Root disease in pulses – cause of poor performance?

Take home messages

  • Root disease is common in pulses and appears to be causing varying levels of yield loss.
  • Five hundred and thirty-three pulse root survey samples were assessed in 2020, building on previous work. Pythium spp., root lesion nematode, Phoma pinodella and Rhizoctonia solani AG8 are common across a range of pulses.
  • Less common but potentially more damaging Aphanomyces and Phytophthora spp. continue to be detected; these are found across Australia but only infrequently at this stage.
  • Partial control of root disease in field trials in 2020 corresponded with yield increases of up to 0.62t/ha. Pulse root diseases are likely to be having significant yield impacts across Australia.

Introduction

Australian growers are increasingly incorporating legumes into rotations for benefits such as nitrogen fixation, broadleaf weed control and disease break effects. More recently, high prices for food legumes such as lentil and faba bean have driven high frequency (e.g., wheat-lentil rotation) pulse cropping. However, despite an eagerness to grow more legumes, growers remain wary, with poor performance and occasional crop failure a concern.

Poor performance of pulses is likely due to multiple factors. Many obvious above-ground issues have been resolved through resistance breeding and the development of insecticide and fungicide strategies and products. However, unexplained poor performance continues to be a frequently reported issue. Increasingly, soil abiotic and biotic constraints are being investigated as the cause of poor performance.

International experience, particularly in North America and Europe, indicates that as pulse cropping frequency increases, soilborne pathogens build up and can cause substantial reductions in yield. Priority targets for international research include Aphanomyces euteiches, Fusarium spp., Phoma pinodella and Phytophthora spp.

This paper summarises the findings of surveys of pulse roots diseases (three years in South Australia (SA) and two years nationally) and preliminary results of yield loss trials conducted in 2020.

Detecting pathogens in pulse roots

Methods

Root samples of poor performing legume crops in SA were sent to SARDI by growers and agronomists. From 2019, the survey was expanded to include AgVic, NSW DPI, DPIRD and USQ to provide national coverage of legume crops. The surveys focused on the roots and lower stems.

In 2020, 533 samples were processed, root health was scored and photographed, then DNA was extracted by the SARDI Molecular Diagnostic Centre. The extracted DNA was tested using a suite of quantitative polymerase chain reaction (qPCR) tests to quantify known pulse pathogens, and by next generation sequencing (NGS) (Illumina® MiSeq®) to identify potentially important pathogens for which SARDI does not have qPCR tests. Three DNA libraries were prepared using primer pairs that target oomycetes (e.g., Aphanomyces, Phytophthora and Pythium spp.) and fungal species (e.g., Fusarium and Sclerotinia). The 2020 samples are currently being sequenced and the results will be reported at a later date.

Results

The survey is providing insight into crop symptoms which were previously unexplained (e.g., poor establishment, reduced vigour or early/uneven senescence (as seen in Figure 1)).

Image of yellowing chickpea crop in the South-East of South Australia in 2017, with poor vigour and patches of premature senescence, which are symptoms of root disease. The roots were assessed as part of the National Pulse Root Disease Survey and contained multiple pathogens, including Phytophthora megasperma, a likely cause of the observed rapid die-back.

Figure 1. Yellowing, poor vigour and patches of premature senescence are symptoms of root disease in this chickpea crop grown in the South-East of SA in 2017. The roots were assessed as part of the National Pulse Root Disease Survey and contained multiple pathogens, including Phytophthora megasperma, a likely cause of the observed rapid die-back.

The most common pathogens detected using qPCR were Pythium spp., Pratylenchus spp. (root lesion nematodes), Rhizoctonia solani AG8, and Phoma pinodella.

Pythium and Pratylenchus spp. are known to have broad host ranges, R. solani AG8 prefers cereals but will infect a broad range of plants. Phoma pinodella along with Didymella pinodes causes blackspot of field pea, but it has a much broader host range.

There were also infrequent detections of Aphanomyces and Phytophthora genera. These genera have been reported to cause severe and widespread yield losses in pulses in Europe and North America.

