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A plant disease potentially devastating to Australian forests and industries
I spy with my drone eye: Remote and near-range sensing of Myrtle Rust
‘‘Some species are seriously threatened, with significant decline in all stands
visited…the worst area in the Bellinger Valley [NSW] where hundreds of plants have
died…’’ (Richard Johnstone, Seed Bank Officer/Botanist, The Australian Botanic Garden Mount
Annan, July 2014)
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Personal Introduction
2René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
René Heim
Bachelor of Science in Bioengineering/Biotechnology
University of Applied Sciences, Hamburg/Germany 2008-2012
Semester Abroad and Language Studies
University of València, València/Spain 2010
Master of Science in Biology (Focus: Plant Ecology/ Vegetation Sensing)
University of Hamburg, Hamburg/Germany 2012-2014
PhD Candidate (Focus: Plant Pathology/ Vegetation Sensing)
Macquarie University, Sydney/Australia 2015-today
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What kind of Disease?Threat and Distribution of Myrtle Rust
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Impact in Australia
4René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Introducing Myrtle Rust (Puccinia psidii)
Syzygium wilsoniiMelaleuca spec.R. rubescensEucalyptus spec.Callistemon spec.
• Fungal disease (spores) which affects the plant family Myrtaceae.
• Australia has orders of magnitude more Myrtaceae species than any other country.
• Bottlebrush (1), Eucalyptus (2), R. rubescens (3), Paperbark (4), Lilly Pilly (5)
• Government invested > $1.5 million to manage and eradicate MR (unsuccessful)
• Structure and function of ecosystems could be adversely affected.
• Some species have already been severely damaged.
Source: 17 Source: 14 Source: 18 Source: 19 Source: 15
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Impact in Australia
5René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Introducing Myrtle Rust (Puccinia psidii)
Attacks soft, actively growing leaves, shoot tips
and young stems.
Plants do not drop dead but are severely inhibited in reproduction
and growth……because fruits…
…and flowers which produce seeds are
infected.
Source: 16Source: 21 Source: 20 Source: 18
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Distribution of Myrtle Rust
6René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
1884
Source: 4
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Distribution of Myrtle Rust
7René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
1913
Source: 4
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Distribution of Myrtle Rust
8René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
1936
Source: 4
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Distribution of Myrtle Rust
9René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
1977
Source: 4
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Distribution of Myrtle Rust
10René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
2002
Source: 4
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Distribution of Myrtle Rust
11René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
2009
Source: 4
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Distribution of Myrtle Rust
12René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
2015
Source: 4
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Impact in Australia
13René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Increase in host species after reaching Australia
Why this escalating infection rate?
• Usually rust fungi have just a few hosts
species myrtle rust has hundreds of
possible hosts.
• 2250 native Australian myrtaceous
species and the half of it in climatically
suitable areas for the fungus.
Source: 1Before After
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Impact in Australia
14René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
• Not possible to predict spore dispersal of myrtle rust efficiently.
• No detection possible before damage has been caused.
• Can’t predict the long term impact on Australia's ecosystems.
• Fungicides can be applied but have toxic side effects and are expensive.
• Need large scale monitoring for the vast range of host species.
• Understanding the variability in species susceptibility is critical in order to optimize
scarce resources for potential species recovery plans.
Why is monitoring necessary?
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How can I Track the Disease?Detection and Monitoring of Plant Diseases
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Vegetation Sensing
16René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Principles
Source: 1
Source: 5
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Vegetation Sensing
17René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Principles
Source: 6 Source: 7
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Vegetation Indices
18René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Monitoring Plant Stress
Source: 13Source: 13
Problem: Vegetation indices
can be very non-specific for
your application!
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Disease Specific Index
19René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Developing a new Index
Recording Spectral
Signature
Generate classes e.g. healthy and
infected
Select spectral features
which explain most
varying sections
Relate selected
features to determine the specific
index
Source: 9
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Disease Specific Index
20René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Preliminary Data from a Lemon Myrtle Plantation
Low
Source: 1 Source: 1
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Disease Specific Index
21René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Preliminary Data from a Lemon Myrtle Plantation
19) 20)
Moderate
Source: 1 Source: 1
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Disease Specific Index
22René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Preliminary Data from a Lemon Myrtle Plantation
High
Source: 1 Source: 1
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Disease Specific Index
23René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Preliminary Data from a Lemon Myrtle Plantation
Source: 1
Source: 7
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What about drones now?UAS, Ecology and its future
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Unmanned Aerial System
25René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Our low budget equipment (~1200$AUS)
DJI Phantom 2 (Drone) + GoPro Hero4 Black (Camera) + Specific Dualband Filter
Source: 10 Source: 11
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Unmanned Aerial System
26René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Plantations are very suitable for drone monitoring.
• No exhaustive screening by eye.
• No contamination of clothing.
• Faster screening on constantly
growing farmland
• Drones are cheap and available.
