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Session 2 2019_final

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2019 TERN Surveillance Training course
Session 2

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Session 2 2019_final

  1. 1. AusPlots Training Session 2
  2. 2. Presentations before lunch Current Stratification Techniques – Ben (For Greg Guerin) Site Selection (Field) - Ben Permitting and Permissions - Sally Pre-Survey Planning - Emrys How to best engage volunteers - Sally Survey Equipment needed - Nikki OHWS Considerations – Sally and Nikki
  3. 3. TERN Ecosystem Surveillance Quantitative review of the AusPlots sampling scheme Greg Guerin, Kristen Williams, Samantha Munroe, Ben Sparrow
  4. 4. Review components • Stocktake – How has sampling performed to date? • Gaps analysis – Where are gaps in the environmental coverage? • Re-sampling strategy – Which sites should be monitored more frequently? • Power analysis – What is the change detection capacity of the network?
  5. 5. Iterative process • Assessment of gaps and representation will be updated as new sites are surveyed
  6. 6. Stocktake • Environmental coverage compared to alternative sampling strategies AusPlots Retrospective schemes
  7. 7. Stocktake • Environmental coverage compared to alternative sampling strategies – visual
  8. 8. Stocktake • Environmental coverage compared to alternative sampling strategies – multivariate dispersion
  9. 9. Gaps analysis • GDM based on AusPlots species composition
  10. 10. Gaps analysis • Optimise distance to most similar AusPlots
  11. 11. Gaps analysis • Optimise ‘Maximum Diversity’ across all sites
  12. 12. Survey Gap Analysis Tool – Glenn Manion, Simon Ferrier, Dan Faith, Kristen Williams Facilitates optimal selection of candidate survey sites to fill gaps in environmental space (eg GDM) Applies principle of biodiversity complementarity Iteratively selects locations with highest complementarity in environmental space, adds the XY coordinates to existing survey sites and repeats the process
  13. 13. A 999 group classified representation of the GDM model of vascular plants used in the analysis Williams, Kristen; Harwood, Tom; Manion, Glenn; Ferrier, Simon; Perry, Justin; Rosauer, Dan; Laffan, Shawn (2013): VAS_v5_r11: Generalised dissimilarity model of compositional turnover in vascular plant species for continental Australia at 9 second resolution using ANHAT data extracted April 2013. v1. CSIRO. Data Collection. https://doi.org/10.4225/08/557FB520465F7 ‘environmental diversity model’
  14. 14. 28,527 9sec ‘sample locations’ used in 1.5M site-pairs for vascular plant GDM (Source: ANHAT database, April 2013) Site pair sampling used 9sec aggregated sites with # species >10, stratified by IBRA bioregions, with random site-pair sampling weighted 10% more within than between bioregions to increase frequency of site-pairs that are closer in geographic and environmental space; locations in sparsely sampled regions tend to be sampled more often (and therefore have more weight in the model) Natural breaks 28,527 9-sec ‘sample locations’ used in 1.5M site-pairs for vascular plant GDM (Source: ANHAT database, April 2013) Lighter points = less often used in the GDM model response variable (bioregional stratified random sampling) Observation data
  15. 15. Demand point distribution (100,000) consistent with pattern of environmental diversity based on continuous GDM space (vascular plants) Geographic density correlates with environmental diversity Input to Complementarity model
  16. 16. AusPlots existing survey points used in the analysis 651 sites As at 14 August 2018 ‘Existing survey sites’ as baseline
  17. 17. Iteration 1 (run 2) Percent-clip legend style Selection is similar to iteration 1 from run 1 Iteration 1
  18. 18. 18 Iteration 2 (run 2) Percent-clip legend style Selection is similar to iteration 5 from run 1 Iteration 2
  19. 19. 19 Iteration 3 (run 2) Percent-clip legend style Selection is similar to iteration 3 from run 1 Iteration 3
  20. 20. 20 Iteration 4 (run 2) Percent-clip legend style Selection is similar to iteration 8 from run 1 Iteration 4
  21. 21. 21 Iteration 5 (run 2) Percent-clip legend style Selection is similar to iteration 9 from run 1 Iteration 5
  22. 22. 22 Iteration 6 (run 2) Percent-clip legend style Selection is similar to iteration 11 from run 1 Iteration 6
  23. 23. 23 Iteration 7 (run 2) Percent-clip legend style Selection is similar to iteration 12 from run 1 Iteration 7
  24. 24. 24 Iteration 8 (run 2) Percent-clip legend style Selection is similar to iteration 13 from run 1 Iteration 8
  25. 25. 25 Iteration 9 (run 2) Percent-clip legend style Iteration 9
