meth_1.2 Soil Sampling for UTAS Urban Soil and Aerial Microbiome Study

Contributor(s): Penelope Jones (Penelope.Jones@utas.edu.au); Emily Flies (Emily.Flies@utas.edu.au)

Citation:

AM Project ID: AM0010 & AM0011

Modified from the BASE protocols (1.1, Bissett et al., 2016).

Soil sampling protocol 2019

  • Residential soil sampling

Materials

  • Clipboard with:
    • Information and consent form (x 2 per participant)
    • Housing questionnaire
    • Soil field data sheet
  • Pens
  • Gloves
  • Permanent marker for labelling
  • 2 x Large zip-lock plastic bags
  • Soil corer & mallet
  • Small trowel
  • Scrubbing brush for corer
  • Spray bottle of bleach
  • Measuring tape
  • Tent pegs
  • Digital camera
  • Small digital scale for weighing soil samples
  • Rubbish bag
  • Hand-held GPS
  • Photographic ID on lanyards
  • Plastic box for carrying samples and kit
  • Falcon tubes

  1. Before you visit Check all visits have been confirmed.
  2. Check you have the spreadsheet with names, addresses, contact details and visit dates with you and that you are wearing photographic ID.
  3. Pre-label the soil sample bag and dust swab transport tubes, writing directly onto the bags/tubes.
  4. Pre-fill the study-IDs & AMI codes on the questionnaires and soil data sheets.

 

When you visit

  1. Introduce yourselves and the purpose of your visit.
  2. Provide the participant with the information sheet and consent form and review it with them. They will already have been sent the information sheet via email before signing up, so acknowledge this but explain that you need to run through it once more and have them sign the consent form while you are there. Get them to sign two copies: leave one signed copy with them and take the other with you for filing. Key points to check re consent: OK to take photos, OK for soils data to be contributed to the Australian Microbiome Initiative*.
  3. Fill in the housing questionnaire with the participant. Ask if you can read the questions to them and record the response (preferable), but if they wish they can fill it in themselves.
  4. Take the soil sample:
    1. Put on a fresh pair of gloves.
    2. Scrub any chunks of dirt off the soil corer (inside/out) and then spray with bleach. Allow bleach to sit for 30 seconds – 1 minute, then take a “cleansing” soil core (to remove any bleach). Replace this core back into the yard and proceed to collecting actual soil samples.
    3. Use the measuring tape to set up a grid across the grassy areas only of the backyard. This can be a 3 x 3 OR a 5 x 2 grid depending on the space but make the grid as large as possible (up to 25 x 25 m square). Mark out the grid corners with the tent pegs and record the grid size on the soils metadata sheet.
    4. Use soil corer to take 12-15 sub-samples at 0-10 cm depth across the grid. Each time, turn the corer upside-down and dump the soil into the bag (keep your hands outside on the bag). Take the actual bits of grass off before putting it in the bag. Use the trowel (cleaned with bleach) to help if the ground is very hard. Stomp down the area around the hole to minimize the hole’s visibility. Homogenise as you go if you can.
    5. In addition to the grid, take some additional samples if there is ‘habitat variation’ (e.g., slope differences), that you need extra samples not on the grid to capture.
    6. Make sure you have at least 1 kg of soil.
    7. Homogenise all sub-samples into the same bag to make a pooled sample; with the bag zipped closed and with gloves on, squish the cores of soil so that they mix together. Be careful not to rip the bag. Double bag the soil bag if you are concerned it may rip.
    8. Record all other local contextual data listed on the soils metadata field sheet.
    9. Photograph the label of the bag. Then take photos of plot – soil and surrounding environment (only if the participant has consented to photography). Make sure that there is nothing identifiable in the photos: e.g., the house, a letterbox, the streetscape.
  5. Thank the participant. Let them know that we hope to have results early next year and will provide them with an individual report as soon as we can.

 

After you have completed the day’s sampling run:

  1. Return to the lab.
  2. Fill in the sample visit log sheet, noting whether all samples collected successfully.
  3. File ALL paperwork in the locked drawer.
  4. Label and fill a 50 mL Falcon tube with a sub-sample of the soil for DNA analysis (make sure it was adequately homogenised before you do this). Leave 1-2 cm space at top of tube.
  5. Place the falcon tubes of soil AND the dust swabs in the -80 °C The falcon tubes should go into Freezer X in freezer boxes. The swabs should go into the upright freezer, laying down in a freezer box which should be labelled on the side (they won’t fit with the lid).
  6. Leave the bags of soil to air dry on the benches with the bag top open.
  7. Fill in the sample storage log sheet.
  8. Check on the air-drying bags of soil. If needed, shake it around to make sure the bottom bits of soil are open to the air. Once the soil is dry (this might take a few days), close the bag.