• Once a monitoring is established
adaptable on other plantations…
• …and other diseases.
• Less complex than satellite or airplane
monitoring.
• Better spatial and temporal resolution
than satellite/airplane monitoring.
• Adaptable on natural environments?Source: 1
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Ideas
27René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
How do I proceed?
Spectral characterizations of myrtle rust (MR).
Developing a MR specific disease index (SDI).
Applying the SDI on lemon myrtle plantations with the UAS.
Developing an early detection method for MR (thermal or spectral?).
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Possibilities
28René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
How to get involved?
• Do you…• …want to cooperate?
• …have a real drone?
• …have a multi-hyperspectral camera?
• …have thermal cameras?
• …have a similar problem?
• …need more information.
• …have ideas that need to be incorporated?Source: 12
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Thanks for the attention!Questions?
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30René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Literature
1. Carnegie, A.J., Kathuria, A., Pegg, G.S., Entwistle, P., Nagel, M., and Giblin, F.R. (2015). Impact of the invasive rust
Puccinia psidii (myrtle rust) on native Myrtaceae in natural ecosystems in Australia. Biol. Invasions 1–18.
2. http://www.dpi.nsw.gov.au/biosecurity/plant/myrtle-rust
3. Giblin, F. (2013). Myrtle rust report: New Caledonia (Maroochydore, Queensland, Australia: University of the Sunshine
Coast).
4. Mahlein, A.-K., Rumpf, T., Welke, P., Dehne, H.-W., Plümer, L., Steiner, U., and Oerke, E.-C. (2013). Development of
spectral indices for detecting and identifying plant diseases. Remote Sens. Environ. 128, 21–30.
5. Makinson, B. (2014). Myrtle Rust - what’s happening? Australas. Plant Conserv. J. Aust. Netw. Plant Conserv. 23, 13.
6. Lein, J.K. (2012). Environmental Sensing (New York, NY: Springer New York).
7. http://www.planthealthaustralia.com.au/national-programs/myrtle-rust/
8. Sankaran, S., Mishra, A., Ehsani, R., and Davis, C. (2010). A review of advanced techniques for detecting plant
diseases. Comput. Electron. Agric. 72, 1–13.
9. Xavier, A.A., da Silva, A.C., da Silva Guimarães, L.M., Matsuoka, K., Hodges, C.S., and Alfenas, A.C. (2015). Infection
process of Puccinia psidii in Eucalyptus grandis leaves of different ages. Trop. Plant Pathol. 40, 318–325.
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31René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences
Figure Sources
1. Rene Heim
2. Source:www.noosanativeplants.com.au.plants.341.melaleuca-quinquenervia
3. https://en.wikipedia.org/wiki/Eucalyptus_grandis#/media/File:Eucalyptus_grandis_Kerewong_State_Forest_55_metres_tall.jpg
4. http://onlinemaps.blogspot.com.au/2011/11/blank-world-map.html
5. Lein, J.K. (2012). Environmental Sensing (New York, NY: Springer New York).
6. https://www.youtube.com/watch?v=rxOMhQwApMc&list=PLM5Qn7cNEHDSSOEWE9jIgwi4CXL5cb3vY
7. http://precisionagricultu.re/misconceptions-about-uav-collected-ndvi-imagery-and-the-agribotix-experience-in-ground-truthing-these-images-for-agriculture/
8. http://geotekno.tumblr.com/
9. Mahlein, A.-K., Rumpf, T., Welke, P., Dehne, H.-W., Plümer, L., Steiner, U., and Oerke, E.-C. (2013). Development of spectral indices for detecting and
identifying plant diseases. Remote Sens. Environ. 128, 21–30.
10. http://elisa.vo.llnwd.net/v1/deals/Phantom-2-V2exp-.jpg
11. http://www.peauproductions.com/collections/filters/products/f-vis940-g
12. http://www.techtimes.com/articles/102639/20151103/maybe-fallouts-vault-boy-isnt-giving-us-the-thumbs-up-after-all.htm
13. Gennaro Cappelluti - http://www.seiswaves.com/cappelluti/docs/anims/leicester/, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=12876160
14. https://www.savethekoala.com/sites/default/files/9.jpg
15. https://southgippsland.wordpress.com/2008/05/17/lilly-pilly-berries/
16. https://www.daf.qld.gov.au/__data/assets/image/0005/59927/geraldton-wax-flower.jpg
17. http://www.duchyofcornwallnursery.co.uk/cpimages/product_zoomimage/PSH-CALPEPI.jpg
18. https://anbg.gov.au/gardens/images/200-vertical/myrt-rust-Rhodamnia-rubescens-fr-carnegie.jpg
19. http://tasteaustralia.biz/bushfood/wp-content/uploads/2013/09/paperbark-tree.jpg
20. http://www.dpi.nsw.gov.au/__data/assets/image/0010/362782/myrtle-rust-agonis.jpg
21. R. Makinson