• TERN Geospatial Catalogue
  •   Search
  •   Map

Fletcherview Tropical Rangelands Soil Environmental DNA (eDNA) Dataset

This dataset contains soil microbial and genomic analysis files of 9 soil samples from each of three plots at Fletcherview, Northern Queensland (NQ) processed by the <a href=' https://agrf.org/ '>Australian Genome Research Facility Ltd (AGRF) </a>. The files are available as compressed FastQ formatted sequence files.<br>


For the nine Far North Queensland (FNQ) new plots (3 plots in Fletcherview and six plots at Wambiana), soil sampling additional to that done as component of plot installation by TERN have been undertaken. This is aligned with potential future exploratory work on soil eDNA proposed for WA. The protocol is a modified version of the <a href=" https://doi.org/10.1186/s13742-016-0126- 5">BASE sampling protocol</a>, combined with soil sampling as per <a href=" https://www.tern.org.au/wp-content/uploads/TERN-Rangelands-Survey-Protocols-Manual_web.pdf ">White et al. (2012)</a>. <br>


DNA extracted from the soil samples and Metagenomics 10Gbp (giga base pairs) bundle as per AGRF protocol.

Simple

Identification info

Date (Creation)
2022-07-26
Date (Publication)
2022-08-01
Date (Revision)
2025-12-10
Edition
1

Publisher

Terrestrial Ecosystem Research Network
Building 1019, 80 Meiers Rd
Indooroopilly
QLD
4068
Australia
+61 7 3365 9097

Author

James Cook University - Edwards, Will (Associate Professor)
1 James Cook Drive, Bebegu Yumba campus, 4811, Douglas, Australia
Bebegu Yumba campus
Douglas
4811
Australia
Website
https://www.tern.org.au/

Purpose
This is aligned with potential future exploratory work on soil eDNA. Resolve microbial diversity for the TERN Fletcherview site (3 plots), plus provide reference sequence collection to assess ability to detect ant species collected at same time and location. Used in biodiversity monitoring assessment. Ants identified by Alan Anderson (CDU) and sequenced. Also allow test of ability to detect vertebrates from eDNA using vertebrate sequences collected by Prof Lin Schwarzkopf (JCU).
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
This work was jointly funded by the Terrestrial Ecosystem Research Network (TERN), an Australian Government National Collaborative Research Infrastructure Strategy (NCRIS) project, and the Queensland Government Research Infrastructure Co-investment Fund (RICF).
Status
Completed

Point of contact

James Cook University - Edwards, Will (Associate Professor)
1 James Cook Drive, Bebegu Yumba campus, 4811, Douglas, Australia
1 James Cook Drive
Bebegu Yumba campus
Douglas
4811
Australia
Topic category
  • Environment
  • Biota

Extent

Description
Plots QDAEIV0008; QDAEIV0009, QDAEIV0010
N
S
E
W


N
S
E
W


N
S
E
W


Temporal extent

Time period
2021-10-19 2021-10-19
Maintenance and update frequency
Not planned
GCMD Science Keywords
  • SOILS
  • ANIMALS/INVERTEBRATES
ANZSRC Fields of Research
  • Soil sciences
  • Sequence analysis
TERN Platform Vocabulary
  • Fletcherview Tropical Rangeland, QDAEIU0008
  • Fletcherview Tropical Rangeland, QDAEIU0009
  • Fletcherview Tropical Rangeland, QDAEIU0010
TERN Instrument Vocabulary
  • Illumina NovaSeq 6000
TERN Parameter Vocabulary
  • sequencing reads
  • Unitless
  • gene family abundance
  • Reads per Kilobase
QUDT Units of Measure
  • Unitless
  • Reads per Kilobase
GCMD Horizontal Resolution Ranges
  • 1 meter - < 30 meters
GCMD Vertical Resolution Ranges
  • < 1 meter
GCMD Temporal Resolution Ranges
  • one off
Keywords (Discipline)
  • species presence
  • metabarcoding
  • soil biodiversity

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
Linkage
https://w3id.org/tern/static/cc-by/88x31.png

Title
Creative Commons Attribution 4.0 International Licence
Alternate title
CC-BY
Edition
4.0
Website
https://creativecommons.org/licenses/by/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}.

Resource constraints

Classification
Unclassified

Distribution Information

Distribution format

Distributor

Distributor

Terrestrial Ecosystem Research Network
80 Meiers Road, Indooroopilly, Queensland, 4068, Australia
Indooroopilly
Queensland
4068
Australia
OnLine resource
Soil eDNA Data Files

