• NERC Data Catalogue Service
  •  
  •  
  •  

Numbers of reads of fungal operational taxonomic units in a soil warming experiment at Mars Oasis in maritime Antarctica from 2007-2012

The datasets consist of three csv files containing: (i) the numbers of DNA reads of 415 operational taxonomic units of fungi in 64 plots of a soil warming experiment sampled in 2007, 2009, 2010, 2011 and 2012, (ii) the taxonomic placements of the fungi and (iii) the treatments applied to the plots.

The research was funded by an Antarctic Funding Initiative grant from the UK Natural Environment Research Council (NE/D00893X/1), a NERC GW4+ Doctoral Training Partnership studentship (grant number NE/L002434/1), NERC core funding to the British Antarctic Survey Long Term Monitoring and Survey programme, and monies derived from the University in Svalbard Arctic Mycology course (for which reference numbers are not available).

Simple

Date (Creation)
2021-10-18
Date (Revision)
2021-10-18
Date (Publication)
2021-10-18
Date (released)
2021-10-18
Edition
1.0
Unique resource identifier
https://doi.org/10.5285/97a08dd9-3b17-49a2-b2d2-aacf67c4cf15
Codespace
doi
Unique resource identifier
GB/NERC/BAS/PDC/01576
Codespace
https://data.bas.ac.uk/
Unique resource identifier
NE/D00893X/1
Codespace
award
Unique resource identifier
NE/L002434/1
Codespace
award
Other citation details
Please cite this item as: Davey, M., & Newsham, K. (2021). Numbers of reads of fungal operational taxonomic units in a soil warming experiment at Mars Oasis in maritime Antarctica from 2007-2012 (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/97a08dd9-3b17-49a2-b2d2-aacf67c4cf15
Credit
No credit.
Status
completed Completed
Author
  Norwegian Institute for Nature Research - Davey, Marie L ( Researcher )
Author
  British Antarctic Survey - Newsham, Kevin K ( Researcher )
Point of contact
  NERC EDS UK Polar Data Centre
British Antarctic Survey, High Cross, Madingley Road , Cambridge , Cambridgeshire , CB3 0ET , United Kingdom
+44 (0)1223 221400
https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/
Maintenance and update frequency
asNeeded As needed
Maintenance note
completed Completed
Global Change Master Directory (GCMD) Science Keywords
  • EARTH SCIENCE > Biosphere > Fungi
  • EARTH SCIENCE > Biosphere > Fungi Taxonomy
Theme
  • Antarctica
  • climate change
  • filamentous fungi
  • fungi
  • glucose
  • glycine
  • growth substrates
  • irrigation
  • lichenised fungi
  • open top chambers
  • soil
  • tryptone soy broth
  • warming
  • yeasts
Place
  • Mars Oasis, Alexander Island Antarctica
GEMET - INSPIRE themes, version 1.0
  • Habitats and biotopes
Access constraints
otherRestrictions Other restrictions
Other constraints
no limitations to public access
Access constraints
otherRestrictions Other restrictions
Other constraints
no limitations
Use constraints
license License
Other constraints
Open Government Licence v3.0
Use constraints
otherRestrictions Other restrictions
Other constraints

.

We strongly encourage contacting Kevin Newsham (kne@bas.ac.uk ) for more information regarding this dataset, including guidance on its reuse.

Use constraints
otherRestrictions Other restrictions
Other constraints
No restrictions apply
Unique resource identifier
url
Codespace
url
Association Type
crossReference Cross reference
Spatial representation type
textTable Text, table
Metadata language
engEnglish
Character set
utf8 UTF8
Topic category
  • Biota
N
S
E
W
thumbnail


Begin date
2007-12-01
End date
2012-12-01

Vertical extent

Minimum value
0.0
Maximum value
5.0

Vertical CS

No information provided.

Vertical datum

No information provided.
Supplemental Information
It is recommended that careful attention be paid to the contents of any data, and that the author be contacted with any questions regarding appropriate use. If you find any errors or omissions, please report them to polardatacentre@bas.ac.uk.
Date (Publication)
2008-11-12
Publisher
  European Petroleum Survey Group
https://www.epsg-registry.org/
Unique resource identifier
urn:ogc:def:crs:EPSG::3031
Version
6.18.3

Distributor

Distributor
  NERC EDS UK Polar Data Centre
British Antarctic Survey, High Cross, Madingley Road , Cambridge , Cambridgeshire , CB3 0ET , United Kingdom
+44 (0)1223 221400
https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/
Units of distribution
bytes
Transfer size
342016
OnLine resource
Get Data ( WWW:LINK-1.0-http--link )

Download data

Hierarchy level
dataset Dataset
Statement

Methodology:

The field experiment was deployed in November 2007 at Mars Oasis on the south-eastern coast of Alexander Island in the southern maritime Antarctic. It consisted of 64 circular plots of 1 m diameter deployed on barren fellfield soil in a periglacial habitat. The soil at Mars Oasis is free of snow and ice cover for c. 10 weeks (early December - mid February) and is permanently frozen for c. 39 weeks of each year. It has a mean pH value of 7.9, mean water potentials measured within a month of snowmelt of between -1 MPa and -7 MPa, and mean organic C and N concentrations of 0.26 percent and 0.02 percent, respectively. Three substrates were applied to the soil. The soil in 48 plots was amended yearly with either powdered glucose, glycine or tryptone soy broth (TSB), with soil in 16 plots receiving each substrate. Within each group of 16 plots, eight were warmed for the duration of the experiment with conical polycarbonate open top chambers (OTCs), and eight were irrigated annually with 1.5 L of water applied to a 0.05 m2 central area in each plot, raising soil water concentrations to 100 percent of water holding capacity. The experimental layout resulted in 16 OTC-irrigation-substrate treatments, each replicated four times in a randomised design.

