Date (Creation)

2025-07-14

Date (Revision)

2025-07-14

Date (Publication)

2025-07-14

Date (released)

2025-07-14

Edition

1.0

Unique resource identifier

https://doi.org/10.5285/d93d9ae6-4eff-4d9a-9997-d0ed06c3df1b

Codespace

doi

Unique resource identifier

GB/NERC/BAS/PDC/02081

Codespace

https://data.bas.ac.uk/

Unique resource identifier

NE/P003079/1

Codespace

award

Other citation details

Please cite this item as: Newsham, K.K., Biersma, E.M., Prieme, A., Molina-Montenegro, M.A., & Goodall-Copestake, W.P. (2025). Richness and abundance of plant and animal pathogenic fungi in Patagonian, sub-Antarctic and Maritime Antarctic soil samples collected January-February 2018 (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/d93d9ae6-4eff-4d9a-9997-d0ed06c3df1b

Credit

No credit.

Status

Completed

Point of contact

Organisation name	Individual name	Electronic mail address	Role
British Antarctic Survey	Newsham, Kevin K		Author
Natural History Museum of Denmark	Biersma, Elisabeth M		Author
University of Copenhagen	Prieme, Anders		Author
University of Talca	Molina-Montenegro, Marco A		Author
Royal Botanic Garden Edinburgh	Goodall-Copestake, William P		Author
NERC EDS UK Polar Data Centre		PDCServiceDesk@bas.ac.uk	Point of contact

Maintenance and update frequency

As needed

Maintenance note

Completed

Global Change Master Directory (GCMD) Science Keywords

• EARTH SCIENCE > Biosphere > Fungi

Theme

• air temperature

• animal pathogenic fungi

• emerging pathogens

• phytopathogens

• plant pathogenic fungi

• precipitation

• soil pH

Place

• Torres del Paine, moraines near Frances Glacier Chile

• Tierra del Fuego, beach near Porvenir Chile

• Fuerte Bulnes Chile

• Busen Region, Pohlia Falls South Georgia Island

• Busen region, Upper Husdal Valley South Georgia Island

• Thatcher Peninsula, Maiviken South Georgia Island

• Tierra del Fuego, pass near Karukinka Natural Park Chile

• Signy Island, Backslope South Orkney Islands

• Livingston Island, Hannah Point South Shetland Islands

• Antarctic Peninsula, Marguerite Bay, Lagoon Island Antarctica

• Antarctic Peninsula, Marguerite Bay, Léonie Island Antarctica

• Antarctic Peninsula, Marguerite Bay, Lagotellerie Island Antarctica

GEMET - INSPIRE themes, version 1.0

• Habitats and biotopes

Access constraints

Other restrictions

Other constraints

public access limited according to Article 13(1)(e) of the INSPIRE Directive

Use constraints

License

Other constraints

Open Government Licence v3.0

Use constraints

Other restrictions

Other constraints

Data released under Open Government Licence V3.0:

Use constraints

Other restrictions

Other constraints

This dataset is under embargo until the publication of the relevant manuscript.

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url

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url

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dependency

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dependency

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url

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Spatial representation type

Text, table

Language

English

Character set

UTF8

Topic category

• Biota

Begin date

1981-01-01

End date

2010-12-31

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.

Title

European Petroleum Survey Group (EPSG) Geodetic Parameter Registry

Date (Publication)

2008-11-12

Cited responsible party

Organisation name	Individual name	Electronic mail address	Role
European Petroleum Survey Group		EPSGadministrator@iogp.org	Publisher

Unique resource identifier

urn:ogc:def:crs:EPSG::3031

Version

6.18.3

Hierarchy level

Dataset

Statement

Methodology:

Soil samples were collected in January-February 2018 from 12 sites between Torres del Paine (Chile) and Lagotellerie Island (Maritime Antarctica). Four to five samples of barren soils (c. 20 g fresh weight) were sampled 1-2 m from Colobanthus quitensis plants into sterile containers that were stored at c. 4 °C before being frozen at -20 °C, prior to transfer to the lab, also at -20 °C.

The samples were defrosted and mixed. Soil pH value was measured in a suspension of 5 g soil and 20 ml of distilled water. Soil C/N ratio was calculated following measurement of total C and N in freeze-dried soils using a TruSpec CN analyser. Water-soluble carbon (C) and nitrogen (N) were extracted from 5 g of fresh soil in 25 ml distilled water for 60 min. After filtration through filter paper, the concentrations of total dissolved organic C were measured using a Shimadzu TOC-L CSH/CSN total organic C analyzer. Total dissolved N was measured with a FIAstar 5000 flow injection analyser after digesting extracts in sulphuric acid with selenium as the catalyst. Dissolved concentrations of NO3--N and NH4+-N were measured using a FIAstar 5000 flow injection analyser using cadmium reduction and indophenol blue and molybdenum blue methods, respectively.

