Abstract:
The dataset consists of the relative abundances of the DNA and RNA of a fungus in soil samples from Signy and Leonie Islands, along with physico-chemical parameters (moisture concentration, pH value, total carbon and nitrogen concentrations, delta-carbon-13 content, carbon-14 enrichment, and mean carbon residence time).
Funding was provided by NERC grants NE/H014098/1 and NE/H014772/1 and NE/H01408X/1
Keywords:
Antarctica, Carbon-13, Carbon-14, Helotiales, soil age
Robinson, C., Cox, F., Garnett, M., Horrocks, C., Dungait, J., & Newsham, K. (2020). Relative abundances of DNA and RNA of a previously undescribed Helotiales species in soils from Signy Island and Leonie Island, along with edaphic factors (Version 1.0) [Data set]. UK Polar Data Centre, Natural Environment Research Council, UK Research & Innovation. https://doi.org/10.5285/65359151-158c-47d1-8c04-a59bc3a28f53
| Creation Date: | 2020-10-07 |
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| Dataset Progress: | Planned |
| Dataset Language: | English |
| ISO Topic Categories: |
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| Parameters: |
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| Personnel: | |
| Name | Dr Clare Robinson |
| Role(s) | Metadata Author, Investigator |
| Organisation | University of Manchester |
| Name | Dr Filipa Cox |
| Role(s) | Investigator |
| Organisation | University of Manchester |
| Name | Dr Mark Garnett |
| Role(s) | Investigator |
| Organisation | NERC |
| Name | Dr Claire Horrocks |
| Role(s) | Investigator |
| Organisation | Rothamsted Research |
| Name | Dr Jennifer Dungait |
| Role(s) | Investigator |
| Organisation | Rothamsted Research |
| Name | Dr Kevin Newsham |
| Role(s) | Investigator |
| Organisation | British Antarctic Survey |
| Parent Dataset: | N/A |
| Reference: | Cox, F., Newsham, K.K., Bol, R., Dungait, J.A.J., Robinson, C.H. (2016). Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic. Ecology Letters 19, 528-536. Cox, F., Newsham, K.K. & Robinson, C.H. (2019). Endemic and cosmopolitan fungal taxa exhibit differential abundances in total and active communities of Antarctic soils. Environmental Microbiology 21, 1586-1596. Horrocks, C.A., Newsham, K.K., Cox, F., Garnett, M.H., Robinson, C.H. & Dungait, J.A.J. (2020). Predicting the impacts of climate warming on maritime Antarctic soils: a space-for-time substitution study. Soil Biology and Biochemistry 141, 107682. Newsham, K.K., Garnett, M.H., Robinson, C.H. & Cox, F. (2018). Discrete taxa of saprotrophic fungi respire different ages of carbon from Antarctic soils. Scientific Reports 8, 7866. Related datasets: DNA and RNA sequences have previously been deposited in the NCBI Sequence Read Archive (accession numbers SRP068654 and PRJNA518063, respectively). |
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| Quality: | Instruments were calibrated according to laboratory practices, with standards being deployed where necessary. No data losses and no data cleaning. | |
| Lineage: | Soils used in the analyses were sampled in October and November 2011 from active layers overlaying permafrost in six pits (0.40 x 0.40 m) dug under turves of Antarctic Hairgrass (Deschampsia antarctica). Three pits were dug at Polynesia Point on Signy Island (60.7107 deg S, 45.5849 deg W; altitude 34-45 m a.s.l.) in the South Orkney Islands and three were dug on Walton Terraces, on the north-eastern side of Leonie Island (67.5984 deg S, 68.3561 deg W; altitude 50-60 m a.s.l.) in the southern maritime Antarctic. The three pits at each island were separated by a mean distance of 311 m. Soils were sampled by hammering five sterile tubes (50 ml capacity) horizontally into the vertical faces of each pit at depths of 2, 4 and 8 cm, generating a total of 90 soil samples. Further details of sampling are provided in Cox et al. (2016; 2019) and Newsham et al. (2018). Soil was frozen at -20 deg C or -80 deg C within a few hours of sampling and was transported back to the UK at these temperatures, where it was thawed prior to analyses. Soil pH, moisture and C and N concentrations were measured in bulked soils from each of the three depths in the three pits dug at each island, generating 18 samples in total. Soil pH was measured by adding approximately the same volume of deionised water to each soil sample to generate slurries and recording pH with a glass electrode (pH 21, Hanna Instruments, Leighton Buzzard, UK). Soil moisture was measured gravimetrically after drying c. 1 g of fresh soil at 105 deg C for 17 h. Sub-samples (c. 2.5 mg) of air-dried soil were weighed