meth_1.1 Soil Sampling for Biomes of Australian Soil Environments BASE

Contributor(s): Biomes of Australian Soil Environments

Citation: Bissett, A., Fitzgerald, A., Meintjes, T., Mele, P.M., Reith, F., Dennis, P.G., Breed, M.F., Brown, B., Brown, M.V., Brugger, J., Byrne, M., Caddy-Retalic, S., Carmody, B., Coates, D.J., Correa, C., Ferrari, B.C., Gupta, V.V.S.R., Hamonts, K., Haslem, A., Hugenholtz, P., Karan, M., Koval, J., Lowe, A.J., Macdonald, S., McGrath, L., Martin, D., Morgan, M., North, K.I., Paungfoo-Lonhienne, C., Pendall, E., Phillips, L., Pirzl, R., Powell, J.R., Ragan, M.A., Schmidt, S., Seymour, N., Snape, I., Stephen, J.R., Stevens, M., Tinning, M., Williams, K., Yeoh, Y.K., Zammit, C.M., Young, A., 2016. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. GigaScience 5, 21. https://doi.org/10.1186/s13742-016-0126-5

AM Project ID: AM_BASE

Method:

  1. 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).
  2. Collect soil (comprising between 9-30 samples) from the plot in a manner that adequately samples the whole plot and ensures biological integrity of the sample. These can be sampled regularly on a grid if you think there is not much microgeographic variation, or the sample points could be stratified to take account of anything you think might be important.
  3. Collect the samples as two depths (1) top 10 cm; (2) 20 cm and below (define). Homogenise all within plot sub-samples to make a pooled sample for each of the two depths. Samples are best mixed in the field in a large ziplock plastic bags from which aliquots can easily be drawn. Sieve if needed.
  4. Ensure collection of adequate soil for nucleic acid extraction and contextual data generation from each sampling unit (e.g., 1 kg from each depth).
      • For DNA extraction: fill 50 mL Falcon tube with soil for DNA analysis (leaving 1-2 cm of space at top of tube) and freeze as soon as possible (see DNA analysis section).
      • Samples must be gently air dried for all remaining workflows:
        • For chemical analysis, sample 250 g dry weight of soil (see chemical analysis section),
        • For particle size, 180 g dry weight of soil (see particle size analysis section).

  5. Assign unique sample identifiers to each sample using the last digits after the “/” i.e. 102.100.100/8202 would be called 8202. Each depth is to have a separate identifier.

  6. Collect and record all other local contextual data listed in the Australian Microbiome contextual data template spreadsheet (admin/Sample_metadata_submission at main · AusMicrobiome/admin (github.com))
  7. Take photos of plot – soil and surrounding environment (example below).  
  8. Send each sample for DNA analysis, chemical analysis as described in sections 1.1.3 and 1.1.4 (contact the Project Manager (Sophie Mazard, smazard@bioplatforms.com) for initiative specific information).
  9. Submit contextual data in the excel sheet (admin/Sample_metadata_submission at main · AusMicrobiome/admin (github.com)) to the Project Manager (Sophie Mazard, smazard@bioplatforms.com).