Pathology challenges in the production & manufacturing industries. Dr Kim Plummer.

Transcription

1 Pathology challenges in the production & manufacturing industries Dr Kim Plummer

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

3 fungicide resistance new virulence, contaminants, opportunists, new arrivals resistant or susceptible cultivars, new crop species climate uncertainty, CO 2 + extreme weather, new cropping regions, marginal zones, other microbes

4 Changes in climate? Watch this space.. Luck et al, (2011) pathogens vary but overall negative effects predicted Murray and Brennan 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

5 Losses due to pathogens 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

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

7 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

8 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)

9 Arms race between plants & invaders Current research Con looking men at the biotrophs weapons = on rusts both sides of the battle Thugs necrotrophs, Yellow & Tan Spots

10 -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..)

11 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

12 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

13 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

14 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 Dr Ross Mann Untreated versus Mycofumigated with endophyte

15 Cool Temperate Grasses/Epichloe Symbiosis 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 Lolitrem B 0- < 0.1 μg/g dwt - Antimammalian - Genes known Peramine μg/g dwt - Insecticidal - Genes known Alkaloids Ergovaline < 0.2 μg/g dwt - Antimammalian / Insecticidal - Genes known Janthitrems - Antimammalian / Insecticidal - Genes unknown 1/Lesson12/L12_01.htm Dr Ross Mann e/agro851/lesson12/l12_01.htm

16 Adaptive Symbiotic Technologies Development of BioEnsure Slides courtesy of Dr Rusty Rodriguez Plants in nature are symbiotic with bacteria, mycorrhizae and fungal endophytes An industry compatible seed treatment that allows plants to tolerate drought, temperature and salt stress. Fungal Endophytes can confer stress tolerance Fungal Endophytes are analyzed in the greenhouse and developed in the lab to produce BioEnsure

17 Cowpea seedlings protected from disease by inoculation with endophyte fungus com/press--publications.html; vegetables_australia_sept_oct_pg_32-33

18 Total Ear Weght (g) Average Ear wt (g) BioEnsure Yield Increase versus Stress 2015 (extreme drought) 2015 (low stress) % % Untreated BioEnsure 320 Untreated BioEnsure 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).

19 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

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

21 Stowaways: movement of pests & pathogens 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 mil passengers on ~46,000 inbound international flights in mil passengers on ~88,000 flights, Incursions have increased during this time (rusts, Prof Robert Park) Port of Melbourne >2.5 million containers (~7000 per day!) The average international container vessel carrying ~3,100 containers

22 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

23 Unwanted pathogens on the radar , 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 Sth America Karnal bunt Barley stripe rust (Puccinia striiformis f. sp. hordei)

24 Wheat stem rust (Puccinia graminis f. sp. tritici) Ug99 lineage out of Africa The Borlaug Global Rust Initiative with Gate s foundation funding monitoring spread. 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 % 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

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26 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 1 st detected in 1930 s in India, now in many middle-eastern countries. Present but confined in Sth America, Sth Africa, USA masses of powdery spores discolour grain and grain products

27 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 protocols for 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

28 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. Symptoms similar to Fusarium head blight 1 st 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

29 ealthaustralia.com. au/wpcontent/uploads/2 012/11/Biosecurity -Manual-for-Grain- Producers.pdf