Profiling Microbial Diversity in Environmental Sediments

DNA extraction and sequencing was conducted according to Seidel et al. (2022a) (link),Seidel et al. (2022b) (link) and briefly, sediment DNA extraction was performed using the DNeasy^® PowerSoil Extraction Kit (QIAGEN, Germany) according to the manufacturer’s guidelines. 16S rRNA gene amplification was performed using the PCR primers 341f and 805r (Hugerth et al., 2014 (link)) and the library for sequencing was prepared and sent for sequencing to the Science for Life laboratory (SciLifeLab) in Stockholm, Sweden. The raw sequencing data were trimmed, denoised, merged, and chimeras removed using the nf-core ampliseq (v. 2.4.0dev) pipeline built in Nextflow (v. 22.04.4) (Straub et al., 2020 (link)) running within the UPPMAX cluster (Uppsala Multidisciplinary Center for Advanced Computational Science). The sequences were trimmed at 269 bp forward and 209 bp reverse and the settings—-double primer were set to “true” to run cutadapt (v. 3.4) twice to ensure the removal of primers, as well as the—-sample_interference were set to “independent.” After chimera removal, the taxonomy was assigned to the SBDI-GTDB (Sativa curated 16S GTDB database, R06-RS202-1, FigShare. doi: 10.17044/scilifelab.14869077.v3). Further data analysis was conducted using R (v. 4.0.4) (R Core Team, 2018 ).