High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration: OTU raw data matrix
We present a High-throughput eDNA dataset of fungi to track functional recovery in ecological restoration in the form of an OTU raw data matrix. We generated a total of 4,993,144 ITS fungal raw reads (118,884 ± 42,210 SD per replicate) across the 42 replicates. A total of 4,955,680 fungal sequences (117,430 ± 42,164 SD per replicate) remained for further analysis after quality filtering. The OTU data provide information on fungal flux at this restoration site through a stagger of years and can be used accordingly.
Simple
Identification info
- Date (Creation)
- 2014-12-18
- Date (Publication)
- 2017-03-16
- Date (Revision)
- 2024-05-12
- Edition
- 1
Identifier
Publisher
Author
University of Adelaide - Gellie, Nicholas ()
Waite Road, Waite, South Australia, 5064, Australia
Waite
South Australia
5064
Australia
Co-author
University of Adelaide - Yan, Dongfeng ()
Waite Road, Waite, South Australia, 5064, Australia
Waite
South Australia
5064
Australia
Co-author
University of Adelaide - Mills, Jacob ()
Waite Road, Waite, South Australia, 5064, Australia
Waite
South Australia
5064
Australia
Co-author
University of Adelaide - Lowe, Andy (Professor)
Waite Road, Waite, South Australia, 5064, Australia
Waite
South Australia
5064
Australia
Co-author
Flinders University - Breed, Martin (Senior Lecturer in Biology)
Sturt Road, Bedford Park, South Australia, 5042, Australia
Bedford Park
South Australia
5042
Australia
- Website
- https://www.tern.org.au/
- Purpose
- This project was conducted during the author's PhD. The OTU data was generated for the manuscript titled "High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration" that uses eDNA assessment to provide a significant extension to current restoration monitoring practice.
- Credit
- We at TERN acknowledge the Traditional Owners and Custodians throughout Australia, New Zealand and all nations. We honour their profound connections to land, water, biodiversity and culture and pay our respects to their Elders past, present and emerging.
- Credit
- We thank A. Bissett, S. Kennedy, Z. Baruch, S. Caddy-Retalic, L. Clarke, S. Kennedy, I. Fox, M. Laws, K. McCallum, and J. McDonald for technical and field assistance. We are grateful for support from the BASE project, Australian Genome Research Facility, BioPlatforms Australia, and SA Water. This work was supported by Australian Research Council funding to AJL and MFB (DE150100542; DP150103414), and China Scholarship Council funding to DY (201408410176). We would also like to acknowledge the contribution of the BASE project partners DOI 10.4227/71/ 561c9bc670099, an initiative supported by Bioplatforms Australia with funds provided by the Australian Commonwealth Government through the National Collaborative Research Infrastructure Strategy.
- Status
- Completed
Point of contact
University of Adelaide - Gellie, Nicholas ()
Waite Road, Waite, South Australia, 5064, Australia
Waite Road
Waite
South Australia
5064
Australia
- Topic category
-
- Biota
Extent
- Description
- Our study system was an active restoration site at Mt Bold, a water catchment reserve of the Mt Lofty Ranges in South Australia (35.07;S, 138.42 E). This catchment was dominated by an open eucalypt woodland that has historically been subjected to tree clearance and grazing that began early in the 20th century. In this context, the native understory and most of the overstory was cleared and replaced by a grassland dominated by introduced grasses. At our study site, grazing ceased in 2003 when South Australia's water utility (SA Water) took over management. SA Water has actively restored the study site since 2005, with the restoration goal of recreating the local Eucalyptus leucoxylon dominated grassy woodland community.
