example_qsip: Example qSIP dataset

In bramstone/qSIP: Quantitative stable isotope probing for microbial ecology

Example qSIP dataset

Description

A data set demonstrating the general organization and data necessary for the calculation of fractional enrichment via qSIP

Usage

data(example_qsip)

Format

A data.table with 14387 rows and 18 variables

Details

• asv_id. unique identifier for individual microbial taxa (here, amplicon sequence variants or ASVs) as identified by 16S amplicon sequencing

• sampleID. unique identifier or code for experimental replicates

• fraction. the fraction number of a replicate (1–22)

• timepoint. the time of sampling for a replicate in days (0, 7)

• isotope. factor of isotopes added to sample (values: NA, 16O, 18O)

• iso_trt. factor specifying whether isotopes were added (light, label)

• ecosystem. the site where soil samples originate from Northern Arizona (MC = mixed conifer, GL = grassland)

• treatment. factor of nutrient amendments added (control, C for glcuose, CN for glucose and ammonium)

• rep. numeric replicate from each plot (1–4 for unlabeled samples, 1–3 for labeled samples)

• Density.g.ml. the density of individual fractions in grams per milliliter (1.6509988–1.736474)

• avg_16S_g_soil. the concentration of bacterial 16S copies of individual fractions expressed per g dry soil (47–803,489)

• seq_abund. the number of sequence reads per taxon (1–20,186)

• Kingdom. the assigned kingdom of a taxon (Archaea, Bacteria, Unassigned, or Eukaryota)

• Phylum. the assigned phylum of a taxon

• Class. the assigned class of a taxon

• Order. the assigned order of a taxon

• Family. the assigned family of a taxon

• Genus. the assigned genus of a taxon

Source

<https://github.com/bramstone/density-dependence-qSIP/tree/main/data>

References

https://doi.org/10.1007/s00442-023-05322-z

bramstone/qSIP documentation built on Nov. 22, 2023, 9:11 p.m.