The Dataset

This dataset consists of 16S-V4 gene-marker sequence data collected from soil DNA samples collected from an Ohio rye cover cropping experiment.

Four treatments correspond to different cover crop management regiments:

  • T1 = no cover crop
  • T2 = Early termiation (2 weeks before soybean planting)
  • T3 = Mid termination (1 day before soybean planting)
  • T4 = Late termination (5 days after soybean planting).

Samples were collected at two time points:

  • S1 = Fall 2019 (baseline)
  • S4 = Summer 2020 (soybean seedling stage).

DNA samples were subjected to PCR using 16S-V4 paired primers.

Amplicons were then pooled and analyzed by 300 cycles of Illumina paired-end sequencing.

The Workflow

  1. Primer and adapter trimming

    • Using cutadapt

  2. ASV inference and taxon assignment (with DADA2)

    • Trim and filter reads.

    • Infer sequence variants from reads.

    • Merge sequence variants from Forward and Reverse reads to obtain full-length Amplicon Sequence Variants (ASVs).

    • Estimate phylogenetic relatedness using the phangorn R package.

    • Assign taxonomy using a marker gene database (SILVA).

  3. Analyzing ASV Data

    • Contaminant identification and removal with decontam R package.

    • R packages: phyloseq, ampvis2, DESeq2, etc.




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