into foil capsules and were analysed for total C and N. Carbon-14 and Carbon-13 determinations were made on the five replicate soils sampled from depths of 2, 4 and 8 cm in one of the three pits dug at each island, generating 30 samples in total. The soils were sent to the NERC (now NEIF) Radiocarbon Laboratory, where the samples were converted to carbon dioxide using either bomb combustion in a high-pressure oxygen atmosphere, or an elemental combustion system. Sample carbon dioxide was cryogenically purified under vacuum and split into aliquots. The delta carbon-13 (relative to the Vienna PDB standard) was determined on one aliquot of sample carbon dioxide by isotope ratio mass spectrometry. A second aliquot was converted to graphite using Fe: Zn reduction and analysed for carbon-14 content using accelerator mass spectrometry at the Scottish Universities Environmental Research Centre (East Kilbride, UK). Carbon-14 results were normalised to delta carbon-13 = -25 per mille and expressed as %modern and conventional radiocarbon ages (in years BP, where 0 BP = AD1950). Final mean residence time (MRT) of C in soil was determined using the Meathop Model, as described by Horrocks et al. (2020). The model calculates a maximum carbon-14 concentration of 114.33 %Modern (for a MRT of 30 years). This MRT was assigned to all values of >114 % Modern. Note that for sample FC_31, there were two solutions to the model, because of the rising and falling parts of the bomb-carbon-14 curve. Also note that for carbon-14 enrichment values of <97% Modern, a conventional radiocarbon age (CRA) was assigned for mean residence time since these samples showed no evidence of bomb-carbon-14 incorporation (Bol et al., Eur. J. Soil Sci. 50, 41-51, 1999). As described by Cox et al. (2016; 2019), DNA and RNA were extracted simultaneously from soil samples (5 mg) taken from the 50 ml-capacity tubes using RNA PowerSoil Total RNA Isolation and DNA Elution Accessory kits (MoBio Laboratories, Carlsbad, CA, USA). Extracted RNA was treated with a Turbo DNA-free kit (Life technologies, Carlsbad, CA, USA), checked for contaminant DNA using PCR, and reverse transcribed using AccuScript High-Fidelity Reverse Transcriptase (Agilent, Santa Clara, CA, USA) and random nonamers. Internal transcribed spacer (ITS) regions in the extracted DNA and cDNA were amplified in triplicate PCR reactions using ITS1F and ITS4 primers. The ITS4 primer was modified with the Roche 454 A adapter and a 10 bp barcode specific to each sample, and the ITS1F primer was modified with the 454 B adaptor. The triplicate PCR products were pooled and purified using AMPure XP bead purification and quantified using a Qubit dsDNA HS Assay before normalization to consistent concentration. The purified and normalized PCR products were run on the 454 Roche Titanium FLX platform at the Liverpool Centre for Genomic Research. The DNA and RNA sequences were processed using the QIIME pipeline. Sequences were filtered to remove reads that were of low quality, <300 bp or >1200 bp, and were split according to barcodes. The remaining sequences were denoised, and checked for potential chimeras. The ITS2 regions of the remaining sequences were extracted using ITSx and grouped into operational taxonomic units (OTUs) at 97% sequence similarity using USEARCH 6.1. |
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| Temporal Coverage: | |
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| Start Date | 2011-11-01 |
| End Date | 2015-12-31 |
| Spatial Coverage: | |
| Latitude | |
| Southernmost | -67.5984 |
| Northernmost | -60.7107 |
| Longitude | |
| Westernmost | -45.5849 |
| Easternmost | -68.3561 |
| Altitude | |
| Min Altitude | 35 |
| Max Altitude | 60 |
| Depth | |
| Min Depth | N/A |
| Max Depth | N/A |
| Location: | |
| Location | Antarctica |
| Detailed Location | Polynesia Point, Signy Island |
| Location | Antarctica |
| Detailed Location | Walton Terraces, Leonie Island |
| Data Collection: | The following instruments were used in the analyses: 1. Total nitrogen and organic carbon concentrations: Carlo Erba NA1500 elemental analyser, CE Instruments, Wigan, UK 2. pH value: Hanna Instruments pH meter, Leighton Buzzard, UK 3. Elemental combustion: Costech ECS 4010, Italy 4. Isotope ratio mass spectrometry: Delta V, Thermo-Fisher, Germany 5. Bead purification: Beckman Coulter, Inc, Brea, CA, USA 6. Qubit dsDNA HS Assay: Life Technologies, Carlsbad, CA, USA |
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| Data Storage: | Three CSV files. |
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