16S rRNA gene amplicon dataset of soil bacterial communities under three legume species and nitrogen or phosphorus fertilisation

16S rRNA gene (V3–V4) amplicon sequencing of 27 rhizosphere soil samples from a greenhouse pot experiment established on 24 October 2017 in Troubsko, Czech Republic (49.17357 N, 16.50691 E). Three forage legumes: crimson clover (Trifolium incarnatum), white clover (Trifolium repens) and black medick (Medicago lupulina) — were grown for 178 days under three fertilisation regimes (nitrogen, phosphorus, unfertilised control) in three replicates, one pot per sample. Rhizosphere soil was sampled on 20 April 2018. DNA was extracted with the QIAamp PowerFecal DNA Kit (Qiagen); the V3–V4 region was amplified with primers 341F/806R and sequenced on an Illumina NovaSeq 6000 (250 bp paired-end) by Novogene Co., Ltd. Contents (single archive, 71 files, 1.41 GB): raw_reads/ – demultiplexed raw paired-end reads, 54 gzip-compressed FASTQ files (two per sample), with in-line barcode and primer retained; otu/ – OTU table at 97 % identity (7,998 OTUs) in non-rarefied and rarefied (122,454 tags per sample) form, OTU representative sequences (FASTA), taxonomic assignments against SILVA release 132, and a phylogenetic tree of the representatives (Newick); diversity/ – per-sample alpha-diversity indices; qc/ – per-sample sequencing quality statistics and DNA extraction QC; chemistry/ – soil chemistry of the same 27 pots at two sampling times and of the soil used to fill the pots; sample_metadata.csv – links every sample and read file to treatment, plant species, replicate and barcode pair; data_dictionary.csv – defines every column of every table; README.txt, LICENCE.txt, CHECKSUMS.md5. Sample codes are <treatment><species><replicate>: C control, N nitrogen, P phosphorus; I T. incarnatum, P T. repens, T M. lupulina; replicate 1–3. The soil chemistry in chemistry/ was first published in Kintl et al. (2020), SGEM 20, 533–540, https://doi.org/10.5593/sgem2020/3.1/s13.069; please cite that article when using it. The dataset is described in an accompanying data article in Data in Brief (submitted).