  26. 26. 26 Iteration 10 (run 2) Percent-clip legend style Iteration 10
  27. 27. 27 Iteration 20 (run 2) Percent-clip legend style Iteration 20
  28. 28. 28 Iteration 30 (run 2) Percent-clip legend style Iteration 30
  29. 29. 29 Iteration 40
  30. 30. 30 Iteration 45
  31. 31. Rapid in filling to achieve continental balance of complementarity Finer scaling of complementarity
  32. 32. 32 Difference between Iteration 28 and 29 Similarity to selected site 28 Percent-clip legend style Run 2 Iteration 29 The difference between successive iterations (eg 28-29) shows ‘options’ for locating a new survey Example ‘difference grid’ to assist decision making
  33. 33. Re-sampling strategy • Climate change sensitivity – GDM predictions
  34. 34. Re-sampling strategy • Optimise species representation without species richness bias: 5-yearly
  35. 35. Power analysis • Power to detect variable woody cover trend across the network – 2 revisits • Power influenced by: – Trend size – Number of sites monitored – Non-linear sampling:power relationship
  36. 36. Power analysis • Power to detect regional woody cover trend (individual groups of sites) • Influenced by: – Trend size – ‘Noise’ – Number of replicates – Spatial variance
  37. 37. Method Locating the Plot Plot Layout Positioning
  38. 38. Locating the Site 1 2 3 4 & 5 6 7
  39. 39. Locating the Site – Community 1 1 2 3 4 & 5 6 7
  40. 40. Heterogeneous Not Community 1 Heterogeneous Locating Plots – Community 1
  41. 41. Locating the Site – Community 2 1 2 3 4 & 5 6 7
  42. 42. Locating Plots – Community 2
  43. 43. Locating the Site – Community 3 1 2 3 4 & 5 6 7
  44. 44. Locating Plots - Community 3
  45. 45. Locating the Site – Community 4 & 5 1 2 3 4 & 5 6 7
  46. 46. Locating Plots - Community 4 & 5
  47. 47. Locating the Site – Community 6 1 2 3 4 & 5 6 7
  48. 48. Locating Plots – Community 6
  49. 49. Locating the Site – Community 7 1 2 3 4 & 5 6 7
  50. 50. Locating Plots – Community 7
  51. 51. Exceptions
  52. 52. Where to put sites • Homogeneous or constantly mixed (Veg, Slope, relief, soil) • Aligned to grid • 100 x 100 (1 ha) • Avoid roads, cattle yards, fences, bores etc. • Consider access now and in the future
  53. 53. Organising a Survey Emrys
  54. 54. Funding and Expenses • Wages • Vehicles and fuel • Accommodation • Equipment costs – Stationary, printing, maps etc • Licence and access fees – Existing data, permits, etc • Food and living expenses • Petty cash – Unexpected repairs, consumables, other expenses • Consultant fees • Additional wages or survey-specific expenses
  55. 55. Biosecurity • Chytrid fungus, Phytopthora, Myrtle Rust • Crazy ants, Cryptosporidiosis, etc • Avoid or limit movement of specimens between sites • Follow local hygiene protocols - clean vehicles, boots, clothes and survey equipment • Contact local agencies to be aware of local risks
  56. 56. Cultural Considerations • Proclaimed Aboriginal Lands or areas owned by Indigenous communities require advanced planning and permission – sacred sites (gender and initiation considerations) – disturbance of significant landscape features – removal or disturbance of sacred plants and animals – entry permits – local communities may wish to be actively involved in survey activities (and may ask for payment) • Aboriginal Consultative Committees can advise best approach to take (and timeframes required)
  57. 57. Landholders and Local Community • Consult after funding and permits have been secured to plan specifics of survey • Explain aims and constraints, ask for views • Landholder may wish to be involved in survey • Publicise activities in local community, particularly with local rangers, Landcare groups, etc • Consider notifying Police
  58. 58. Reconnaissance Trips • Check survey sites prior to survey beginning • Area may have changed significantly since selection • Fire, flood, agriculture or other disturbance may render site unsuitable • Logistical challenges best identified in advance (access, etc)
  59. 59. Confirmation with Landholders • Once sites and survey dates have been confirmed, all landholders and managers should be contacted to confirm arrangements • Identify any areas to be avoided • Ensure access (keys etc) • Check which radio frequencies are used locally
  60. 60. Field Equipment and Vehicles • Ensure equipment and vehicles are suitable for conditions and provide adequate contingency Terrain: 4WDs, radios – Remote: Satellite phone, radios, extra fuel and water etc – Weather: wet weather gear, extra water, mosquito protection, warm clothes, etc
  61. 61. Survey Specific Items Make Sure you have Everything before you go!!!