Aphanomyces euteiches was detected in six faba/broad bean samples from SA and New South Wales (NSW) and one lentil sample from Victoria (Vic); the collecting agronomists reported large yield loss in many of these paddocks.

Phytophthora medicaginis, a known problem in northern NSW, was detected in 26 (25 chickpea, 1 faba bean) samples from northern NSW; P. megasperma was detected in 33 samples (multiple crop types) across Australia, and P. drechsleri (tentative identification), was detected in 14 samples, mostly lupin from Western Australia (WA); this species was also detected in SA, Vic and southern NSW. SARDI is currently undertaking work to confirm the identity of this species.

Bar graph showing frequency of detection over threshold levels of pathogens using qPCR in samples of field pea, chickpea, lentil, faba bean, lupin and vetch, received nationally in 2020.

Figure 2. Frequency of detection over threshold levels of pathogens using qPCR in pulse samples received nationally in 2020.

Next generation sequencing has been a valuable research tool to identify pathogens not covered by existing qPCR tests. Three primer pairs were developed to amplify gene regions selected to identify different pathogen groups.

It was the NGS technology that first identified P. megasperma and P. “drechsleri”. It also detected a range of Aphanomyces and Fusarium species, Sclerotinia trifolorium and Thielaviopsis basicola. Fusarium spp. such as F. avenaceum, while not likely to cause total crop loss, are increasingly being viewed as important internationally due to their ability to affect a wide host range (including cereals) and cause considerable reduction in root mass, and thereby reduce yields under tough conditions.

Confirming pathogenicity of fungal isolates

To confirm the role of specific organisms in causing root disease, fungi and oomycete species were isolated from the diseased pulse samples. An isolate collection of 200+ suspected pathogens have been put in long-term storage for future investigations.

Methods

Preliminary pathogenicity and host range tests have been conducted for Fusarium, Phytophthora and Phoma isolates in replicated controlled growth room bioassays (pot tests). Isolates were evaluated on lentil, faba bean, chickpea, field pea and lupin seedlings grown in sand/vermiculite soil mix inoculated with agar plugs of growing culture. Disease symptoms were evaluated visually after 4-6 weeks growth in controlled environment rooms.

Results

Fusarium avenaceum isolates were highly pathogenic on all crops tested, with just one strain appearing non-pathogenic (Table 1). Infection was characterised by the development of black lesions on the stem base and roots and yellowing and early senescence of above ground plant parts (Figure 3).

First image shows faba bean seedlings grown in a controlled environment without pathogen. Second image shows a seedling exhibiting symptoms after being inoculated with Fusarium avenaceum from faba bean grown in South-East South Australia in 2019. Third image shows the root symptoms of the inoculated seedling

Figure 3. 1) Faba bean seedlings grown in controlled environment without pathogen, 2) Symptoms exhibited by seedling inoculated with Fusarium avenaceum from faba bean grown in South-East SA, 2019. 3) Root symptoms of inoculated seedling.

Fusarium oxysporum and F. redolens isolates’ pathogenicity varied between crops, but all isolates of both species were highly pathogenic on chickpea.

Fusarium tricinctum isolates were highly pathogenic on chickpea and moderately pathogenic on faba bean, lentil and lupin.

P. pinodella isolates were highly pathogenic on chickpea, field pea and lentil, but less so on faba bean and lupin (Table 2).

Table 1. Frequency of detection of Fusarium spp. in 2019 survey samples using next generation sequencing and pathogenicity of representative isolates collected from 2018-2019 crop samples. Pathogenicity on each crop is indicated as ‘-‘ non-pathogenic, ‘+’ weakly pathogenic, ‘++’ moderately pathogenic or ‘+++’ highly pathogenic.