DNA was extracted from 0.25 g subsamples of freeze-dried soil using a FastDNA Spin Kit for Soil. The internal transcribed spacer (ITS) 2 region of fungal DNA was amplified using the primers ITS4 and ITS7. PCR amplifications consisted of two steps: (i) primers and template DNA (1 µl) were added to Illustra puReTaq Ready-To-Go PCR Beads and were thermocycled at 94 °C for 2 min, then 35 cycles at 94 °C for 30 s, 56 °C for 30 s and 72 °C for 30 s, followed by an extension step at 72 °C for 5 min and (ii) 2 µl of the diluted PCR product was added to a reaction mixture consisting of 0.15 µl DNA polymerase (AccuPrimeTM Taq DNA Polymerase High Fidelity, Invitrogen), 2 µl 10 x AccuPrimeTM PCR Buffer II, 1 µl (770 nM) of custom-tagged forward and reverse primers and 13.85 µl sterile water. Mixtures were thermocycled at 94 °C for 2 min, then 14 cycles at 94 °C for 30 s, 56 °C for 30 s and 72 °C for 30 s, followed by an extension step at 72 °C for 5 min. Amplicons were purified in 1% agarose gels using a Montage Gel Extraction Kit. The concentrations of amplicons were measured using Qubit dsDNA HS assays and fluorescence was measured using a Qubit fluorometer. Samples, pooled in equimolar amounts, were paired-end sequenced over two Illumina MiSeq flowcells.

Demultiplexed sequences from each sample were trimmed of primers using cutadapt 1.18. DADA2 v1.22.0 was subsequently used in R v 4.1.1 for quality filtering, amplicon sequence variant inference and taxon assignment. Quality filtering removed all sequences with ambiguous bases (trncQ=11), >2 expected errors and lengths <50 bp. Error rates were estimated for forward and reverse sequences and amplicon sequence variants inferred before merging with a 30 base pair minimum overlap. Chimeras were removed and taxonomies assigned to resulting amplicon sequence variants using the RDP classifier with the sh_general_release-dynamimc_all_25.07.2023 reference from UNITE. The decontam v1.14.0 package was then used to remove putative contaminants identified in negative controls (threshold value 1.0). Taxonomies and occurrences of the removed amplicon sequence variants were cross-checked through manual inspection. The taxonomy-assigned, decontaminated amplicon sequence variants were clustered into operational taxonomic units (OTUs) at 98% similarity over 90% of sequence length using the BLASTCLUST algorithm in the package blast-legacy v2.2.26. For each OTU, the taxonomies for its constituent amplicon sequence variants were compared to validate the OTU taxonomy used for all subsequent analyses.

Le...(20)

Data collection:

Instruments

Qubit fluorometer (Thermofisher, USA)

Illumina MiSeq System (Illumina, San Diego, California, USA)

TruSpec CN analyser Leco (St Joseph, MI, USA)

Shimadzu TOC-L CSH/CSN total organic C analyzer (Shimadzu, Kyoto, Japan)

FIAstar 5000 flow injection analyser (Foss Tecator, Hoganas, Sweden)

Software

R versions 4.1.1 and 4.1.3

R packages: terra v 1.6-47, glmnet v4.1-8, DADA2 v1.22.0, decontam v1.14.0 and indicspecies v1.7.15

Python: cutadapt 1.18

UNITE: RDP classifier with sh_general_release-dynamimc_all_25.07.2023

blast-legacy v2.2.26

Web of Science

CHELSA database v. 2.1

CHELSA-BIOCLIM+ database

iNEXT package

Data quality:

Raw data are shown. The data have not been cleaned.

Metadata

File identifier

d93d9ae6-4eff-4d9a-9997-d0ed06c3df1b XML

Metadata language

English

Character set

UTF8

Hierarchy level

Dataset

Hierarchy level name

dataset

Date stamp

2025-07-14

Metadata standard name

ISO 19115 Geographic Information - Metadata

Metadata standard version

ISO 19115:2003(E)

Metadata author

Organisation name	Individual name	Electronic mail address	Role
NERC EDS UK Polar Data Centre		polardatacentre@bas.ac.uk	Point of contact