Pathology challenges in the production & manufacturing industries

Dr Kim Plummerk.plummer@Latrobe.edu.au

Au$288M Agricultural Biosciences R & DLa Trobe University, ~110 staff + PhD students; Vic Gov Dept. of Economic Development, Jobs, Transport and Resources, ~350 staff + PhD students

http://www.croppro.com.au/crop_disease_manual/ch01s01.php

resistant or susceptible

cultivars, new crop species

climate uncertainty, ↑CO2 + ↑ extreme weather, new cropping regions, marginal zones, other microbes

fungicide resistance new virulence,contaminants, opportunists,new arrivals

• Luck et al, (2011) pathogens vary but overall negative effects predicted

• Murray and Brennan 2009 - higher current estimates of loss (over their previous predictions) may be associated with changes in climatic conditions since the last survey (in 1998).

• increases in potential loss from stem and stripe rusts could be caused by temperature increases, while drier conditions could be associated with increased losses from crown rot.

• Pathogens are likely to adapt to change scenarios, crops slower to adapt

• Also dependent on grower responses to changes, marginalisation of existing farms or moving into new cropping areas

Changes in climate? Watch this space…..

• Pre-harvest: • pathogens (viruses, bacteria, fungi, oomycetes) compete for

photosynthates

• Reduce yield & lifespan of perennial species

• Controls: cost of agrichemicals – financial, environmental impact & health concerns, toxicity to plants (e.g. copper accumulation)

• Post-harvest• Reduced quality (seed viability) & impact on food safety

(contaminants, biological & chemical residues), export market limitations

• Cost of finding new, effective pesticides (resistance) or producing, e.g. breeding resistant plants

Losses…due to pathogens

average annual

loss of $913

million, or $76.64

per hectare

= 19.5% average

annual value of

wheat crop over past decade.

If the current control

measures were not

in place, losses would be far higher.

http://grdc.com.au/uploads/documents/GRDC_WheatDiseaseLoss_Report_final.pdf

Estimated costs of wheat disease in AustraliaGordon M. Murray and John P. Brennan 2009, for GRDC

Differences between potential & present losses in

wheat crop reflect the value of current control

measures.

New pathogen variants (mutants) can challenge these gains, have to keep pace with these.

Gordon M. Murray and John P. Brennan 2009, for GRDC

Plants vs pathogens

• Most plants are naturally resistant to most pathogens

• Conversely most pathogens infect few host plants

• In natural populations plants & pathogens coexist

• Disease epidemics - symptom of cultivation systems (monocultures)

Arms race between plants & invaders

http://www.funnysalescartoons.com/photo/funny-sales-cartoon-castle-attack?context=latest

Thugs – necrotrophs, Yellow & Tan Spots

Con men – biotrophs = rustsCurrent research looking at the weapons on both sides of the battle

-Omics discovery age, extra weapons Host plant genomes/transcriptomes/proteomes….• Identification of resistance genes

• Host and non-host resistance genes (most R genes in wheat are from other species)

• Assisted breeding plus potential for stacking multiple disease resistance genes for durable resistance.

Pathogen genomes/transcriptomes etc• Most genes - function unknown

• We can now work out how they get in – counter intelligence

• Smart breeding choices for durable resistance

• Population genetics (breeding potential of pathogens)

• Facilitating pathogen identification (generally…..)

http://www.nwroc.umn.edu/Cropping_Issues/2009/May_26/PreventingEarlySeasonLoss/index.htm

• Patho-genomics/transcriptomics of tan spot and yellow spot fungi

• necrotrophic diseases not so thuggish

• plant breeding against host susceptibility genes rather than host disease resistance genes, i.e. sometimes less, is more

Wrangling beneficial microbes

• Using -omics to understand microbial communities = microbiomes (in particular the soil environment)

• Secondary metabolites – bioactive molecules

• Bioactive compounds: antibiotics, fungicides, bio-fumigants

• Beneficial interactions, novel, stable, bioactives

• Co-opt non-pathogens to promote plant defences, outcompete or attack pathogens directly

