Using Landcare Research s collections to find answers to PSA on kiwifruit
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1 Using Landcare Research s collections to find answers to PSA on kiwifruit Pathogens don t carry passports! Bevan Weir Landcare Research, Auckland Biosecurity Bonanza 19 May 2014
2 Outline Pathogens don t carry passports How do we know what they are? How taxonomy + collections + databases are important for biosecurity With reference to the recent Psa kiwifruit disease But relevant to many plant pathogens and fungi PTA, Myrtle rust, Citrus canker, Xylella etc.
3 What is Psa? A bacterial disease of kiwifruit Leaf spots, canker, death Pseudomonas syringae pv. actinidiae bacterium
4 Severe kiwifruit disease Psa-V Statistics 8 May orchards have Psa-V 81% of New Zealand s kiwifruit hectares Not Nelson or Whangarei kvh.org.nz
5 Why Landcare Research? History DSIR split into CRIs in 1992 The PDD of DSIR was split between Crop & Food, Hort Research, AgResearch, and Landcare Research Landcare retained: National collections (CHR, PDD, NZAC, ICMP) Taxonomists
6 DSIR Bacteriology 1988
7 Psa response
8 Genome sequence November 2010 from Te Puke MAF ID d bacterium as Psa But which strain? Asian Italian Asked by MAF to do whole genome sequence Sequenced in 3 days EcoGene
9 Gene Genome analysis Japan 84, Italy 94 avrpto1 - - avrd1 + + avrae1 + + hopa1 - + hopb1 - - hopc1 - - hopd1 + + hopf2 - - hopg1 - - hrpk1 + + hopaf1 ± - hopan1 + + Coronatine ± - Phaseolotoxin + - Italy 08/09 NZ 2010
10 Gene Genome analysis Japan 84, Italy 94 Italy 08/09 NZ 2010 avrpto avrd avrae hopa hopb hopc hopd hopf hopg hrpk hopaf1 ± - - hopan Coronatine ± - - Phaseolotoxin + - -
11 ICMP: International Collection of Microorganisms from plants National coll. of living bacteria and fungi All of NZ, stakeholders Liquid N 2 19,371 cultures 50%:50% Bact:Fungi 57%:43% NZ:World Important collection of plant pathogenic bacteria type of Psa + 700
12 New or Old disease in NZ? Was Psa-V a recent introduction? Or present for a long time? changing conditions caused severe disease? Screened 40 years of ex- kiwifruit bacteria in the ICMP looking for Psa Found no matches from 143 Value of collections to NZ Keep collecting NZ material
13 Different Psa populations in NZ? The genome matched Italian Diagnostic test of the time did not differentiate populations Testing from around the country indicated Psa was widespread Impacted policy & biosecurity decisions But subsequent sequencing revealed a novel Psa population in NZ Psa-V: strong pathogen, canker Psa-LV: Leaf spots, plants survive, been here a while
14 Psa global populations I-Psa Z Italy (2008) I-Psa 8 Italy (2008) CRA-FRU Italy (2008) CFPB 7286 Italy (2008) CRA-FRU 8.43 Italy (2008) CRA-FRU 8.76 Italy (2009) CRA-FRU Italy (2010) CRA-FRU Italy (2010) CRA-FRU Italy (2010) CRA-FRU Italy (2010) I D1 Italy (2010) I Italy (2010) T10_04758 New Zealand (2010) T10_04782 New Zealand (2010) T10_05815 New Zealand (2010) T10_05454 New Zealand (2010) T10_06115 New Zealand (2010) T11_0918 New Zealand (2011) CH China (2010) Psa1A Chile (2010) Psa1B Chile (2010) Chile (2010) 2871B5 Chile (2010) 287A63 Chile (2010) 1 ICMP 9855 Japan (1984) MAFF Japan (1987) NCPPB 3739 Japan (1984) PT 1 MAFF Japan (1984) MAFF Japan (1988) PA 459 Japan (1988) NCPPB 3871 Italy (1994) NCPPB 3873 Italy (1994) KACC Korea (1997) 1 KACC Korea (1998) KACC Korea (1997) T10_04976 New Zealand (2010) T10_05163 New Zealand (2010) T10_05188 New Zealand (2010) T10_05195 New Zealand (2010) 1 T10_05196 New Zealand (2010) T11_01581 Australia (1990) T11_01369A Australia (2011) T11_01395A Australia (2011) Australia (2011) Psa3 (Psa-V) Psa1 Psa2 Psa4 (Psa-LV) Chapman et al doi: /phyto r
15 Diagnostics
16 Psa diagnostic service CRIs have immediate capability Did 300+ Psa tests by isolation + seq. Living bacteria gold standard Into the ICMP Trained commercial labs Tech transfer Now occasional tests Did sequencing for MAF weekends
17 New diagnostic tests Helped validate new diagnostic tests Faster, more specific Directly from plant tissue Provided positive controls and 150+ DNA genetically similar pathovars other ex-kiwifruit bacteria Based on P. syringae taxonomy research Validation very important False positives have economic consequences
18 NZfungi database Database of Fungi and bacteria Pansectorial, national database Taxonomy (What is the current name?) Biostatus (Is this organism here? Exotic or native?) Associations (What plant is it found on?) Collection specimen data Feeds through to NZOR
19 NZfungi database
20 NZfungi database
21 Armillaria novae-zealandiae
22 Management of Psa? Psa can be controlled by antibiotics improper use problem Resistance problem EU zero residue problem Problems can be mitigated Need a novel biological solution: KVH Investigating biologicals Screened ICMP collection for anti-psa bacteriocins Found 10 promising candidates (from 200)
23 Management of Psa?
24 Conclusions Pathogens don't carry passports Can t check everything at the border Collections are important Reference material Historic collections Biological resource Taxonomy changing rapidly need to stay up to date with what is in NZ LCR databases
25 Acknowledgements LCR technical staff Maureen Fletcher, Paula Wilkie, Elsa Paderes Duckchul Park MPI PHEL Tamaki Brett Alexander, Rob Taylor Funding LCR, KVH, MPI
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