  62. 62. Survey Participants Adequate expertise and support  Scientific expertise, drivers, hazardous goods handlers, etc  Ensure there is someone familiar with the method  Ensure roles are clearly identified  Medical information Volunteers  Should be reimbursed for out of pocket expenses  Make it clear what costs they will need to cover
  63. 63. Pre-Survey Meeting • Ensures everyone is on the same page • Survey team gives overview of methodology, location of survey site, accommodation, etc • Collection of keys, local contacts, facilities, etc • Local issues – Biosecurity – Cultural considerations • Handouts – Include the above – contact information for all participants – What to Bring
  64. 64. Transport • Appropriate vehicles • Vehicle checklists and backup gear – Well ahead of time and prior to departure • Driver training – Manual cars, 4WD, towing, heavy vehicles, etc – Winch and radio operation • Meeting points
  65. 65. Packing • Ensure enough space for personal gear – let participants know beforehand what they will need and how much they can bring • Pack as much as possible ahead of time • Pack safely – tie down loose items – Don’t overload vehicles and trailers
  66. 66. AusPlots Rangelands Survey Equipment Manual
  67. 67. Index 1. Setting out Hectare Plot 2. Vegetation collection 1. Collection 2. Barcoding, Pressing and Storage 3. Vegetation Point intercept 4. Soil sampling and collection 1. Pit 2. Soil Analysis 3. Bulk Density 4. Metagenomics 5. Subsites 6. Drying and storage 5. Panoramic Photo 6. Leaf Area Index 7. Basal Wedge 8. Miscellaneous 9. Equipment Checklist
  68. 68. 1. Setting out Hectare Plot 1. Mallet – To hammer tent pegs into the ground 2. Tent pegs – To mark each transect lines start and finish point (Measuring tape attachment point) attach bright flagging tape for easy visibility. 3. Clothes pegs – Attached above tent pegs, usually in a tree with bright flagging tape for easy visibility. 4. 100m fibreglass measuring tape – Used as vegetation transect lines. Tape measure double sided and fibreglass for easy visibility if tape flips, as well as durability 5. DGPS – Used to accurately mark out 1 hectare plot and transect lines (Approximately 0.50m accuracy) 5.1. DGPS attachment – For improved accuracy 1 2 3 4 5 5.1 6 6.1 6. Galvanised Star Pickets – 1800mm pickets mark out each corner and centre of plot 6.1. Star picket hammer – To secure pickets in place, as they are left at each site
  69. 69. 2.1 Vegetation Collection 1. Paper bags – To put plant samples in. 1 per bag for ease of keeping specimens separated, especially small samples. Ensure bags are good quality to avoid tearing. 2. Large heavy duty plastic bag – Carry around site to place paper bags with samples in. Heavy duty to avoid tearing in field. 3. Secateurs – To collect samples with ease (thick, spikey plants etc.) 4. Trowel/Shovel – To remove plants from the root without causing damage to the specimen 5. Shoulder Bag – Used to place tools, paper bags in to carry around plot 1 2 3 4 5
  70. 70. 2.2 Vegetation Barcoding, Pressing and Storage 1. Tablet – Used for site description, entering plant ID’s and allocating barcodes to specimens 2. Sistema Container – 2L or 3L airtight container used to place leaf tissue samples (in tea bags). Site code, date, location added to each container on lid and side of container 1. Teabag with leaf tissue sample and barcode for reference 2. Silica – Used to dry leaf tissue samples and preserve specimens (approx. 4 cups) 3. Barcodes – Placed on leaf tissue teabags and herbarium samples and scanned into tablet 4. Teabags – For leaf tissue samples, 1 per teabag 1 2 2.2 2.1 3 4 5 5. Plant press – 3 pieces of newspaper between cardboard for adequate drying. 1 sample with barcode per piece of newspaper. Write site code, date and location on top cardboard.
