Processed 16S rRNA gene amplicon data from a long-term fertilization experiment in a subtropical tea plantation

Description

This dataset contains the surviving processed bacterial 16S rRNA-gene V3–V4 amplicon data supporting exploratory bacterial-community analyses of a 12-year fertilization experiment in a subtropical tea plantation. It includes metadata for 24 plot-by-depth soil samples, sequencing quality-control summaries, a locked abundance matrix containing 7,554 amplicon sequence variants and 1,624,230 processed counts, representative ASV sequences, taxonomic assignments, diversity and ordination inputs, figure source data, and analysis code. The analyses reported in the associated Geoderma manuscript used the final vendor-released Summary/Summary dataset dated 24 November 2022. The original paired-end FASTQ files were deleted from the sequencing provider’s archive and could not be recovered, and no retained soil or DNA was available for resequencing. Accordingly, this deposit enables reproduction from the processed-ASV stage but not independent repetition of demultiplexing, read merging, primer removal, quality filtering, denoising, chimera removal, index-bleed assessment or contaminant screening. The bacterial-community results should therefore be interpreted as exploratory configuration-level corroboration rather than treatment-specific mechanistic evidence.

Steps to reproduce

Begin with 03_ASV_abundance/ASV_abundance_counts.csv and join sample information using 01_sample_metadata/sample_metadata_final.csv. Convert ASV counts to within-sample relative abundances without rarefaction. Recalculate observed ASV richness, Shannon diversity using logarithm base 2, Simpson diversity and Pielou evenness. Calculate Bray–Curtis dissimilarities from relative abundances and derive principal-coordinate analysis coordinates. Aggregate phylum-level relative abundances using the supplied taxonomic assignments. The processed-data statistical analyses and figure generation can be reproduced using the scripts and notebook in 08_analysis_code. The original paired-end reads are unavailable; therefore, demultiplexing, paired-read merging, primer removal, quality filtering, denoising, chimera removal, index-bleed assessment and contaminant filtering cannot be independently repeated.

Institutions

• Nanjing Agricultural University

  Jiangsu, Nanjing
• Jiangsu Academy of Agricultural Sciences

  Jiangsu, Nanjing
• Guangdong Academy of Agricultural Sciences

  Guangdong, Wushan

Categories

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