Macquarie Island Soil Mesocosm qPCR Data for Hydrocarbon Toxicity

February 2013 to April 2015 data from an in-situ mesocosm experiment on Macquarie Island assessing the toxicity of residual hydrocarbons on soil microbial communities. The dataset contains semi-processed and processed microfluidic qPCR results for 90 soil samples, assaying 14 functional genes, generated by the Australian Antarctic Data Centre. It includes gene copy numbers, treatment concentrations, and environmental parameters.

Use Cases

• Model the relationship between Treatment (nominal spiking concentration) and Factor qPCR corrected copies/g to quantify dose-response effects of hydrocarbons on specific genes.
• Analyze temporal changes in gene abundance by correlating Time (sample set) with Copies/ul or Factor qPCR corrected copies/g for different Assay targets.
• Investigate correlations between environmental variables in the 'Environmental' tab (e.g., TPH data, vegetation coverage percentage) and microbial gene copy numbers (Factor qPCR corrected copies/g).
• Assess technical reproducibility by comparing results across the three Fluidigm chips (Plate column: 90, 91, 92) for the same sample conditions.
• Calculate gene copies per gram of soil using the provided G of soil and Initial volume columns to standardize measurements across samples.

Strengths

• Data spans a 26-month experimental period from initial setup in February 2013 to final sampling in April 2015.
• Includes 90 distinct soil samples analyzed with assays for 16 different genes, 14 of which produced valid results.
• Provides both semi-processed qPCR outputs and a processed Biological spreadsheet with corrected gene copy numbers per gram of soil.

Limitations

• Sample size is limited to 90 selected replicates from an initial pool of 270 extractions.
• qPCR data is semi-processed as the Fluidigm platform does not allow export of raw fluorescence values.
• Chemical data (TPH) and vegetation observations are only provided for a single time point, limiting longitudinal environmental analysis.

Provenance

Source

Australian Antarctic Data Centre (AU_AADC), accessed via NASA Earthdata.

Collection Method

Data generated from a controlled in-situ mesocosm experiment; soil DNA was extracted and analyzed using Automated Ribosomal Intergenic Spacer Analysis (ARISA) and microfluidic quantitative PCR (Fluidigm).

Time Range

February 2013 to April 2015

Freshness

Data was last updated in March 2015.

Geography

Macquarie Island