Getting to the Root of and Root Rot Pathogens

Syama Chatterton, Lethbridge Research Centre CropSphere January 10-11, 2017, Saskatoon, SK

Overview

• Root rot surveys in 2016 – Distribution of pathogens in SK • Intro to causal agents – Risk factors for root rot – Host range of Aphanomyces • Current research projects – Field trials – Inoculum dose – Field mapping

2 Field surveys for root rot of pea and in 2016 • 67 lentil and 68 pea fields surveyed during flowering • Samples sent to Lethbridge for rating and analysis • Diagnostic DNA tests for common pathogens

3 Disease severity rating scale

1 2 3 4 5 6 7 Healthy Moderate Severe

4 Healthy Moderate Severe

5 Healthy Moderate Severe

6 7 Lentil root rot by soil zones in 2016

Incidence Incidence DS > 1 DS > 3 (healthy – severe) (moderate + severe) Mean DS

Black 93.5 47.7 3.5

Dark Brown 96.0 33.9 3.0

Brown 88.0 21.6 2.7

8 Pea root rot by soil zones in 2016 Incidence Incidence DS > 1 DS > 3 Mean DS

Grey 85.3 14.0 2.4

Black 91.8 46.2 3.5

Dark Brown 81.3 40.0 3.1

Brown 91.9 63.5 4.3 9 Percent fields positive for Aphanomyces euteiches 80 71.4 73.3 68.8 69.6 70 66.7 66.7

60 54.2 50

40

30

20

10

0 Black Dark Brown Brown Grey Black Dark Brown Brown Pea

10 Lentil fields Pea fields 40 40 Test 1 Test 2 Test 1 Test 2 35 35

30 30

25 25 in each category in each 20 20

15 15

10 10

Number of fields fields of Number 5 5

0 0 0 1-25 26-50 51-75 76-100 0 1-25 26-50 51-75 76-100 % positive samples % positive samples

11 Other soilborne fungi….

100 90 80

70 60 50 40

% positive fields % positive 30 20 10 0

Virulent Weak Wheat Root rots are caused by a complex of organisms

• Two main pathogen groups of focus – Aphanomyces euteiches – highly aggressive on pea and lentil, long-lived resting spore – Fusarium spp. - distributed widely • F. avenaceum and F. solani most virulent species

13 Aphanomyces euteiches: First report for Saskatchewan in 2012 • or water mould http://cronodon.com/images/ • Zoospores - dependent on water for free-swimming stage • Produces long-lived resting spores (oospores) • Only registered chemical = ethaboxam • Very difficult to isolate using conventional methods, requires a DNA test 14

Fusarium root rot

• Fusarium is a very large Genus with hundreds of different species • One of the most common fungi in the soil • Plant pathogens - not all species are equal

Fusarium graminearum (FHB) Fusarium avenaceum 15 Root rot infection stage

• Aphanomyces root rot: – Infection can occur at any time in the growing season – Most important factor is presence of soil moisture for zoospore infection • Fusarium root rot: – Most susceptible stage to infection seems to be at seedling stage – Symptoms don’t compound until late flowering • Peas can sustain a fair amount of Fusarium root rot before yield impacted

16 Lethbridge, AB Taber, AB 7 7

6 6

5 5

4 4 Fusarium 3 3 Fusarium Aphanomyces Aphanomyces Disease Disease severity 2 2

1 1

0 0 0 1000 2000 3000 4000 0 1000 2000 3000 4000 Yield (kg/ha) Yield (kg/ha)

17 18 Aphanomyces versus Fusarium?

Yellowing and Shoots wilting of remain shoots healthy

Pinching of Blackened tap epicotyl, stops root, starts at abruptly at seed soil line attachment Lateral roots Healthy watery and lateral honey-brown roots decay

Aphanomyces Fusarium 19 Symptom expression is not clear-cut

Most often roots are infected with a pathogen complex

20 Root rot symptoms on pea and lentils

21 Risk factors for root rot Factor Effects

Crop history 4-5 cropping cycles with susceptible host Soil moisture – Oospores germinate in dry soil (SWP > -20 kPa), but Aphanomyces hatch zoospores in wet soil (SWP > 5 kPa) Soil compaction Conducive soils with 35-40 % clay content prone to compaction and water-logging Soil pH Acidic soils, pH range 5.6 – 6.6 Soil temp Optimal temp for infection is 24oC Other soilborne Root rots usually caused by a complex that act pathogens synergistically to increase disease

22 Control options – what can you do right now?

• If you have had a history of root rots – get soil tested to confirm presence of Aphanomyces • Avoid planting peas and lentils in Aphanomyces- infested fields • Prolonged rotations of susceptible hosts (peas and lentils) in infested fields (6 – 8 years) • Consider using a seed treatment that targets the root rot complex • An in-crop fungicide application will not have any effect

