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 Australian Genome Research Facility Ltd (AGRF) . The files are available as compressed FastQ formatted sequence files.
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 BASE sampling protocol, combined with soil sampling as per White et al. (2012).
DNA extracted from the soil samples and Metagenomics 10Gbp (giga base pairs) bundle as per AGRF protocol.
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 BASE sampling protocol, combined with soil sampling as per White et al. (2012).
DNA extracted from the soil samples and Metagenomics 10Gbp (giga base pairs) bundle as per AGRF protocol.
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.
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).
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).
Lineage
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.
Sample Collection and Processing
Preparation for eDNA extraction and sequencing
Samples sent to AGRF under ice. to AGRF Ltd., Plant Genomics Centre, Waite Campus, Hartley Grove, Urrbrae SA 5064.
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 AGRF Service Guide Whole Genome Metagenomics.
Sample Collection and Processing
- 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.
- 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)
- 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 – see results from Anderson) as well as plant canopies via the Ozplots transects which may allow for possible test of detection distances for eDNA.
- Prior to collection, scrape all surface material (biological material) from the surface.
- 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.
- Remove any obvious twigs or leaf material prior to sampling
- Sieve if needed .
- Collect 2 samples – 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 (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)
- Ensure collection of adequate soil for nucleic acid extraction (approx. 50 gms)
- Wash/rinse all sampling material with bleach between samples.
- Contextual data generation from each sampling site is generated as part of
- Surveillance soil sampling and is not required to be collected.
- 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 = “frozen, D = “dry”), second (F = site identifier (i.e. “Fletcherview”), then numeral (site = 1, 2, 3, etc), numeral (row = 1, 2, 3) and sample on row (1, 2, 3) as per figure above).
Preparation for eDNA extraction and sequencing
Samples sent to AGRF under ice. to AGRF Ltd., Plant Genomics Centre, Waite Campus, Hartley Grove, Urrbrae SA 5064.
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 AGRF Service Guide Whole Genome Metagenomics.
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