1. Australian Antarctic Data Centre
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4. AAS_4135_Hydrocarbon_Toxicity

Description

This data set is the product of three high-throughput qPCR dynamic array Fluidigm chips. Data is semi-processed, as Fluidigm software does not allow the export of raw fluorescence data.

In-situ soil mesocosms (n=20) were set up on Macquarie Island in February 2013. Following a year's equilibration, mesocosms were spiked in triplicate with a fuel mixture mimicking the composition of aged fuel spills on Macquarie Island, in addition to five solvent-only controls. Spiking concentrations range from 50mg/kg to 10000 mg/kg, all in triplicate, in addition to 5 solvent - only controls. Soils have been sampled from initial set up until April 2015, with a total of 2 pre-spike and 4 post-spike sample sets.

DNA was extracted from soil in triplicate. Automated Ribosomal Intergenic Spacer analysis (ARISA) was conducted for both Fungal and Bacterial soil communities across all extractions (n = 270). ARISA results confirmed uniformity of replicate extractions. One replicate for each sample was selected for further work (n=90).

Microfluidic qPCR was conducted with the 90 samples and assays for 16 different genes, 14 of which worked. See Thesis in publications section for more details.

First dataset is the semi-processed data output from Fluidigm program (it does not allow the export of un-processed data).

Consult Fluidigm Real-Time PCR Analysis User Guide (PN 68000088 J1) for more information on columns A-N (ID, Type, relative Conc, Value, Calibrated rConc, Quality, Threshold, In Range, Out Range, Peak Ratio).
Assay = gene assayed, see Thesis in publication for more details. Name = sample name and individual extraction replicate; A,B,or C. Plate = individual Fluidigm chip; three were run, 90, 91 and 92. Time refers to sample set, see Question 2. Treatment = nominal spiking concentration of mesocosm. Dilution factor = dilution factor of sample prior to submission for microfluidic qPCR. Copies/ ul = gene copy number of DNA sample. Initial volume = extraction volume. G of soil = weight of soil extracted. Comb_cond is purely for ease of processing with factor qPCR. Factor qPCR corrected copies/g = output once interpolate differences were corrected with factor qPCR.


Processed gene copy number data (copies/g) is provided in second spreadsheet in 'Biological'. 'Environmental' tab provides additional data on samples, including TPH data and vegetation observations at one time point (expressed as percentage of coverage). Contact Sarah Houlahan for more information on chemical data.

Quality

The experiment was to continue into 2016, however elephant seals destroyed a number of the mesocosms on the Island.

Several genes had very low efficiencies, so data for these genes should be used discerningly.
See Thesis listed in publications for more details on individual genes.

Sample Set/Action, Date, Weeks after spiking
Establishment, 17/01/2013, -45 weeks
P1, 01/02/2013, -43 weeks
P2, 30/10/2013, -3 weeks
Spiking, 19-25/11/2013, 0 weeks
T1, 10/12/2013, 2 weeks
T2, 30/03/2014, 18 weeks
T3, 07/01/2015, 59 weeks
T4, 24/03/2015, 69 weeks

Access

These data are publicly available for download from the provided URL.

Temporal Coverages

• Start date: 2013-01-17 - Stop date: 2015-03-24

Spatial Coverages

Science Keywords

• EARTH SCIENCE > HUMAN DIMENSIONS > ENVIRONMENTAL IMPACTS > CONTAMINANT LEVELS/SPILLS
• EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > CONTAMINANTS > PETROLEUM HYDROCARBONS
• EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > CONTAMINANTS > TOXIC CHEMICALS

Use Constraints

This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/).

Please follow instructions listed in the citation reference provided at http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_4135_Hydrocarbon_Toxicity when using these data.