23 Host range testing of Aphanomyces Crop Disease reaction Oospores

Peas Susceptible Yes

Lentils Susceptible Yes

Cicer milkvetch Susceptible Yes

Dry bean Variable Few

Alfalfa Variable Yes

Chickpeas Resistant Few

Sainfoin Resistant Few

Faba bean Resistant No

Soybean Non-host No

Fenugreek Non-host No 24 Research projects on the go 1. Survey and map root rot incidence and severity in Alberta and Saskatchewan 2. Evaluate field-based solutions to reducing root rot impact – seed treatments, cultivar effects, soil amendments 3. Develop inoculum quantification tools for predicting root rot risk in Canadian prairie soils 4. Determine spatial distribution of A. euteiches in vertical and horizontal soil profiles, and in different soil zones 5. Identify interactions between species that affect root rot development

25 Field-based solutions

• Most are in the research phase… • Ethaboxam (Intego Solo) – Registered for early suppression of Aphanomyces root rot – Must be used in combination with other seed treatments with actives against Fusarium and other damping-off pathogens • Phostrol (phosphite salts) – Not registered on pulse crops – Good efficacy in trials in the U.S. on processing pea when applied at seeding or emergence – More widespread trials taking place in 2016  Won’t provide full-season protection 26 Results A. euteiches + ethaboxam in the greenhouse Results - Field Trials Control options

• Liming or Ca+ amendments – Calcium prevents zoospores from germinating – Feasibility of applying and incorporating calcium? • Brassica cover crops – Green manure break-down products “biofumigate” soil and suppress oospores – Feasibility in no-till systems if green manure needs to be incorporated? – Increased disease risk to canola?  Long-term effects as amending inoculum levels in soil

29 Aphanomyces inoculum dose-response curves

• Soil test to quantify inoculum potential and disease risk before planting peas  How many oospores/ g soil cause disease?  Does this differ between soil zones?  Is it influenced by other soilborne pathogens?

30 31 Disease progression in dark brown soil zone

32 Swift Current – Brown soil

5 4.5 4

3.5 3 2.5 2

1.5 Disease Severity Disease 1 Auto 0.5 Non 0 0 0.5 1 1.5 2 2.5 3 3.5 log oospores/g soil

33 Autoclaved No added inoculum in brown soils

Natural

Presence of Fusarium spp. confounds Aphanomyces research 34 Aphanomyces dose-response curves

• Variable dose-response curves between soil zones in autoclaved soils, Dk. Brown > Brown > Black – 100 oospores/g in dark brown soils – 750 oospores/g in brown and black soils • Presence of Fusarium spp., particularly in brown soils, increases disease severity – 100 oospores/g in all soil types

35 Distribution of A. euteiches in the soil profile

• Collected soil samples in October 2015/2016 from 3 fields in each of the 3 soil zones of Saskatchewan

20 40 60

36 Highest inoculum levels in the top 20 cm

Fields Soil zone 0-20 20-40 40-60 K Dark Brown 3.9 3.3 2.8 E Brown 4.5 3.5 2.2 C Dark Brown 3.1 2.6 2.7 G Dark Brown 4.6 3.7 3.4 B Black 4.8 4.0 3.7 H Brown 3.9 3.6 3.3 P Black 4.3 4.1 3.7 L Brown 4.7 4.1 3.2 N Black 4.9 4.6 4.1 37 Distribution of A. euteiches in field G (dark brown) 5 4.5 4

3.5

3 2.5 20

2 40 Diseaserating 1.5 60 1 0.5 0 1 2 3 4 5 6 7 8 9 10 11 GH Ctrl Site 38 Distribution of A. euteiches in field N (black)

5 4.5 4

3.5

3 2.5 20

2 40 Diseaserating 1.5 60 1 0.5 0 1 2 3 4 5 6 7 8 9 10 11 GH Ctrl Site 39 Why all plant pathologists need a drone!

40 Conclusions

• Root rots are widespread, but have less of an impact in dry years • Aphanomyces and Fusarium root rots occur as a complex, are difficult to distinguish and act synergestically • Long rotations between susceptible pulse crop only control option • Faba beans, soybean and chickpeas best pulse crop option in infested fields

41 Conclusions

• Inoculum potential differs between soil types, dark brown soils most conducive • Presence of other pathogens, especially Fusarium spp., increases inoculum potential • Threshold dose for Aphanomyces root rot = 100 oospores/g soil • A. euteiches decreases with increasing soil depth – highest in the top 20 cm • Horizontal distribution varies by field, uniform or patchy

42 Collaborators • Sabine Banniza, U of S • Sherillyn Phelps and Brian Olson, SPG • Bruce Gossen, AAFC • Mike Harding and Robyne Bowness, Alberta Agriculture

Technical Assistance • Carol Mueller, Scott Erickson • Trina Dubitz • Dustin Burke, Carol Pugh • Cheryl Cho • Telsa Willsey (MSc student) • A lot of coop students 43