OnLine resource
File naming

OnLine resource
ro-crate-metadata.json

Resource lineage

Statement
Thorough documentation of the collection procedures will ensure maintenance of sample value. This protocol is modification of BASE and designed to “nest” the soils samples within the space defined by the pitfall traps. <br><br> Sample Collection and Processing <br> <ol> <li>Select a 20 x20m plot at the sample site in a reasonably homogenous environment that reflects the characteristics of the site (based on soil, vegetation and land use). We used Sth Wst corner of plots starting at the star picket for the pitfalls, and embedded the 20m x 20m soil at its centre. It could really be anywhere within the 100m x 100m plot, as long as the design above is maintained.</li> <li>Collect soil (9 samples) regularly on a grid (as done in QLD plots). The Surveillance protocol is slightly different and covers the entire plot area. (Having a set of samples in this grid design plus the 9 from surveillance will allow test of whether the results from these approached differ. Having a grid is easier to recommend for non-specialists since it requires no decision making about unique habitats and so would be less reliant on individual choice and be easier protocol to engage land managers/land owners etc)</li> <li>Collect the samples in top 5cm. For Qld plots samples are kept individual to allow spatial reference of results from unique soil samples and results from unique pitfalls (ant IDs and abundances are resolved at a per trap level &ndash; see results from Anderson) as well as plant canopies via the Ozplots transects which may allow for possible test of detection distances for eDNA.</li> <li>Prior to collection, scrape all surface material (biological material) from the surface.</li> <li>Soil can be dug with standard trowel or similar and should be well-mixed. Dig a hole approx. 5cm diameter and use trowel to homogenise dislodged soil prior to transfer into samples.</li> <li>Remove any obvious twigs or leaf material prior to sampling</li> <li>Sieve if needed .</li> <li>Collect 2 samples &ndash; one as per Surveillance protocol (individual samples stored in material bags, placed within zip-lock bags containing silica gel and all samples from one site placed into single larger material bag and labelled. One large bag per site. All samples are returned to the lab and oven dried (we did 48 hrs at 60OC). - the second, collected into 50ml sterile tubes &nbsp;(in field these are placed in cooler bags (standard Coles etc shopping type), preferably with ice-pack if possible. Further, in FNQ these samples were stored in car fridge as cold as possible in field and returned and placed into fridge freezer that day. Stored in Freezer (-80oC) on return to lab. (this could provide test of difference in outcome from diff sampling techniques)</li> <li>Ensure collection of adequate soil for nucleic acid extraction (approx. 50 gms)</li> <li>Wash/rinse all sampling material with bleach between samples. &nbsp;</li> <li>Contextual data generation from each sampling site is generated as part of</li> <li>Surveillance soil sampling and is not required to be collected.</li> <li>Assign unique sample identifiers to each sample using as above. For FNQ, example sample coding was: F.F.1.1.1 (first letter denoting sampling regime (F = &ldquo;frozen, D = &ldquo;dry&rdquo;), second (F = site identifier (i.e. &ldquo;Fletcherview&rdquo;), then numeral (site = 1, 2, 3, etc), numeral (row = 1, 2, 3) and sample on row (1, 2, 3) as per figure above).</li> </ol> <br><br> Preparation for eDNA extraction and sequencing <br> Samples sent to AGRF under ice. to AGRF Ltd., Plant Genomics Centre, Waite Campus, Hartley Grove, Urrbrae SA 5064. <br>DNA extraction from 27 soil samples and Metagenomics 10Gbp bundle as per AGRF protocol. The Illumina DNA Preparation (M) method (formally known as Nextera Flex library preparation) was used for sequencing; for more information, see <a href ="https://static1.squarespace.com/static/5c6a2bfa11f7845bc7a99405/t/6260b8637ad4156742ea94db/1650505842062/SVG2202WGM_Service+Guide_Whole-Genome+Metagenomics.pdf">AGRF Service Guide Whole Genome Metagenomics</a>.
Hierarchy level
Dataset
Title
AGRF Service Guide Whole Genome Metagenomics
Website
https://www.agrf.org.au/service-guides

Method documentation

Reference System Information

Reference system identifier
EPSG/EPSG:4326

Reference system type
Geodetic Geographic 2D

Metadata

Metadata identifier
urn:uuid/ee08bdaf-28b7-4b15-9f74-6fc1acd6b039

Title
TERN GeoNetwork UUID

Language
English
Character encoding
UTF8

Point of contact

Terrestrial Ecosystem Research Network
Building 1019, 80 Meiers Rd
Indooroopilly
QLD
4068
Australia
+61 7 3365 9097

Type of resource

Resource scope
Dataset
Metadata linkage
https://geonetwork.tern.org.au/geonetwork/srv/eng/catalog.search#/metadata/ee08bdaf-28b7-4b15-9f74-6fc1acd6b039

Point-of-truth metadata URL

Date info (Creation)
2022-07-26T00:00:00.000000+00:00
Date info (Revision)
2025-12-10T10:09:42.473259+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

Code
10.5281/zenodo.5652221
Website
https://github.com/ternaustralia/TERN-ISO19115/releases/tag/v1.0

 
 

Overviews

Spatial extent

N
S
E
W


N
S
E
W


N
S
E
W


Keywords

ANZSRC Fields of Research
Sequence analysis Soil sciences
GCMD Science Keywords
ANIMALS/INVERTEBRATES SOILS

Provided by

Share on social sites

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

Associated resources

Not available


  •   About
  •   Github
  •