Microbial good guys - endophytes

• Fungi and bacteria living inside the plant leaves (endophytes) and roots (mycorrhizae)

• Mutually beneficial, improve plant growth

• Assist with tolerating plant stress (e.g. drought)

• Provide resistance to pathogens, insects, but can also impact mammals (us and other herbivores)

• Similar genera to pathogens – ID very important

Mycofumigation = process of using volatile chemicals produced by a fungus to control soil-borne pathogens, weeds and insects (Stinson et al. 2003). Fungi evaluated for mycofumigation have all been isolated as endophytes

Untreated versus Myco-fumigated with endophyte

Dr Ross Mann

Benefits to the plant, protection against

• herbivores (fungal alkaloids)• some abiotic stresses• pests (e.g chinch bug)• disease (eg. dollar spot -Sclerotinia)

Benefits to fungi• Protection, dissemination, nutrition

http://www.ntep.org/endophyte.htmhttp://turfgrass.cas.psu.edu/graduate/Agro85

1/Lesson12/L12_01.htm

http://turfgrass.cas.psu.edu/graduat

e/Agro851/Lesson12/L12_01.htm

Lolitrem B0- < 0.1 μg/g dwt

Peramine15-30 μg/g dwt

Ergovaline< 0.2 μg/g dwt

Janthitrems

- Antimammalian- Genes known

- Antimammalian / Insecticidal- Genes known

- Insecticidal- Genes known

- Antimammalian / Insecticidal- Genes unknown

Alkaloids

Cool Temperate Grasses/Epichloe Symbiosis

Dr Ross Mann

Adaptive Symbiotic Technologies Development of BioEnsure®

Fungal Endophytes can confer stress

tolerance

An industry compatible seed treatment that allows plants to tolerate drought, temperature and salt stress.

Plants in nature are symbiotic with bacteria, mycorrhizae and fungal endophytes

Fungal Endophytes are analyzed in the greenhouse and developed in the lab to produce BioEnsure

Slides courtesy of Dr Rusty Rodriguez

Cowpea seedlings protected from disease by inoculation with endophyte fungus

http://www.adaptivesymbiotictechnologies.com/press--publications.html; vegetables_australia_sept_oct_pg_32-33

BioEnsure® Yield Increase versus Stress

Cumulative results from six test plots (100’ x 60’) established by independent cooperator in CA. BioEnsure® increased yield an average of 8.85% across replicates with a range of 5-14%, (T test, p<0.01).

8.85%

320

330

340

350

360

370

380

Untreated BioEnsure

Ave

rage

Ear

wt

(g)

2015 (low stress)

375%

0

2000

4000

6000

8000

10000

Untreated BioEnsure

Tota

l Ear

We

ght

(g)

2015 (extreme drought)

AST’s Approach to the Future of Food Security

Developing microbial consortia to confer benefits to plants:

• Improved nutrition

• Biotic stress protection

• Enhanced seed viability & germination

• Improved seedling growth, development and health

• Abiotic stress tolerance

• Improved soil health

• Increased yields

• Expansion onto marginal lands

Breed a new generation of plants with enhanced symbiotic communication

New cultivation strategies to enhance soil health & symbiotic benefits

The Future is Symbiotic and Synergistic

Australia is relatively free of major pests and diseases found worldwide…..

https://www.youtube.com/watch?v=o4g930pm8Ms

• International air and cargo traffic has increased the risk of pathogens and pests accompanying passengers arriving in Australia.

• In 1956, ~64,000 people arrived on 1,825 flights to Australia (including Melbourne Olympic Games)

• In 2000 8.3 mil passengers on ~46,000 inbound international flights

• in 2014 16.6 mil passengers on ~88,000 flights,

• Incursions have increased during this time (rusts, Prof Robert Park)

Stowaways: movement of pests & pathogens

http://bitre.gov.au/statistics/aviation/international.aspxhttp://bitre.gov.au/statistics/aviation/domestic.aspx http://portcapacity.portofmelbourne.com

• 2012‐13 Port of Melbourne >2.5 million containers (~7000 per day!)

