Interplay between geological and contemporary environments on soil microbial communities across various sedimentary rocks
Description
Paired-End rDNA raw sequences
Files
Steps to reproduce
After conducting high-throughput PCR amplification on different soil DNA templates, paired-end sequences of soil microorganisms (primarily bacteria and fungi) were obtained using the Illumina MiSeq platform with dual-index sequencing. For soil bacteria, we selected V4 region as the amplification region and 515F and 806R as universal primers. For soil fungi, we selected ITS1-5F region as the amplification region and ITS5-1737F and ITS2-2043R as universal primers. The unoise3 was used for amplicon sequence variant (ASV) denoising processing and the ASV representative sequences and ASV feature tables were constructed after predicting the actual biological sequence and removing the chimeras. We annotated the bacteria and archaea species with 16S SILVA database, annotated the fungi species with ITS UNITE database, filtrating chloroplast and mitochondrial sequences and then standardized the feature tables. To eliminate the sequencing depth differences among the samples, subsamples (rarefies) with the default depth set 100,000, thus the standardized feature tables that can be used for downstream analysis created. We used Usearch tool to conduct the abundance statistics and summaries at different taxonomic levels, which were used for the subsequent analysis.
Institutions
- Yunnan University