  71. 71. 3. Vegetation Point Intercept 1. Densitometer and pole – To Measure vegetation height and to intercept exact transect point (densitometer needs to be constructed please ask for instructions). 2. Laser pointer – Attached to pole with duct tape facing down, used to intercept point on transect line. 3. Voice Recorder on Lanyard – Used to record every transect, data to be entered into tablet. 1 1.1 2 1.2 3 *Pole with measurements to allow for easier/quicker height description. *Applying Green cellophane with a rubber band over the top of the densitometer (Image 1.1) to avoid glare looking directly at mirror. *Shoulder bag recommended to carry spare batteries for voice recorder and laser, as well as paper bags for collecting plants that may be missed by collections person.
  72. 72. 4.1 Soil Pit • Auger – To collect soil samples from solid pit (clay etc.) • Maddock – Break through hard surfaces (rock, clay or tree roots) • Shovel/spade – To dig pit and remove excess soil 1 2 3 4 5 6 7 1. 1m soil profile tape– To check depth of pit, horizons and for pit photograph 2. Soil handbook – Useful for soil texturing and characterisation 3. Munsell colour chart – Soil colour at each layer/horizon 4. Ziplock bags - To collect soil samples (0-10cm,10-20cm etc.), site code, date, pit, depth to be on each bag. 5. Soil data sheet and pen – To be filled out in field 6. Spray bottle with water – For texturing samples 7. 2mm sieve – For soil characterisation and texturing
  73. 73. 4.2 Soil Analysis 1. Demineralised water – Only use demineralised water to complete pH and conductivity analysis as it has a neutral pH level 2. Sieve – If completing analysis back in the lab, soil samples may need to be sieved for correct consistency. 3. Datasheet – Analysis added to datasheet 4. Ec-pctestr35 Probe - Used for pH and conductivity analysis 5. 250ml Beaker – Demineralised water and correct amount of soil sample added to perform analysis 6. Hydrochloric acid, plate & pipette – Used to test the effervescence of each soil sample by placing a small amount of soil on plate a using the pipette to drop the acid. 1 2 3 4 5 6
  74. 74. 4.3 Bulk Density 1. Mallet – To hammer in density ring (tanner kit). 2. Cloth tape – Used to seal the two lids and prevent lids falling off. Write site code, date, and depth on the tape. 3. Tanner kit – Used to assist with extracting bulk density samples. 4. Paint scraper – Used to slide under bulk density sample to remove it from the ground without losing any of the sample, also useful for removing excess soil from either end. 5. Stanley knife – Assist with levelling off the soil and removing any organic matter. 6. Bulk density ring and lids– Ring is set volume, once soil is collected, a lid is attached to either end. 7. Nail clippers – Can be used to cut out small roots or organic matter before placing the lids on the bulk density ring. 8. Geopick – Assists with extracting the ring from the ground by removing soil from around the ring. 1 2 3 4 5 6 7 8 6.1
  75. 75. 4.4 Metagenomics 1. Shovel/trowel – To dig and collect metagenomics sample. 2. Spray bottle with Ethanol – Used to sanitize shovel between each metagenomics site. 3. Tablet - Used to write description, location and take photo of site. 4. Numbered tag – Placed next to metagenomics site for photo reference (do this before taking sample). 5. Small Calico bags – Approx. 300mm x 450mm, Used to place metagenomics samples into, to then be placed inside large zip lock bag with silica. 6. Zip Lock bag and silica – Approx. 255mm x 375mm, used to put calico bag containing metagenomics in, with approximately ¾ cup of silica. Labelled with site code, date and metagenomics number. *Place all metagenomics in one large calico bag for easy transport. 1 2 3 4 6 5
  76. 76. 4.5 Subsites 1 4 2 3 5 1. Calico Bag – Approximately 300mm x 450mm, used to keep each of the soil subsites together (you should have 1 calico bag containing 3 soil samples per subsite). Each bag to be labelled with site code, date and subsite number. 2. Zip lock bags - Approximately 175mm x 312mm, used to collect soil samples from 0-10cm, 10-20cm and 20-30cm from each subsite. Each zip lock bag to be labelled with site code, date, subsite number and depth. 3. Spray bottle with ethanol – Used to sanitize shovel/spade between subsites. 4. Shovel/trowel – Used to dig subsites 5. Tablet – Used to enter GPS location, photo and description of each subsite. *The tablet will mainly be used when taking original Metagenomics data, but extra information may be entered in relation to digging the subsites.
