This training session will cover several topics: vegetation vouchering, collecting vegetation samples for genetics and isotope analysis, soil metagenomics sampling, and developing fauna survey protocols. For vegetation vouchering, samples should be large enough and include flowers, fruits, bark, roots or leaves as appropriate. Samples are labeled with a barcode and field name and pressed. Additional samples are taken for genetics and isotope analysis. Soil samples involve scraping surface soil and placing in a labeled silica bag. Developing fauna survey protocols will refine purposes and methods, target taxa, involve experts, and produce a manual. A potential new method for estimating basal area from photopoints was also discussed.

1. Training Session 4
Topics to cover:
Vegetation vouchering
Vouchering for genetics
Vegetation isotope analysis
Soil metagenomics
Fauna protocols
Photopoints

2. MethodVegetation Vouchering

3. 1.Collect sample
–ensure large enough sample (to cover an A3 sheet of paper)
–flowering/fruiting, bark where possible –root for grasses + leaves (use an envelope for easily lost bits)

4. 1.Attach barcode (well) to non-diagnostic part of the sample
2.Scan barcode in Vouchering module
3.Provide a field name
•either a good guess at taxonomic name OR
•a descriptive name that is only current for that site
4.Place in plastic bag
Use a small amount of this material for genetic sample ( as discussed in the genetic section)

5. Press
Change Papers
Deliver to herbarium

7. Method: Vegetation DNA Samples& Leaf Isotope Analysis

8. Why?
DNA
•evolutionary relationships
•phylogenetic diversity and endemism
•evolutionary adaption
•refugia
•colonisation/contraction dynamics
Isotope
•the reason that the teabag needs to be synthetic
•accurate info on carbon and nitrogen content of the leaves
•can inform on plant stress, adaption to climate change, assist with modelling etc.

9. Sampling from voucher specimens
1. Take around 10cm2from each voucher specimen
2. Place into a synthetic tea bag and seal
3. Label with adhesive voucher label and scan with app
4. Place bag in box with ⅓ cup silica granules (self indicating and non-indicating granules)
5. Seal box and ensure it is labelled with plot identifier. Preferably 1 box per plot.
Change silica every few days until indicator no longer changes colour.
6. Samples can then be used for isotope and DNA analyses

10. Sampling from dominant perennial species
For each dominant perennial species in the plot (i.e. FPC >2% or opaque canopy cover >5%) Additional leaf samples should be taken from four individuals across the plot
1. Take around 5cm2from each of four individuals
2. Place into a synthetic tea bag and seal
4. Place in sealed box as before
5. These samples will be used for DNA analyses only.
3. Label with adhesive voucher label and scan with app (to link to voucher specimen and plot)

12. MethodSoil Metagenomics

13. 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.

14. 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.

15. MethodFauna SurveySally O’Neill

16. •Improve our understanding of fauna:
–distributions
–abundance
–richness
•Provide a baseline against which future change can be assessed
•Build understanding of the relationship between habitat dynamics and faunal species population dynamics
•Lead to efficiencies in biodiversity monitoring
Fauna Protocol Broad Aims

17. Rationale for Fauna Protocol
•No existing standardisednational fauna monitoring method
•High level of interest in establishing ‘biodiversity monitoring’ in rangelands
•Complement the existing AusPlotsRangelands Survey Protocols Manual

18. … lots of details TBA!
?
?

19. Considerations
•Refine details of the purpose
•Who will be doing the surveys?
•Trapping –types, duration, effort, timing
•Logistics
•Targeted species/guilds/keystones?
•Vouchering?
•Genetic samples?
•Observation methods
•Bats?

20. •Collation and review of methods currently (and previously undertaken)
•Review of agency requirements (legislative)
•Consult with experts -state agencies, researchers and universities, museums, NRM groups and (reserve) landholders
•Draft the method selection
•Field trials
•Development of the survey protocols manual
•Release on the website
•…. then what?
Development Process

21. 1
Ben Sparrow TERN Ausplots
Basal Area from Photopoints…..
Isitpossible?

22. Ways it is currently obtained
22
Basal Wedge
DBH Measurement
Terrestrial LiDAR

23. An Alternative: A New Photopoint methodPhoto Layout
23
•24mm Focal Length
•Aperture = F11
•ISO 100
•Raw Format (+/-JPG)
•1.3m to centre of lens
•Calibration target used
•2.5m Baseline
•DGPS Location recorded

24. A New Photopoint methodThe Tripod
24
Tripod and Star Picket setup
If terrain not flat then attempt to copy the average slope.

25. A New Photopoint methodRaw outputs
25
ETC.

26. The Scene Reconstruction Process
26
IdentifesLike features in images pairs
Uses this to calculate camera location
Using Camera location information projects information into 3d space

27. DBH Calculations
Trunks then identified Spectrally, but including 3D information
A Cylinder is fitted to each trunk
The Cylinder is cut at 1.3m (DBH) and the area of the cross section is calculated (DBH for the individual tree)
These DBH’s are then summed for the whole site.
Currently hasa max depth of view, but improvements being worked on.

28. Trunk Identification and Basal area calculation
28

29. Other outputs: pointclouds
29

30. Other Outputs: Panoramas
30

31. Benefits
31

32. Benefits
32
Method
Cost Equipment
Cost Staff
Time
Accuracy
Direct Harvesting
*
***
***
***
Basal Wedge
*
*
*
*
DBH measures
*
***
***
***
LIDAR
***
***
***
***
Photopoints
**
*
*
**

33. Future work
33
Take account of Occlusion
Trial and accuracy assess in a variety of ecosystems
Determine method variation needed for different environments
Automate processing (Work Commenced)
–Submission for the public using a web interface
Manage Huge Datasets
Process our archive of 300+ Sites

34. Link To Video