• The average international container vessel carrying ~3,100 containers

Key risks for Australia in relation to incursions:

• growing tourism & trade, increasing people & plant product movements

• Deliberate introductions of exotic pathogens (bioterrorism?)

• evolution of potentially more pathogenic strains (by mutation in pathogen populations);

• changes in climate and ecology, with associated changes in vector-borne disease spread and occurrence;

• limited capability for coordinated surveillance and response capacity in exporting countries and inland, combined with large scale movements of an increasingly diverse range of plant products

Unwanted pathogens on the radar• 2012–13, grain production (wheat, barley,

canola, sorghum, oats, and lupins) was valued at $12.7 billion.

• wheat, accounts for > half of total production

• Several pathogens recently emerged or evolved

• Wheat stem rust Ug99 (= race TTKSK)

• Wheat blast - extensive epidemics in SthAmerica

• Karnal bunt

• Barley stripe rust (Puccinia striiformis f. sp. hordei)

http://www.fao.org/agriculture/crops/rust/stem/rust-report/stem-ug99racettksk/en/

http://www.planthealthaustralia.com.au/wp-content/uploads/2012/11/Biosecurity-Manual-for-Grain-Producers.pdf

Wheat stem rust (Puccinia graminis f. sp. tritici) Ug99 lineage out of Africa

• Race identified in Uganda in 1999, spread to Egypt, Yemen, Iran

• 2014 ~50,000 Ha wheat killed by stem rust in Ethiopia

• yield losses of 70-100% • 80-90% of global wheat

cultivars susceptible• variants overcomes many R

genes, Sr31, Sr24 & Sr36 • rust spores spread 1000s km

by wind or via accidental human transmission (infected clothing or plant material).

• Australia preparing for Ug99s

http://www.fao.org/agriculture/crops/rust/stem/stem-rustmapper/en/

The Borlaug Global Rust Initiative with Gate’s foundation funding monitoring spread.

http://www.fao.org/agriculture/crops/rust/stem/stem-rustmapper/en/

Karnal bunt fungus: Tilletia indica• affects wheat, durum, triticale

• recognised by a ‘dead fish’ smell

• not detected in Australia but looks similar to other diseases present in Australia

• a major threat to grain export markets, many countries have import restrictions

• 1st detected in 1930’s in India, now in many middle-eastern countries.

• Present but confined in SthAmerica, Sth Africa, USA

http://www.planthealthaustralia.com.au/wp-content/uploads/2013/01/Karnal-bunt-FS.pdf

masses of powdery spores discolour grain and grain products

Karnal bunt Case Study• In 2004 Pakistan claimed Karnal Bunt, was present in Australian

wheat shipments.

• claim affected $500 million of wheat on the water at the time.

• offloading product from ships carrying Australian wheat was potentially affected in all ports of the world.

• in order to prove area freedom in Australia from this disease, 28,000 samples were tested.

• PHA commissioned leading experts to develop diagnostic protocolsfor use in Australia and Pakistan.

• All samples were negative, and trade was able to resume.

• Highlights importance of capability!

• Need for forensic microbiology diagnostics, future-proofing against possible sabotage, deliberate versus accidental introduction of pathogens

http://www.grainproducers.com.au/component/k2/item/48

Wheat blast• emerging threat worldwide (also

infects triticale & barley)

• caused by fungus, Magnaporthe oryzae/Pyricularia grisea (same species, different host range to rice blast pathogen)

• Triticum population of M. oryzae is closely related to pathogen of perennial & annual ryegrasses in U.S.

http://www.k-state.edu/wheatblast/about/

Symptoms similar to Fusarium head blight

• 1st detected in southern Brazil in 1985, spread to Bolivia, and Paraguay (1 infected head in Kentucky, USA)

• Crop losses common 40%, up to 100% • Currently, no commercially resistant varieties, fungicides targeting wheat blast not

effective• infected/infested seeds via trade and travel most likely mechanism for spread• Bad news/good news: power of comparisons between blast pathogens – genomics,

transcriptomics, proteomics, metabolomics

http://www.planthealthaustralia.com.au/wp-content/uploads/2012/11/Biosecurity-Manual-for-Grain-Producers.pdf