Soil was sampled from the central region of each plot into sterile plastic tubes in early December 2007, 2009, 2010, 2011 and 2012, and was stored at c.-3 deg C for 96 h (2010) or 16-24 h (other years), before being frozen at -20 deg C and being transported, at the same temperature, to the UK. There, the soil from each plot was defrosted and passed through a 2mm sterile mesh under aseptic conditions. Total DNA was then extracted from 1.1g (fwt) sub-samples of soil and was dried under aseptic conditions prior to shipping to Norway, after which it was resuspended in 30 micro-litres of sterile distilled water. The internal transcriber spacer region or ribosomal RNA genes was first amplified with the primers ITS1F (5'-CTTGGTCATTTAGAGGAGTAA-3') and ITS4 (5'-TCCTCCGCTTATTGATATGC-3'). The ITS1 region was then tagged in a second, nested PCR using fusion primers consisting of the primers ITS1F and ITS2 (5'-GCTGCGTTCTTCATCGATGC-3') and one of 96 unique 6 basepair multiple identifier combinations. PCR reactions were conducted in 25 micro-litre reactions. Final concentrations of reagents were as follows: 1x gold buffer, 0.2 mM dNTPs, 1.5 mM MgCl2, 0.2 micro-metre each of the forward and reverse primers, 2 micro-litres of template DNA and 0.75 units of AmpliTaq Gold DNA Polymerase (ThermoFisher Scientific). Reaction conditions were as follows: initial denaturation at 95 deg C for 5 minutes, followed by 30 cycles (initial amplification) or 20 cycles (nested amplification) of denaturation at 95 deg C for 30 seconds, annealing at 55 deg C for 30 seconds, elongation at 72 deg C for 1 minute, and a final elongation step of 72 deg C for 7 minutes. Amplicons were purified with Agencourt AMPure beads (Agencourt Bioscience, Beverly, United States) and DNA concentrations were measured by Qubit assays. Samples were combined into equimolar pools of 96 uniquely tagged samples that were then submitted to StarSeq GmbH (Mainz, Germany) where each of the four pools of 96 samples were further indexed using the Illumina Nextera Library Prep kit before sequencing in a paired end run on an Illumina MiSeq platform.

Samples were demultiplexed and primer sequences were identified and removed from both the 5' and 3' ends of forward and reverse reads using cutadapt v.1.9.1, allowing up to 15 percent mismatch across the length of the primer. The DADA2 v1.18 package in R was used for quality filtering, error correction and chimera detection. Reads were quality filtered to remove all sequences with ambiguous bases, more than 2 expected errors in the forward direction, more than 4 expected errors in the reverse direction, and length of les...(18)

Data collection:

Instrumentation:

1. Qubit dsDNA HS assays: Life Technologies, Carlsbad, CA, USA

2. Amplicon sequencing: Illumina MiSeq platform, Illumina Inc., San Diego, USA

3. cutadapt v. 1.9.1: Martin (2011) doi: 10.14806/ej.17.1.200

4. DADA2 v. 1.18: Callahan et al. (2016) doi: 10.1038/nmeth.3869

5. RDP classifier v. 2.13: Wang et al. (2007) doi: 10.1128/AEM.00062-07

6. UNITE v. 8.3: Nilsson et al. (2018) doi: 10.1093/nar/gky1022

7. FUNguild v. 1.0: Nguyen et al. (2016) doi: 10.1016/j.funeco.2015.06.006

Data quality:

Instruments were calibrated according to laboratory practices, with standards being used where necessary. No data losses and no data cleaning. Columns MB-MG and MO contain missing values (entered as asterisks) when an OTU could not be confidently assigned to a phylum, class, order, family, genus or species, or a guild or growth form.

File identifier
97a08dd9-3b17-49a2-b2d2-aacf67c4cf15 XML
Metadata language
engEnglish
Character set
utf8 UTF8
Hierarchy level
dataset Dataset
Hierarchy level name
dataset
Date stamp
2021-10-18
Metadata standard name
ISO 19115 Geographic Information - Metadata
Metadata standard version
ISO 19115:2003(E)
Point of contact
  NERC EDS UK Polar Data Centre
British Antarctic Survey, High Cross, Madingley Road , Cambridge , Cambridgeshire , CB3 0ET , United Kingdom
+44 (0)1223 221400
https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/
 
 

Overviews

Spatial extent

N
S
E
W
thumbnail


Keywords

Antarctica climate change filamentous fungi fungi glucose glycine growth substrates irrigation lichenised fungi open top chambers soil tryptone soy broth warming yeasts
GEMET - INSPIRE themes, version 1.0
Habitats and biotopes
Global Change Master Directory (GCMD) Science Keywords
EARTH SCIENCE > Biosphere > Fungi EARTH SCIENCE > Biosphere > Fungi Taxonomy

Provided by

logo

Share on social sites

Access to the portal
Read here the full details and access to the data.

Associated resources

Not available


  •  
  •  
  •