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.
3. 1.Collect sample
โensure large enough sample (to cover an A3 sheet of paper)
โflowering/fruiting, bark where possible โroot 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
โขeither a good guess at taxonomic name OR
โขa 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)
8. Why?
DNA
โขevolutionary relationships
โขphylogenetic diversity and endemism
โขevolutionary adaption
โขrefugia
โขcolonisation/contraction dynamics
Isotope
โขthe reason that the teabag needs to be synthetic
โขaccurate info on carbon and nitrogen content of the leaves
โขcan 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 โ 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)
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 โmax 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.
16. โขImprove our understanding of fauna:
โdistributions
โabundance
โrichness
โขProvide a baseline against which future change can be assessed
โขBuild understanding of the relationship between habitat dynamics and faunal species population dynamics
โขLead to efficiencies in biodiversity monitoring
Fauna Protocol Broad Aims
17. Rationale for Fauna Protocol
โขNo existing standardisednational fauna monitoring method
โขHigh level of interest in establishing โbiodiversity monitoringโ in rangelands
โขComplement the existing AusPlotsRangelands Survey Protocols Manual
19. Considerations
โขRefine details of the purpose
โขWho will be doing the surveys?
โขTrapping โtypes, duration, effort, timing
โขLogistics
โขTargeted species/guilds/keystones?
โขVouchering?
โขGenetic samples?
โขObservation methods
โขBats?
20. โขCollation and review of methods currently (and previously undertaken)
โขReview of agency requirements (legislative)
โขConsult with experts -state agencies, researchers and universities, museums, NRM groups and (reserve) landholders
โขDraft the method selection
โขField trials
โขDevelopment of the survey protocols manual
โขRelease on the website
โขโฆ. then what?
Development Process
21. 1
Ben Sparrow TERN Ausplots
Basal Area from Photopointsโฆ..
Isitpossible?
22. Ways it is currently obtained
22
Basal Wedge
DBH Measurement
Terrestrial LiDAR
23. An Alternative: A New Photopoint methodPhoto Layout
23
โข24mm Focal Length
โขAperture = F11
โขISO 100
โขRaw Format (+/-JPG)
โข1.3m to centre of lens
โขCalibration target used
โข2.5m Baseline
โขDGPS 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.
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 DBHโs are then summed for the whole site.
Currently hasa max depth of view, but improvements being worked on.
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)
โSubmission for the public using a web interface
Manage Huge Datasets
Process our archive of 300+ Sites
