TERN Surveillance Training, Calperum 2019, Day 1 lectures, final session

1. Training Session 4 – Almost There!
Soil - Metagenomics
Soils – Plot Description
Soils – Characterisation to 1m+
Soils – 9 x 30 cm samples
Soils – Bulk density
Soils – Sample collection
Leaf Area Index Meter (LAI)
The App
Fauna Protocols
What’s in store for the week
Summary of the Day

2. Method
Soils: Plot Description

3. Plot
Description
• Plot name
• Plot location – SW corner marker
• Erosion
• Micro relief
• Drainage
• Disturbance
• Surface condition
• Other optional measures if a soil
scientist available – covered in the
field section

4. ¢
¢
¢
¢
¢
¢ ¢
¢ ¢
¢ Soil core to 30cm
1 m core/pit
outside, but adjacent to quadrat
5 samples in
the primary soil
individual (25 x
25m quadrat in
SW corner)
4 other samples
throughout the
bigger quadrat

5. Method
Soils:
Characterization to
1 m

6. Two Options
• Pit or auger
• Advantages and disadvantages to both
• Pit can see profile
• Auger easier – If no experienced soil scientist there is
little benefit from a pit
• Pit can see layers

7. Either way you will lay out
your soil samples for
characterisation
Record – why stopped
Type of observation
Take a photo of the pit if dug
Record depths
Identify horizons
Samples discussed later

8. Photo Colour chart Horizon identification Soil texturing

9. • Optional collections available if a
soil scientist present – Detailed
in the manual
• At least 500 g collected in a
plastic bag for each 10 cm
increment through the profile
(eg. 0-10, 10-20, 20-30, 30-40
etc.
• If experienced can identify
horizons and collect within these
• Sample increased if significant
amount of coarse fragments

10. Method
Soils: Observations
(9 x 30cm samples)

11. Method
Soil Metagenomics

12. Scrape loose material from soil surface
Use a trowel or small shovel to take a sample from the soil
surface
Ensuring that the trowel is not contaminated with soil
from another site.
Do include surface crust occurring at the
site – max depth 3cm.
Place the sample in a calico bag and label with a barcode
Scan the barcode using the app.

13. Tie the calico bag and place in a
labelled plastic bag that contains 1/3
of a cup of silica that contains some
indicator silica
Seal the bag
Replace the silica until the indicator
no longer changes colour
Place the 9 plastic bags from the
one site into a large calico bag
and label for that site.

14. • 9 samples collected throughout the quadrat
• 5 in the primary soil individual
• 4 throughout the rest of the quadrat
• In both cases aim to sample from the variety of
cover / terrain options available.
• Samples collected, bagged and labelled
• At least 500 g from 0-10, 10-20 and 20-30cm
unless stopped
• GPS each location
• 3 samples x 9 locations per site should be placed in
a larger bag and labelled for that site

15. Dig shallow pits
for the 9
samples
Take samples at
10 cm
increments
Store samples in
bags

16. Method
Soils: Bulk Density Measures

17. • Bulk density essential to convert any soil
measures to volume
• Precision required for accuracy
• Start by clearing veg from a small area
• Done at 3 depths

18. 1. Remove the plastic caps
from a stainless steel ring
2. Place the tanner sampler on
flat ground – Push the feet
in gently until the whole
bottom surface is flush with
the ground
3. Load the stainless steel ring
4. Place the top of the sampler
in the top of the tube to rest
on the stainless steel ring
5. Hit this with a rubber mallet
until it is flush with the top
of the device
6. Remove all of the device
leaving the ring in the
ground.

19. Either...
• trim around the ring
enough to place a
cap on it
Insert a trowel well
below the cylinder and
remove it with excess
soil - none of the soil in
the cylinder can be
disturbed

20. Or....
• Dig around the
cylinder carefully
• Place the trowel a
little under the
cylinder and prise
it out of the soil
with excess
• The soil in the ring
cannot be
disturbed

21. Carefully trim excess soil from the edge of the
cylinder – this surface must be flush – this can take
some time to do well
Once one surface is complete, cap that
end, turn the cylinder over and repeat for
the other side
Tape the two caps and the ring together
well
Clearly label and transport
to a drying oven

22. Method
Soils: Sample Collection

23. At the end of
the site you
should have....
• 1 large calico bag containing 9
snaplock bags containing 9 calico bags
with silica for metagenomic samples
• 1 large plastic bag with 9 medium
calico bags each containing x 3 x 500 g
snaplock bags with soil samples (from
9 distributed sites)
• 1 large plastic bag with 10 x 500 g
snaplock bag soil samples from the pit
or core
• 1 medium calico bad with 3 x bulk
density rings in it
• ALL CLEARLY LABELLED!