Species

Isolates Collected

Isolates Tested

Chickpea

Field pea

Faba bean

Lupin

Lentil

F. acuminatum

12

5

56%

77%

84%

71%

89%

   

-/+

-/+

-/+

-/+

-/+

F. avenaceum

6

5

6%

31%

63%

29%

27%

   

-/+++

-/+++

+/+++

-/+++

-/+++

F. culmorum

1

1

6%

8%

21%

7%

6%

   

++/+++

+/+++

+/+++

+/+++

-/+

F. equiseti

4

4

48%

69%

72%

55%

49%

   

-/++

-/+

-/++

-/+

-

F. oxysporum

17

14

91%

100%

91%

80%

73%

   

++/+++

-/+

-/+

-/++

-/++

F. redolens

2

2

31%

0%

16%

9%

29%

   

++/+++

-/+

-/++

-/++

-/+

F. solani

4

4

70%

0%

19%

36%

13%

   

-/+

-/+

-/+

-/+

-/+

F. tricinctum

4

4

5%

31%

37%

30%

2%

   

+++

-/+

-/++

+/++

+/++

Table 2. Frequency of detection of Phoma spp. in 2019 survey samples using next generation sequencing and pathogenicity of P. pinodella isolates collected from samples 2018-2019 toward common pulse crops in controlled environment assay. Pathogenicity is indicated as either non-pathogenic ‘-‘ non-pathogenic, ‘+’ weakly pathogenic, ‘++’ moderately pathogenic or ‘+++’ highly pathogenic.

Species

Unique Isolates

Isolates Tested

Chickpea

Field pea

Faba bean

Lupin

Lentil

Phoma/Didymella spp.

20

16

53.13%

100.00%

90.70%

67.86%

75.00%

   

++/+++

++/+++

+/++

-/++

++/+++

Yield effects of pulse root diseases

In 2020, SAGIT project SUA920 investigated yield losses caused by soilborne diseases of pulses using a mixture of fungicides at 20 sites associated with the GRDC investment Southern Pulse Agronomy program.

Methods

At each site, two suitable legume crops were sown with seed and soil fungicides to control multiple fungal/oomycete/nematode targets.

Plant samples (approximately 15 per plot) were visually assessed and DNA tested using the same ‘Pulse Research’ test panel as for the survey. Trials were harvested to determine any yield response.

Preliminary results are presented in this paper, data analysis is progressing. For simplicity, only lentil and faba bean data are presented.

Results

Table 3 summarises the pathogens present at each site. Other pathogens, including Fusarium spp., for which a PREDICTA®B test has not been developed, could not be quantified but are likely to have been present and possibly played a role in disease development and response. Plant samples will be processed through NGS to detect the presence of Fusarium and other species.

Table 3. Initial density of pathogens detected in soil samples from 2020 field sites. Fungi results are reported as pgDNA/g soil. Pratylenchus neglectus and P. thornei are reported as nematodes/g soil.

Site

Rhizoctonia solani AG2.1

Rhizoctonia solani AG8

Phoma pinodella

Macrophomina phaseolina

Pratylenchus neglectus

Pythium clade f

Pythium clade I

Booleroo

21

62

2

3

0

36

0

Eudunda

1

43

279

2

1

3

5

Farrell Flat

248

48

9

15

1

16

2

Hart

0

0

342

1

1

19

5

Pinery

0

101

0

1

3

28

4

Riverton

0

20

186

2

2

28

13

Tarlee

2

141

104

1

1

36

4

Turretfield

36

4

54

75

2

71

1

Warnertown

4

6

89

15

0

46

7

Pt. Broughton

0

0

11

89

1

13

5

Maitland

18

0

3

1

35

21

57

Kimba

8

60

35

10

2

12

5

Stokes

29

49

103

1

2

239

0

Tooligie 1

0

0

167

6

9

17

0

Tooligie 2

56

75

75

12

1

28

2

Wudinna

0

128

150

1

12

10

3

Yeelanna

0

0

84

20

20

50

19

Bool Lagoon

0

0

1775

222

2

271

28

Coomandook

0

10

25

131

7

36

2

Sherwood

29

4

2373

71

0

67

0

These sites were selected without prior knowledge of disease risk and potentially are representative of the pulse producing areas. Bool Lagoon, Sherwood, Riverton, Tarlee, Eudunda, Hart, Maitland, Wudinna, Pinery, Stokes and Tooligie 1 all had relatively high levels of one or more pathogens detected by the existing qPCR tests.

