Bacterial Rots of Onion:Knowledge Gaps & the USDA SCRI Project

Lindsey du Toit, Washington State UniversityPacific Northwest Vegetable Association Annual Convention & Trade Show

20-21 November 2019, Kennewick, WA

Known bacterial pathogens of onion(Compendium of Onion & Garlic Diseases & Pests, 2nd Edition)

1. Bacillus cereus – soft rot2. Burkholderia cepacia (Pseudomonas cepacia) – sour skin3. Burkholderia gladioli pv. alliicola – slippery skin4. Dickeya chrysanthemi (Erwinia chrysanthemum) - soft rot5. Enterobacter cloacae – Enterobacter bulb decay6. Erwinia rhapontici – soft rot7. Eschericia sp. – soft rot8. Klebsiella sp. – soft rot9. Lactobacillus sp. – soft rot10. Pantoea agglomerans – bacterial leaf necrosis11. Pantoea ananatis – center rot12. Pantoea allii – center rot13. Pectobacterium carotovorum subsp. carotovorum - soft rot14. Pseudomonas aeruginosa – brown rot15. Pseudomonas marginalis pv. marginalis – soft rot16. Pseudomonas syringae – bacterial leaf spot17. Pseudomonas viridiflava – leaf streak/bulb rot18. Serratia marcescens – soft rot19. Xanthomonas axonopodis pv. allii – Xanthomonas leaf blight

Estimated $60 million in losses to bacterial diseases of onion annually in USA

Bacterial soft rots

Pantoea agglomerans, Pectobacterium carotovorum, Dickeya spp.

Bacterial leaf blights/dieback

Bacterial bulb rots

PNW: Burkholderia gladioli, Pantoea agglomerans, Enterobacter cloacae

Factors Favoring Onion Bacterial Diseases

Contaminated seed and transplants

Storm damage, rain, hail, frost damage

Mechanical wounds, insects (thrips), weeds

Irrigation - runoff, excess, overhead irrigation

Excessive fertility, especially post-bulb initiation

Moderate to high temperatures (>30oC), except for some Pseudomonas spp. (cool to warm)

Dense plant stands

Some topping, curing, and handling practices

Irrigation and bacterial bulb rotsTeviotdale et al. 1990. Effect of sprinkler vs. furrow irrigation on

incidence of bacterial bulb rot

Inoc. Inoc.No

inoc.

No

inoc.

Irrigation and bacterial bulb rots

Insects• Erwinia soft rot – onion maggot• Center rot/Pantoea leaf blight - thrips

Weeds• Pseudomonas leaf streak

cutleaf evening primrosedandelionpurple cudweed

• Pantoea leaf blight & center rotcommon cockle burcommon ragweedyellow nutsedge

Seed• Pantoea leaf blight (center rot)• Xanthomonas leaf blight

Factors Favoring Onion Bacterial DiseasesH.F. Schwartz

Management of bacterial diseases • Clean planting material – seed, transplants

• Sanitation - cull piles, volunteers

• Cultivar maturity, scouting, minimize wounding• Preventative sprays: No systemic bactericides

– coppers + EBDC (copper resistance?), disinfectants, Actigard- coverage, non-ionic surfactant, when to apply?

• Cultural practices:- Irrigation management: type, frequency, crop use (monitor soil moisture status), terminating irrigation- N-fertility: amount, final application ~bulb initiation, monitor crop nutrient status, avoid ‘bull necks’

• Curing:- Field curing: undercut bulbs, topping = wounding?- Postharvest curing: forced air, minimal heat

Post-harvest curingSchroeder, Humann, & du Toit. 2012. Plant Dis. 96:1548-1555.

Fig. 2. Burkholderia cepacia Fig. 3. Burkholderia gladioli

Evaluating Irrigation Management and ManKocidefor Internal Dry Scale and

Bacterial Bulb Rots of Onion – 2016 & 2017 trials

Lindsey du Toit and Tim Waters, Washington State UniversityOnion World May/June 2015, pp. 4-7

du Toit, L.J., Waters, T., and Reitz, S. 2016. Internal dry scale and associated bulb rots of onion. PNW 686. 8 pp.

