7c5815a5-7909-418b-87dc-af0cab0e57ce https://ipt.biodiversity.aq/resource?r=soil_fungi_its2_maritime_antarctica Microbial soil Fungi (ITS2) diversity from Maritime Antarctica Kevin Newsham British Antarctic Survey
Cambridge GB
David Hopkins The Royal Agricultural University
Cirencester GB
Lilia Carvalhais The University of Queensland
Brisbane AU
Peter Fretwell British Antarctic Survey
Cambridge GB
Steven Rushton Newcastle University
Newcastle upon Tyne GB
Anthony O'Donnell University of Western Australia
Crawley AU
Paul Dennis The University of Queensland
Brisbane AU
Maxime Sweetlove Royal Belgian Institute for Natural Sciences Research assistent
Rue Vautier 29 Brussels 1000 BE
msweetlove@naturalsciences.be
user 2019-03-19 eng Amplicon sequencing dataset (454) of microbial fungi (ITS2 marker gene) in soils from the Antarctic Peninsula and Maritime Antarctic Islands. Metadata GBIF Dataset Type Vocabulary: http://rs.gbif.org/vocabulary/gbif/dataset_type.xml This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License. Soil samples from the Antarctic Peninsula and Maritime Antarctic Islands. -71.844 -45.661 -60.701 -71.878 microbial soil Fungi, ITS2 marker gene phylum Fungi Fungi unkown Kevin Newsham British Antarctic Survey
Cambridge GB
Paul Dennis The University of Queensland
Brisbane AU
Total DNA was extracted under sterile conditions from 10 g of soil using a PowerMax® Soil DNA isolation kit (MO BIO Laboratories, Inc., Carlsbad, CA, USA) as per the manufacturer’s instructions. The internal transcribed spacer 2 (ITS2) region of the ribosomal RNA encoding genes was amplified by polymerase chain reaction (PCR) using the primers gITS7 (5′ GTGARTCATCGARTCTTTG27) and ITS4 (5′ TCCTCCGCTTATTGATATGC28), which target sites in the 5.8S gene and ribosomal large subunit, respectively. The gITS7 primer was 5’-labelled with the 454 FLX sequencing primer adapter B sequence and the ITS4 primer was 5’-labelled with a sample specific barcode sequence and the 454 FLX sequencing primer adapter A sequence. PCRs were performed in duplicate 50 μl reactions, each containing 5 ng template DNA, 1X Phusion® High Fidelity PCR Buffer (New England Biolabs Inc.), 0.2 mM of each of the dNTPs (Invitrogen), 0.3 μM of the ITS4 primer, 0.5 μM of the gITS7 primer, and 1U of 1X Phusion® High Fidelity DNA Polymerase (New England Biolabs Inc.). Thermocycling conditions were as follows: 98 °C for 30 s, 35 cycles of 98 °C for 10 s, 56 °C for 30 s, 72 °C for 15 s and a final extension at 72 °C for 7 min. Negative controls, consisting of sterile water in place of template DNA, did not yield amplicons. Amplicons were purified using a Wizard® SV Gel and PCR Clean-Up System (Promega), quantified with a Qubit fluorometer with a Quant-iT dsDNA HF assay kit and then 72 ng of each sample was pooled. The pooled sample was purified again using a QIAquick PCR Purification Kit (Qiagen), and then sent to Macrogen (Seoul, Korea) for 454 pyrosequencing. Soils without plant cover were sampled along the climatic gradient in Maritime Antarctica. The uppermost five centimetres of soil was collected in 50 ml DNA/RNAase-treated plastic tubes (30 mm diam.) from each of five locations at each site and was bulked. The soil was then immediately snap-frozen by immersion in a mixture of dry ice and ethanol (c. -80 °C). Samples were maintained at -80 °C from the time of sampling until they were processed. Microbial soil Fungi (ITS2) diversity from Maritime Antarctica David Hopkins This work was funded by a UK Natural Environment Research Council Antarctic Funding Initiative grant (NE/D00893X/1; AFI 7/05) and a University of Queensland Early Career Researcher Award.
2019-01-08T01:05:30.223+01:00 dataset Newsham K, Hopkins D, Carvalhais L, Fretwell P, Rushton S, O'Donnell A, Dennis P (2019): Microbial soil Fungi (ITS2) diversity from Maritime Antarctica. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=soil_fungi_its2_maritime_antarctica&v=1.2 Newsham, K. K., Hopkins, D. W., Carvalhais, L. C., Fretwell, P. T., Rushton, S. P., O’Donnell, A. G., & Dennis, P. G. (2016). Relationship between soil fungal diversity and temperature in the maritime Antarctic. Nature Climate Change, 6(2), 182. 7c5815a5-7909-418b-87dc-af0cab0e57ce/v1.2.xml