Root disease developed at all sites, however severity varied. For example, at Farrell Flat, mean root disease score in untreated lentil was less than 1. This level of disease is unlikely to affect crop growth or yield. At Maitland and Warnertown root disease scores exceeded 3 (Figure 4). Most sites root disease scores were greater than 2 across a range of crop types.

Mean root disease score (0-5 scale where 0 = no disease and 5 = plant death) of faba bean either untreated or treated with a combination of fungicides/nematicides targeting oomycetes, fungi and nematodes at replicated (n=3) field trials at SA sites in 2020. Approximately 10-15 plants per plot were assessed for each replicate of each treatment.

Figure 4. Mean root disease score (0-5 scale where 0 = no disease and 5 = plant death) of faba bean either untreated or treated with a combination of fungicides/nematicides targeting oomycetes, fungi and nematodes at replicated (n=3) field trials at SA sites in 2020. Approximately 10-15 plants per plot were assessed for each replicate of each treatment.

Full treatment with a combination of pesticides appeared to reduce root disease compared with the untreated control at several sites (Figure 4 and 5). There were noticeable root disease responses in lentil at Yeelanna, Tarlee, Maitland and Tooligie 2, and in faba bean at Tarlee, Sherwood, Bool Lagoon and possibly Warnertown.

Mean root disease score (0-5 scale where 0 = no disease and 5 = plant death) of lentil either untreated or treated with a combination of fungicides/nematicides targeting oomycetes, fungi and nematodes at replicated (n=3) field trials at SA sites in 2020. Approximately 10-15 plants per plot were assessed for each replicate of each treatment.

Figure 5. Mean root disease score (0-5 scale where 0 = no disease and 5 = plant death) of lentil either untreated or treated with a combination of fungicides/nematicides targeting oomycetes, fungi and nematodes at replicated (n=3) field trials at SA sites in 2020. Approximately 10-15 plants per plot were assessed for each replicate of each treatment.

Complete disease control was not achieved at any site, despite the number of products applied in combination at robust rates, indicating the necessary combination of products is currently unavailable. For example, the difference at Sherwood was less than one unit of a 0-5 scale.

Despite only partial disease control, significant yield effects were observed at four of the eight lentil sites and five of the 11 faba bean sites (Tables 4 and 5). The yield responses mostly align with observed reductions in root disease (Figures 4 and 5) and pathogen DNA in roots (data not shown). However, the yield responses to various treatments did not follow the same trend across sites. For example, at Tarlee, the oomycete treatment alone improved yield over the untreated treatment by 0.42t/ha, whereas the addition of other chemistry limited yield response to equal or less than the untreated. Pre-sowing Pythium levels at this site were not particularly high, yet the pathogen levels in the lentil roots sampled during the season were high and clearly reduced by fungicides. The same effect was not evident in the faba bean crop grown alongside. Pythium is known to rapidly increase under favourable conditions.

At Bool Lagoon, the addition of the oomycete treatment alone did not improve yield, even though Pythium levels were high at this site. Addition of fungal and nematode treatments saw a 0.62t/ha yield increase. This site had high P. pinodella and Macrophomina phaseolina levels, and therefore, controlling one pathogen only, in a pathogen complex, may not be sufficient to improve yield.

The addition of some fungicides appeared to reduce yield at some sites. The fungicides may have phytotoxic impacts on pulses and reduce yield when the target pathogen is not present. Indirect effects on Rhizobia may also be important.

Table 4. Mean yields and standard error (SE) of treatments applied to lentil seed and soil at soilborne disease response sites 2020. All treatments are currently unregistered and have been coded: O = treatment selected to control oomycetes (Pythium & Phytophthora), F1 = selected to control Rhizoctonia, Phoma etc.., F2 = selected to control Fusarium, N = selected to control nematodes.