2017 Results: Bulbs at harvestInternal dry scale, bacterial rot, black mold, & double centers

Factor Treatment

Dry scale

(0-3 severity

index)

Bacterial

rot (% of

bulbs)

Black

mold (%

of bulbs)

Double

centers (%

of bulbs)

Irrigation Wet 0.68 a 13.9 a 2.3 a 26.5 a

Dry 0.63 b 12.4 a 1.3 a 25.3 a

LSD 0.04 4.9 3.0 5.8

Inoculation Inoculated 0.67 a 21.0 a 2.2 a 22.8 b**

Non-inoculated 0.63 a 5.3 b 1.4 a 29.0 a

LSD 0.05 4.5 1.5 4.8

Bactericide ManKocide 0.67 a 12.5 a 1.8 a 26.3 a

No ManKocide 0.64 a 13.8 a 1.7 a 25.6 a

LSD 0.05 4.5 1.5 4.8

**Difficult to discern doubles on rotten onions

Evaluation of Foliar Applications of Bactericides for Management of Onion Bacterial Rot – 2019 trial

Lindsey du Toit, Tim Waters, Washington State UniversityBeth Gugino, Pennsylvania State University

IR-4 Minor Crops Program

No. Product Active ingredient Rate of applicationNo. of applic.

Application interval

1 Control - - - -

2 ManKocide Mancozeb + CuOH 2.25 lb/A 5 7 days

3 Kocide 3000-O CuOH 1.5 lb/A 5 7 days

4 Champ WG CuOH 1.5 lb/A 5 7 days

5 Oxidate 2.0 H2O2 + peroxyacetic acid 1.25 fl oz/2 ga 7 5 days

6 Kasumin 2L Kasugamycin 32 fl oz/A 4 7 days

7 Kasumin 2L 64 fl oz/A 4 7 days

8 Nano-MgO Nano-magnesium oxide 200 ug/ml 5 7 days

9 Nano-MgO 1,000 ug/ml 5 7 days

10 GWN 10120 Ammonia CuOH 2.0 pt/A 5 7 days

11 SP8010 Unknown 19 fl oz/A 5 7 days

12 SP8010 + Kocide3000-O

Unknown + CuOH 19 fl oz + 1.5 lb/A 5 7 days

13 SP8010 + SP2700 2% SP

Unknown 19 fl oz + 4.2 oz/A 5 7 days

14 Lifegard WG Bacillus mycoides J 4.5 oz/100 gal 5 7 days

15 Instill CuSO45H2O + metallic Cu 0.86 lb a.i./100 gal 3 7 days

• Planted Calibra on 1 April 2019 at 164,000 seed/A• Split-plot RCBD, 4 replications, bactericides to main plots, inoculation

treatments to split-plots = 120 plots• 15 bactericide treatment applications:

– Initiated on 24 July, at 5- to 7-day intervals, 3 to 5 times• Inoculated with B. gladioli and P. agglomerans on 1 & 15 August• Sprinklers turned on in late afternoon every other day for 15 min (Jul.-Aug.)• Rated plots weekly 6x for incidence & severity of bacterial blight (23 July - 27

August), & 2x for phytotoxicity (6 & 27 August)• Bulb yield (size & weight) measured on 7 Oct.• Bulb rot (incidence & severity) rated on 16 Oct.• Bulb rot in storage to be rated in Feb. 2020

2019 Foliar Bactericide Trial

Variable Inoculated Non-inoc. P value

8/20 disease incidence 37.7 ± 2.5% 7.5 ± 1.2% <0.0001

8/27 disease incidence 63.1 ± 3.3% 23.4 ± 2.2% <0.0001

8/20 disease severity (0-7) 4.3 ± 0.2 1.7 ± 0.2 <0.0001

8/27 disease severity (0-7) 5.7 ± 0.2 4.3 ± 0.2 <0.0001

Tops down on 8/06 55.1 ± 3.8% 47.8 ± 4.0% 0.0620

% bulbs with bacterial rot 50.9 ± 2.2% 35.0 ± 2.3% <0.0001

Mean bulb rot severity 16.7 ± 1.1% 8.5 ± 0.8% <0.0001

No. of marketable bulbs/plot 34.0 ± 1.2 37.2 ± 1.3 0.0205

Marketable bulb yield (t/A) 38.7 ± 1.3 45.8 ± 1.3 <0.0001

• B. gladioli & P. agglomerans inoculation caused leaf blight & bulb rot• Symptoms observed 19 days after inoculation• Inoculation affected all variables. Bactericide treatments only affected incidence of bulb rot

at harvest and marketable bulb yield (# of bulbs and tons/acre)• No interaction between inoculation treatments and bactericide treatments