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Temporal extent
- Time period
- 2014-12-17 2014-12-18
- Title
- High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration
- Website
-
High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration
Related documentation
- Maintenance and update frequency
- Not planned
- GCMD Science Keywords
- ANZSRC Fields of Research
- TERN Parameter Vocabulary
- QUDT Units of Measure
- GCMD Horizontal Resolution Ranges
- GCMD Temporal Resolution Ranges
- Keywords (Discipline)
-
- Biodiversity Inventory
- Ecological Succession
- Experimental Ecology
- Landscape Ecology
- Long-Term Community Monitoring
- Long-Term Species Monitoring
- Molecular Ecology
- Restoration Ecology
- Soil Ecology
Resource constraints
- Use limitation
- The Creative Commons Attribution 4.0 International (CC BY 4.0) license allows others to copy, distribute, display, and create derivative works provided that they credit the original source and any other nominated parties. Details are provided at https://creativecommons.org/licenses/by/4.0/
- File name
- 88x31.png
- File description
- CCBy Logo from creativecommons.org
- File type
- png
- Title
- Creative Commons Attribution 4.0 International Licence
- Alternate title
- CC-BY
- Edition
- 4.0
- Access constraints
- License
- Use constraints
- Other restrictions
- Other constraints
- TERN services are provided on an "as-is" and "as available" basis. Users use any TERN services at their discretion and risk. They will be solely responsible for any damage or loss whatsoever that results from such use including use of any data obtained through TERN and any analysis performed using the TERN infrastructure. <br />Web links to and from external, third party websites should not be construed as implying any relationships with and/or endorsement of the external site or its content by TERN. <br /><br />Please advise any work or publications that use this data via the online form at https://www.tern.org.au/research-publications/#reporting
- Other constraints
- Please cite this dataset as {Author} ({PublicationYear}). {Title}. {Version, as appropriate}. Terrestrial Ecosystem Research Network. Dataset. {Identifier}.
- Other constraints
- (C)2017 University of Adelaide. Rights owned by University of Adelaide.
Resource constraints
- Classification
- Unclassified
Distribution Information
Distribution Information
Distribution Information
Distributor
Distributor
Terrestrial Ecosystem Research Network
Building 1019, 80 Meiers Rd, Indooroopilly, QLD, Australia, 4068
Indooroopilly
QLD
4068
Australia
- Distribution format
-
- OnLine resource
- ro-crate-metadata.json
Resource lineage
- Statement
- eDNA metabarcoding: Three 25 m x 25 m quadrats were randomly selected per site, giving a total of 24 quadrats across the 8 sites. Soil was sampled from the 0-10 cm and 20-30 cm soil horizons at each quadrat. A representative 50 g sample of soil was collected at each of these 24 quadrats by pooling nine soil samples from each soil depth, including soil from open areas and under plants. These nine soil samples were pooled into a sterile plastic bag, and homogenized using a sterilized trowel. All soil samples (n = 48) were frozen on site in sterile 50 mL falcon tubes until DNA extraction hereafter referred to as technical replicates.
- Hierarchy level
- Dataset
Reference System Information
- Reference system identifier
- EPSG/EPSG:3577
- Reference system type
- Geodetic Geographic 2D
Metadata
- Metadata identifier
-
urn:uuid/c4484dda-18fd-4949-99ed-5e490ad0bbde
- Title
- TERN GeoNetwork UUID
- Language
- English
- Character encoding
- UTF8
Point of contact
- Title
- Revegetation rewilds the soil bacterial microbiome of an old field- Part 1: OTU raw data matrix
Identifier
- Codespace
- https://geonetwork.tern.org.au/geonetwork/srv/eng/catalog.search#/metadata/
- Description
- Parent Metadata Record
Type of resource
- Resource scope
- Dataset
- Metadata linkage
-
https://geonetwork.tern.org.au/geonetwork/srv/eng/catalog.search#/metadata/c4484dda-18fd-4949-99ed-5e490ad0bbde
Point-of-truth metadata URL
- Date info (Creation)
- 2022-10-25T00:00:00
- Date info (Revision)
- 2024-05-12T00:00:00
Metadata standard
- Title
- ISO 19115-1:2014/AMD 1:2018 Geographic information - Metadata - Fundamentals
- Edition
- 1
Metadata standard
- Title
- ISO/TS 19115-3:2016
- Edition
- 1.0
Metadata standard
- Title
- ISO/TS 19157-2:2016
- Edition
- 1.0
- Title
- Terrestrial Ecosystem Research Network (TERN) Metadata Profile of ISO 19115-3:2016 and ISO 19157-2:2016
- Date (published)
- 2021
- Edition
- 1.0
Identifier
Overviews
Spatial extent
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Associated resources
Not available