  77. 77. 4.6 Lab drying and Storage 1 2 3 4 5 1. Foil Trays - Used to lay soils out in the lab for drying 2. Plastic Tubs – Used for long term storage of soil samples (labelled with site details and barcode 3. Drying Oven - Multiple drying uses including bulk density samples, presses, silica etc. 4. Milk Crates – Storage of tubbed up soil samples (2 crates per site) 5. Roseworthy Storage Facility - All of our soil samples are stored at Roseworthy ready for use.
  78. 78. 5. Panoramic Photo 1 2 3 4 5 6 7 1. Notebook – Used for site description, date, location and to mark the start of each of the 3 photo panoramas (pan #1, #2, #3). 2. Electrical Tape – To mark height on the centre star picket (1300mm high and 250mm below), where camera is aimed. 3. 2m Tape measure – To measure heights on star picket and distance from picket for tripod placement. 4. DSLR or similar – To take panoramic photo, must have capabilities needed for correct photo settings. 5. Tripod – To secure camera in place, must be able to reach a minimum height of 1300mm 6. Tent pegs with flagging tape – To mark the distance from star picket, where the tripod/camera is placed. 7. Permanent marker or pen – Used to fill out notebook, permanent marker is easier to see when photographing.
  79. 79. 6. Leaf Area Index 1 1.1 2 1. Leaf Area Index wand – Measures leaf area 1. Wedge for wand – This is the correct wedge for the wand which blocks your shadow when taking a reading 2. Notebook and pen - Used for site description, date, location and to mark the start and finish time of when the leaf area reading was taken. It may also be helpful to note the amount of cloud cover on the day.
  80. 80. 7. Basal Wedge 1 2 1. Notebook and Pen - Used to note all of the basal wedge data in the field (Site code, location, date, species, fraction and number of hits) 2. Basal Wedge – Used to estimate the width of trees using the fractions etched in the wedge. *A voice recorder can be used instead of the notebook to collect data in the field.
  81. 81. 8. Miscellaneous • Bleach mix – Used to spray down vehicle, tyres and tools to reduce the risk of spreading invasive species and disease, use ethanol to spray shoes. • Extra Backpacks, chaff and calico bags to carry equipment and soil samples. • First Aid Kit • Communication Devices – radios, spot checkers etc. • Enough drinking water (we carry 2x 60L tanks per car) • Safety and protective gear – hats, gaiters, sunglasses, Sunscreen • Laptop – for backing up data
  82. 82. 9. Equipment Check List Field Equipment No. No. No. *Consumables needed per site Soil Analysis Basal Wedge Setting out Hectare Plot Demineralised water 1L Basal Wedge 1 DGPS 1 Sieve 1 Notebook or voice record 1 Galvanised Stakes 5 Datasheet 1 stake dropper 1 Ec-pctestr35 Probe 1 Safety equipment Tent Pegs 20+ 250ml Beaker 2+ Bleach in spray bottle 1 Clothes Pegs 20+ Hydrochloric acid, plate & pipette 1 first aid equipment 1 Hammer 1 Communication devices Calico bag or bum bag for pegs 1 Metagenomics Coloured flagging tape 1 Tablet 1 100m fibreglass measuring tape 10 Small spade or shovel 1 Calico bags (300 X 450mm) 9 Point intercept Large ziplock bags (255 X375mm X 100um) 9 Densitometer pole 1 Alcohol in spray bottle 1 voice recorder on lanyard 1 Silica 9 cups Laser pointer 1 Numbered tags 9 Large calico bags (300 X 600mm) 1 Vegetation collection Paper bags 100+ Subsites Large heavy duty plastic bag 1 Tablet 1 Tea bags 100+ Small Spade of Shovel 1 barcode stickers 100+ Ziplock bags 27 tablet 1 Large calico bags (300 X 600mm) 9 Plant press 1 Measuring tape 1 sistema container 1 Alcohol in spray bottle 1 silica 4 cups Optional - Backpack 1 secateurs 1 shovel/trowel 1 3D Panoramic Photo DSLR Camera 1 Soil sampling and collection (5 steps) Tripod 1 Pit Note book and pen 1 Shovel and or spade 2 2m measuring tape 1 Auger 1 Tent pegs 3 Mattock 1 electrical tape 1 Geo pick 1 1m soil profile tape pvc fiberglass 1 Leaf Area Index Ziplock bags (175 X 312mm X100um) 10 LAI wand kit 1 Bulk density apparatus 1 Notebook 1 Bulk density rings with plastic caps 3 Cloth tape 1 Soil data sheet and pen 1
  83. 83. TERN Field Method Training 29 April 2019                 
  84. 84. Lunch

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