacer (ITS), but the decreasing price of high-throughput sequencing has made shotgun metagenome sequencing increasingly accessible. Here, we describe the shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional 16S and ITS1 amplicon data for 176 of those samples. The samples were dominated by bacteria, with eukaryotes contributing a minority of reads. Microbial membership showed weak associations with both site of origin and plant genotype, which were highly confounded. There is large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and samples of high complexity and a low microbial load as the other extreme. We use the metagenome data, which captures the ratio of plant to bacterial DNA in real leaves, to scale the 16S amplicon data such that they reflect absolute bacterial abundance, and show that this cost effective hybrid strategy overcomes compositionality problems in amplicon data and leads to fundamentally different conclusions about microbiome assembly.