Training Session 4

Topics to cover:

Vegetation voucheringVouchering for geneticsVegetation isotope analysisSoil metagenomicsFauna protocolsPhotopoints

MethodVegetation Vouchering

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)

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)

PressChange PapersDeliver to herbarium

Method:Vegetation DNA Samples& Leaf Isotope Analysis

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.

Sampling from voucher specimens

1. Take around 10 cm2 from 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

Sampling from dominant perennial speciesFor 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 5 cm2 from 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)

MethodSoil Metagenomics

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.

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 bagReplace 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.

MethodFauna Survey

Sally O’Neill

• 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

Rationale for Fauna Protocol

• No existing standardisednational fauna monitoring method

• High level of interest in establishing ‘biodiversity monitoring’ in rangelands

• Complement the existing AusPlots Rangelands Survey Protocols Manual

… lots of details TBA!

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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?

• 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

1

Ben Sparrow TERN Ausplots

Basal Area from Photopoints…..Is it possible?

Ways it is currently obtained

22

Basal Wedge

DBH Measurement

Terrestrial LiDAR

An Alternative: A New Photopoint methodPhoto Layout

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•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

A New Photopoint methodThe Tripod

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Tripod and

Star Picket

setup

If terrain not flat

then attempt to

copy the average

slope.

A New Photopoint methodRaw outputs

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ETC.

The Scene Reconstruction Process

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Identifes Like features in images pairs

Uses this to calculate camera location

Using Camera location information projects information into

3d space

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.

Trunk Identification and Basal area calculation

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Other outputs: pointclouds

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Other Outputs: Panoramas

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Benefits

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Benefits

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Method Cost Equipment Cost Staff Time Accuracy

Direct Harvesting * *** *** ***

Basal Wedge * * * *

DBH measures * *** *** ***

LIDAR *** *** *** ***

Photopoints ** * * **

Future work

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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

Link To Video