meth_1.24 Soil Sampling from Cotton Production Systems

Contributor(s):

Gupta Vadakattu – CSIRO Gupta.vadakattu@csiro.au 08 8303 8579

Oliver Knox – UNE oknox@une.edu.au 02 6773 2946

Citation:  

AM Project ID: AM0003

Modified from the BASE protocols (meth_1.1, Bissett et al., 2016), this abbreviated method concerns itself only with the sampling of soil from cotton production systems.

Data generated from this work allows comparison of cotton fields from different regions with native vegetation soils as reported in the Cottongrower article ‘How does a cotton production system change the soil biology?’ Oct-Nov 2016.

Method:

These sample collection SOPs describe the steps involved in:

  • sampling microbial communities
  • obtaining relevant metadata
  • processing sample for subsequent contextual metadata and sequence analysis

 

Sampling equipment:

  • Soil core (augar) – capable of recovering soil to 30 cm deep.
  • Two large ziplock bags per field to collect and mix samples and send soil to CSIRO
  • GPS enabled camera/phone to capture pictures of site and location details.
  • Record sheet for rotation and location details

 

Sampling:

  1. The project is seeking to undertake and analyse soil from five cotton valleys (Namoi, St George, Darling Downs, Murrumbidgee and Central Queensland) with five fields sampled in each area and four to five native vegetation/riparian site.
  2. Select a 25 x25 m 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 are looking for fields under cotton production and ideally back to back, although realise there may be limitations to this. Please record the fields past three seasons cropping history.
  3. Collect soil (comprising ~10 samples [see 4]) in the plant line, but not directly against the plant, from the plot in a manner that adequately samples the whole plot using either a regularly grid or a stratified approach if you think there may be differences in the field.
  4. Collect the samples as two depths (1) top 10 cm; (2) 20 cm to 30 cm. Place the samples from each depth in a large ziplock plastic bag or bucket, homogenise all within plot sub-samples to make a pooled sample for each of the two depths.
  5. Ensure collection of adequate soil for nucleic acid extraction and contextual data generation from each sampling unit (e.g. minimum 600 g from each depth).
  6. Use the Bags provided with a unique four number sample identifier. These identify the last four digits in the sample identity, of which depth has a separate
  7. Collect and record all other local contextual data listed in the ‘Australian Microbiome contextual data template spreadsheet’. Copy provided.
  8. Take photos of plot – soil and surrounding environment (example below). Please capture the GPS location of the site. This can be done using your phone’s locations settings.                                                                       
  9. Ensure the quarantine forms (supplied) are completed and located on the outside of the postal bags. Without this the samples run the risk of never reaching Adelaide, wasting your input.
  10. Send the soil sample for DNA and chemical analysis using the provided bags and transported in Esky (cooler box) with frozen refrigerant bricks to:

    Dr Gupta Vadakattu, CSIRO Agriculture & Food, Locked bag 2, Glen Osmond, SA 5064, Australia

Sample processing at CSIRO labs:

Assign unique sample identifiers to each sample using the last digits after the “/” of the data handles provided by Bioplatforms Australia, i.e. 102.100.100/8202 would be called 8202. Each depth is to have a separate identifier.

Individual soil samples for each location were mixed, sieved and subsampled for OMICS and contextual data analysis.

For DNA extraction: ~40-50 g of field soil was transferred to a 50 mL Falcon tube and frozen as soon as possible (see DNA analysis section) and delivered frozen to AGRF labs.

Sub samples for the contextual data analyses i.e., chemical and physical properties, were air dried and stored in cold room (4 oC) until analysis.