 

Treatment Mean Yield (t/ha)

Site

Nil

O

N

O + F1

O + F1 + N

O + F1 + N + F2

SE

p-value

Yeelanna

4.55

4.12

4.74

4.15

4.61

4.75

0.24

0.035

Tooligie 2

1.39

1.37

1.35

1.44

1.44

1.09

0.11

0.023

Booleroo

1.94

1.75

1.73

1.65

1.92

1.71

0.28

0.146

Farrell Flat

1.99

2.06

1.97

1.78

2.02

1.84

0.11

0.144

Maitland

2.86

2.99

2.94

2.99

3.07

3.00

0.10

0.007

Tarlee

3.11

3.53

3.17

2.82

3.15

2.86

0.21

<0.001

Pinery

2.72

2.83

2.82

2.71

2.73

2.67

0.05

0.062

Warnertown

2.19

2.27

2.17

2.17

2.18

2.19

0.07

0.577

Table 5. Mean yields and standard error (SE) of treatments applied to faba bean seed and soil at soilborne disease response sites 2020. All treatments are currently unregistered and have been coded: O = treatment selected to control oomycetes (Pythium & Phytophthora), F1 = selected to control Rhizoctonia, Phoma etc., F2 = selected to control Fusarium, N = selected to control nematodes.

 

Treatment Mean Yield (t/ha)

Site

Nil

O

N

O + F1

O + F1 + N

O + F1  + N + F2

SE

p-value

Yeelanna

5.36

5.22

5.29

5.55

5.32

5.38

0.08

<0.001

Sherwood

3.36

3.59

3.51

3.63

3.73

3.70

0.14

0.004

Coomandook

3.83

3.66

3.90

3.74

3.97

3.76

0.19

0.477

Bool Lagoon

4.70

4.64

5.10

5.12

5.32

4.98

0.32

0.005

Booleroo

2.59

2.21

2.36

2.32

2.16

2.32

0.32

0.931

Eudunda

3.97

3.89

3.77

3.74

3.62

3.82

0.09

0.058

Farrell Flat

4.86

4.94

5.07

4.83

5.01

4.84

0.10

0.288

Maitland

4.52

4.47

4.63

4.56

4.68

4.85

0.11

0.199

Riverton

4.37

4.48

4.35

4.08

4.51

4.43

0.14

0.015

Tarlee

3.59

3.72

3.56

3.79

3.58

3.68

0.09

<0.001

Warnertown

2.25

2.30

2.36

2.26

2.33

2.26

0.05

0.478

Conclusion

Surveys undertaken by this project show root disease is common in Australian pulse crops. Pathogens are generally present in a pathogen complex. Some pathogens are very common across grain legume regions and crop types i.e., P. pinodella, P. neglectus, Pythium spp., Fusarium spp. and Rhizoctonia solani AG8. It is suspected that these have some effects on yield across many crops.

Yield losses up to 0.6t/ha yield in faba beans at Bool Lagoon, associated with partial control of moderate-high root disease, is an indication that soilborne diseases can be a substantial constraint to pulse yields.

Several pathogens were detected including Aphanomyces euteiches and Phytophthora spp. that caused substantial yield loss in isolated crops. These pathogens are favoured by wet conditions and could cause large losses in above average rainfall seasons.

Preliminary controlled environment studies have confirmed the pathogenicity of Phoma isolates on roots of chickpea, field pea and lentil, with weaker pathogenicity on faba bean and lupin. Fusarium isolates were more variable, with most isolates of F. avenaceum and F. culmorum highly pathogenic on all tested crops but isolates of F. redolens and F. oxysporum showing a preference for chickpea. Isolates of F. solani and F. acuminatum tested so far have been non-pathogenic or only weakly pathogenic. Several individual isolates appear highly pathogenic on at least one crop and likely caused the poor performance of the original crop from which they were obtained. Future studies will endeavour to prioritise pathogens that have the greatest impact on yield and seek to develop control strategies.

Acknowledgements

The research undertaken as part of this project is made possible by the significant contributions of growers through both trial cooperation and the support of the GRDC, the author would like to thank them for their continued support.

We thank collaborators from DPIRD, AgVic, NSW DPI and USQ for their assistance with the national pulse survey. We also thanks staff in SARDI regional offices in Clare, Port Lincoln, Minnipa and Struan for their assistance in sowing the pulse root disease yield response trials, particularly Penny Roberts and Sarah Day of SARDI Clare for their contribution and collaboration.

Contact details

Blake Gontar
blake.gontar@sa.gov.au

GRDC Project Code: DJP1907-002RMX,