 

*Important note – soil samples and the Australian Microbiome Initiative

Note that the consent form explains that if they agree, the soils data will be contributed to the Australian Microbiome Initiative. This is a national project that is trying to gather as many soil samples as possible from a diversity of Australian environments, to better understand the diversity of soil microbiomes across the continent. If the participant agrees to this, their data will provide part of this national database.

The potential concern for participants is that we have to provide the location of the soil sample (a GPS latitude and longitude), so theoretically someone could work out where the soil sample came from. We would also submit the photographs of the soils and vegetation (taking care that the photos are as non-identifiable). We would not attach any other personal information to the sample – e.g., address, their name or anything from the housing questionnaire. It would simply be the genetic sequences, the GPS location and the contextual data you take on the AMI spreadsheet.

If they are not comfortable with the location of the sample being public, we can still take the sample but we won’t submit it to the Australian Microbiome Initiative (we will process it ourselves).

 

  • Public green space (playground) soil sampling

Materials

  • As for the residential soil sampling
  • Printed and/or email copy of the council permissions

Methods

  1. Identify your “high and low use areas” to sample (ideally ~25 m x 25 m each):
    1. High use areas will be around benches/picnic tables or between pathway/gate and playground equipment
    2. Low use areas will generally be in the centre of the grassy area but not below/too close to trees/other vegetation that would alter the microbial composition
  2. Write a label on the 2 x ziplock bags in permanent marker (sample location, high intensity or low intensity, and date & the AMI code)

FOR THE HIGH INTENSITY AREA:

  1. Put on a fresh pair of gloves.
  2. Scrub any chunks of dirt off of the soil corer (inside/out) and then spray with bleach
  3. Take a “cleansing” soil core (to remove any bleach). Replace this core back into the ground and proceed to collecting actual soil samples.
  4. Use the soil corer provided to take ten sub-samples at 0-10 cm depth from the grassy areas only. Take the core sample, then turn the corer upside-down and dump the soil into the bag (keep your hands outside on the bag). Stomp down the area around the hole to minimize the visibility of the hole.
  5. Distribute the samples across the grassy area in a way that best captures the whole ‘plot’ (preferably sample on a grid if you think there isn’t much microgeographic variation, or the sample points could be stratified to take account of anything you think might be important). Make sure you have at least 1 kg of soil.
  6. Homogenise all ten sub-samples into the same bag to make a pooled sample; with the bag zipped closed and with gloves on, squish the cores of soil so that they can mix together. Be careful not to rip the bag. Double bag the soil bag if you are concerned it may rip.
  7. Collect and record all other local contextual data listed in the ‘soil field datasheet’
  8. Take photos of plot – soil and surrounding environment (make sure not to include people).

REPEAT FOR THE LOW INTENSITY LOCATION

  1. Take photos of high and low use locations

After you have completed the day’s sampling run:

  1. Return to the lab.
  2. Fill in the sample visit log sheet.
  3. Label and fill a 50 mL Falcon tube with a sub-sample of the soil for DNA analysis (make sure it was adequately homogenised before you do this). Leave 1-2 cm space at top of tube.
  4. Place the falcon tubes of soil in the -80 °C
  5. Leave the bags of soil to air dry on the benches with the bag top open.
  6. Fill in the sample storage log sheet.

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Field data-sheet – soil collection

 

UTAS Study ID:                                                                                              

 

AMI code:                                                                                       

Date sampled (YYYY-MM-DD)

Time sampled (hh:mm)

Latitude (decimal degrees)

Longitude (decimal degrees)

Sample site description*

Vegetation total cover %*

Vegetation dom grasses %*

Horizon (O and/or A)*

Elevation (m)

Temperature (deg C)

Grid size & sampling pattern* (draw below if necessary)

 

* See notes below

 

At the end of the day ALL soil metadata needs to be entered into the spreadsheet.

 

Notes for specific fields

 

Sample site

  • For backyards: Backyard + population density band (e.g., 0-500)
  • For playgrounds: Playground + pop density band

Soil Horizons

  • O: The organic or litter layer mainly over the soil surface composed of fresh and decaying plant residue. Typically composed of >25 % organic soil materials. This layer can usually be easily brushed away by hand.

  • A: This is the top layer of soil (often called top soil) that typically has the highest microbial activity. Composed of a mixture of mineral material and accumulated humified organic matter. Also, any plowed or disturbed surface layer

 

Vegetation total cover % and dom grasses %

  • In most cases should be 100 % for both

 

Grid size and sampling pattern

  • Not in AMI metadata but for our purposes
  • What size grid did you lay out? What pattern?
  • Did you sample regularly on the grid and/or vary by topography etc?