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)

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

What kind of Disease?Threat and Distribution of Myrtle Rust

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

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

Distribution of Myrtle Rust

6René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

1884

Source: 4

Distribution of Myrtle Rust

7René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

1913

Source: 4

Distribution of Myrtle Rust

8René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

1936

Source: 4

Distribution of Myrtle Rust

9René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

1977

Source: 4

Distribution of Myrtle Rust

10René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

2002

Source: 4

Distribution of Myrtle Rust

11René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

2009

Source: 4

Distribution of Myrtle Rust

12René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

2015

Source: 4

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

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?

How can I Track the Disease?Detection and Monitoring of Plant Diseases

Vegetation Sensing

16René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

Principles

Source: 1

Source: 5

Vegetation Sensing

17René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Faculty of Science and Engineering I Biological Sciences

Principles

Source: 6 Source: 7

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!

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

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

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

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

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

What about drones now?UAS, Ecology and its future

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

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

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?).

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

Thanks for the attention!Questions?

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.

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