Inci

de

nce

(%

) o

f b

ulb

s w

ith

bac

teri

al r

ot

Incidence (%) of bulb rotANOVA for bactericide = 0.0613ANOVA for bactericide*inoculation = 0.9792

* *

**

Incidence (%) of bulb rotANOVA P value for bactericide = 0.0613

** *

Marketable bulb yield (tons/acre)ANOVA P value for bactericide = 0.0263

2019 IR-4 Foliar Bactericide Trial• Inoculation + frequent overhead irrigation caused

severe bacterial leaf blight and bulb rot

• Bactericides were largely ineffective, except Kocide and Lifegard, despite 2 applications before inoculation

• Management of bacterial bulb rots requires effective pre-harvest cultural practices – irrigation & fertility

Stop the Rot: Combating onion bacterial diseases with pathogenomic tools & enhanced management

strategies

Southeast

11,200 A sweet

Bc Pag Pan

Pv Xaa

Columbia Basin

1,000 A sweet;

24,000 A storage

Bg Ec PagWSU

OSU

UCR

UI

USU CSU

NMSU

TAM

UGA

PSU

Cornell

MSU

Rockies

4,000 A storage

Bg Ec Pag

Pan Xaa

Treasure Valley

23,000 A storage

Bg Ec Pag

Midwest

2,500 A storage

Bc Pag PanNortheast

7,800 A storage

Bc Ec

Pag Pan

Southwest

31,200 A storage;

28,700 A non-storage

Bc Bg Ec Pag

du Toit et al. 2019. USDA NIFA SCRI Project No. 2019-51181-30013

Stop the RotUSDA NIFA SCRI Project No. 2019-51181-30013

• $4,044,300 + $4,200,000 matching (universities, stakeholders)

• 4 year-project: Oct. 2019-Sep. 2023• 24 collaborators

• PD = Lindsey du Toit, WSU• Co-PI’s = Bhabesh Dutta & Brian Kvitko, Univ. of Georgia;

Christy Hoepting, Cornell Extension; Brenna Aergerter, Univ. of California; Mark Uchanski, Colorado State Univ.

• 12 states + Teresa Coutinho, Univ. of Pretoria, South Africa

• 12-member Stakeholder Advisory Panel• Kerrick Bauman, Michael Locati represent PNW

Stop the RotUSDA NIFA SCRI Project No. 2019-51181-30013

• Objective A: Onion bacterial disease characterization• A1 – Survey onion crops nationally for bacterial pathogens• A2 – Genetic analyses, virulence factors, bacterial communities• A3 – Develop molecular diagnostic tools• A4 – Develop methods to screen for resistance to bacterial

diseases of onion

• Objective B: Onion bacterial disease management• B1 – Irrigation practices• B2 – Fertility practices• B3 – Pesticide programs• B4 – Cultural practices• B5 – Postharvest practices• B6 – Bacterial disease modeling/risk prediction• B7 – Economic assessments, Extension/outreach

Stop the RotUSDA NIFA SCRI Project No. 2019-51181-30013

Washington State University team members:• Lindsey du Toit, Plant Pathologist• Tim Waters, Extension Specialist & Entomologist• Gabriel LaHue, Soil Scientist• Kirti Rajagopalan, Computer Scientist• Ananth Kalyanamaran, Data Modeler• Heather MacKay, Project Manager• Graduate students & technical staff

• Onion bacterial samples, fields surveyed• Field trial participation• Economic assessment of bacterial issues/needs• Bacterial disease risk modeling/prediction• Feedback on project direction, progress, etc.

Acknowledgements

Play With Your Food

• USDA NIFA SCRI• Pacific Northwest Vegetable Association• Columbia Basin Onion Research

Committee• WSCPR• IR-4 Minor Crops Program• Onion growers, consultants, seed

companies

WSU: Tim WatersDon Kinion, Jennifer Darner, Erika Ramirez Garcia, Eduardo Sallas, Andrea Vallejo Gutierrez

Mike Derie, Barbara Holmes, Paul Morgan, Erin Miller, Haruka Fukada, Ryan Solemslie