24. Method
Using the LAI

25. LAI Measurements
• AusCover desire to validate LAI and FPC products
• FPC validated by point intercept
• LAI can be validated by Hemispherical Photography
or LAI2200
• Hemispherical Photography
- Potentially more accurate
- Harder to set up in the field
- Lowest height about 40-50 cm above ground level
- Harder to process in the office – more work
- Harder to get high number of samples
- Larger volume of data

26. LAI 2200
– Operates closer to the ground – more appropriate for
Rangelands
– Easy to take a high number of samples
– Instant processing – no work later
– Easy to use for non experts to use in the field
– Much quicker to use
LAI 2200 seen as best outcome considering the needs
of both AusCover (data) and AusPlots (speed and
ease of use)

27. LAI 2200
• Need to avoid direct sunlight
– diffuse light
– constant cloud
– dawn or dusk
• Need above/clear sky reference fairly regularly (issue
in really high canopy areas)
• Recent field trip collected data to inform of optimal
sampling strategy
• Not operationally useful for chenopods
– (re: number of samples)

28. The device will come pre-set up – There will be
no need to connect the “wand” to the console.
You will only need to use the “wand”.
Remove it from the Pelican case. The manual
will be in the case but we ask that you follow
the AusPlots manual in the first instance, and
then attempt calling AusPlots staff before you
use the manual or change any settings. The
device is significantly more complex than our
application.
We have simplified its
operation to make it easier
to use in the field.

29. The Sensor head and fitting
the lens cover

30. Taking an “above” Reference
– Note the overcast sky
The wand set up for logging points and an above reference
Before

31. During After

33. Field data collection:
tooling
• Core function:
support data collection
according to the protocol
• Minimise data double-
handling
• Maximise integrity of data
(e.g. transcription errors)
• Use ‘off-the-shelf’ where
appropriate (rapid
development)
• Be able to function without
a network (remote
locations)
• Offer efficiency gains vs.
traditional data collection
methods

34. System Architecture

35. AuScribe:
Field Data Collection App

36. Plot Creation

37. Site Description

38. DGPS Point collection

39. Site Description

40. Point Intercept

41. Basal Wedge

42. Structural Summary

43. Plot Upload

44. Data Curation (SWARM)

45. Benefits:
• Integrity of data
• Speed of data availability
Challenges:
• Getting the UI right; resistance when it is slower than “recording audio”
(with subsequent data entry later on).
• More automation (Soils and DGPS integration).
• Multi-tablet system.
Reflecting…

46. Any Questions?
andrew.tokmakoff@adelaide.edu.au
Andrew Tokmakoff

47. How to get Further Info
http://www.tern.org.au/AusPlots-pg26979.html
Product /
Service
Description For more information
Accepted
method
The AusPlots Rangelands Survey Protocols Manual provides a simple agreed method for anyone
undertaking research or monitoring in the rangelands. Developed in collaboration with all of the
rangelands' jurisdiction the method is the first nationally agreed and consistent method for
rangelands monitoring. It is freely available, and is supported by a field app that streamlines data
entry and download processes. In 2014 AusPlots will release further protocols so keep an eye on
this website for updates.
The AusPlots Forests Survey Protocols Manual outlines the field methodology for AusPlots Forests.
The background and rationale of the project and details of bioregional stratification and site
selection will be outlined in a separate document. This version of the manual (v1.0) details the
methodology for (a) the installation of plot infrastructure, (b) the description of the site and (c) the
core measurements that form the minimum dataset for AusPlots Forests plots. This draft edition is
provided as an online resource and material from the document or its attachments should not be
republished without written consent. If you have any feedback on this draft version please contact
Dr Sam Wood.
Click here to view or download
the AusPlots Rangelands
Survey Protocols Manual
Click here to view or download
the AusPlots Forests Survey
Protocols Manual
Data
AusPlots data is available via TERN's Soils to Satellites and AEKOS Data Portal. As at March 2014
data from approximately 130 sites is available, with more being added regularly as herbarium
identifications are received. The program has collect >430 plots to date.
AusPlots site locations can be
downloaded here (.kml file)
Soils to Satellites
AEKOS Data Portal
Contact Andrew Tokmakoff
Samples
Soil and plant samples collected by AusPlots are contributed to the CSIRO National Soil Archive and
regional herbaria, with some samples stored at the AusPlots facility. These samples are available for
further use by researchers. Traditional soil samples, soil metagenomic samples, vegetation voucher
samples and vegetation genetic and isotope samples may all be available for use.
For more information on
applying to access and use
these samples, please contact
Ian Fox

71. Practical
What is in store for the rest of the week?

72. Structure of
each Day
From 6:30 am Breakfast
7:30 – 7:45 am Day Plan
8:00 am Leave homestead
8:30 am Arrive at field sites
10:30 am Morning tea
11:00 am Field Training
12:30 am Lunch on Site
1:15 pm Field Training
3:00 pm Arvo tea
3:30 pm Field Training
5:00 pm Return to Homestead then free time
6:30pm Dinner
8:00 pm + Free time/ informal discussions on method

75. Today – 4 Theory
Sessions
• Session 1 Context +
Stratification + Manual
• Session 2 Stratification,
permissions and planning
• Session 3 All Vegetation
Components
• Session 4 Soils and Fauna

76. Summary