Soil tank test microbial data
Description
This dataset records microbial sequencing data collected from soil tank simulation experiments conducted between September 2022 and April 2023 at the Beijing Engineering Research Center for Ecological Restoration and Carbon Fixation of Saline-Alkaline and Desert Land, Tsinghua University. The data represent sequencing data collected from bacterial and fungal communities during two distinct phases of the simulation experiment.
Files
Steps to reproduce
The V3-V4 hypervariable region of bacterial 16S rRNA genes and the ITS1-ITS2 region of fungal rRNA genes were amplified using primer pairs 338F (5'-ACTCCTACGGGAGGCAGCAG-3')/806R (5'-GGACTACHVGGGTWTCTAAT-3') and ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-3')/ITS2R (5'-GCTGCGTTCTTCATCGATGC-3'), respectively. Polymerase chain reaction (PCR) amplification was conducted using a T100 Thermal Cycler (BIO-RAD, USA). PCR products were separated by 2% agarose gel electrophoresis, purified with the AxyPrep DNA Gel Extraction Kit (Axygen, USA) following the manufacturer’s protocol, and quantified using the QuantiFluor™-ST Blue Fluorescent Quantification System (Promega, USA). Amplicon sequencing was performed on an Illumina MiSeq PE300 platform by Majorbio Biopharmaceutical Technology Co. Ltd. (Shanghai, China). Raw FASTQ files underwent quality filtering using fastp (v0.19.6) (Chen, 2023; Chen et al., 2018), and paired-end reads were merged with FLASH (v0.19.6) (Magoč and Salzberg, 2011). Subsequent sequence analysis was conducted using QIIME2, with DADA2 employed for sequence denoising (Callahan et al., 2016). The resulting optimized sequences were utilized to generate amplicon sequence variant (ASV) representative sequences and corresponding abundance profiles.
Institutions
- Tsinghua UniversityBeijing, Beijing