National survey unmasks root disease culprits in pulse crops

New knowledge of soil-borne pulse pathogens surfaces from nationwide study

Legumes & Pulses
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Scientists identify mystery soil pathogen at the root of SA chickpea crop failures.

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South Australian Research and Development Institute (SARDI) research scientist Dr Tara Garrard examines the soil-borne pathogens that cause root diseases in pulse crops as part of a national survey. PHOTO SARDI

South Australian Research and Development Institute (SARDI) research scientist Dr Tara Garrard examines the soil-borne pathogens that cause root diseases in pulse crops as part of a national survey. PHOTO SARDI

New knowledge of the soil-borne pathogens that cause root diseases in pulse crops has started to emerge from a national survey of the southern, western and northern growing regions.

Research leader, Dr Tara Garrard from South Australian Research and Development Institute (SARDI) says the study aims to overcome a knowledge gap in pulse root diseases facing Australian growers.

"We know quite a lot about foliar diseases in pulses, but much less is known about root diseases," Dr Garrard says.

In an effort to better understand the losses that stem from pulse root diseases, the SARDI research team is collaborating with pathologists, growers and agronomists across the country.

Dr Garrard says the national survey, with GRDC investment from 2019 to 2021, originated from another survey limited to south-eastern South Australia, with investment from the SA Grain Industry Trust (SAGIT).

The initial SA survey analysing diseased root samples collected by growers and agronomists from underperforming crops was prompted by reports of chickpea and faba bean crop failures in the state's high-rainfall zone (HRZ).

Dr Garrard says early findings of this work piqued widespread industry interest that saw the scope of the study expanded to include Victoria, Western Australia, New South Wales and Queensland, as well as SA.

Now the SAGIT-funded survey from 2018 to 2020 is running in parallel with, and contributing to, the national GRDC-invested study.

Both the SA and national surveys aim to unmask a range of root disease-causing pathogens with the potential to limit pulse crop performance.

Crops being studied are chickpeas, lentils, faba beans, field peas, lupins, canola, vetch, clover and lucerne.

PATHOGEN TESTING

Dr Alan McKay points out infection from pulse root diseases as part of a 'root health workshop' at Blyth, South Australia, in 2019. PHOTO Blake Gontar, SARDI

Dr Alan McKay points out infection from pulse root diseases as part of a 'root health workshop' at Blyth, South Australia, in 2019. PHOTO Blake Gontar, SARDI

As part of this effort, the SARDI pathology team used "specific DNA tests and sequencing-based methods to help identify pathogens that are difficult to isolate from diseased root samples".

The diseased samples examined were mostly received from SA, Victoria, southern NSW and WA. Drought conditions restricted sampling in northern NSW and Queensland in 2019.

"We initially used 12 existing tests for specific pathogens, but as the DNA sequencing data increased, we found other unexpected pathogens so we started routinely running 24 tests," Dr Garrard says.

Most of these were drawn from the existing suite of PREDICTA®B DNA-based soil tests.

"The DNA sequencing data is revealing many pathogens that might be impacting pulse crop performance.

"And to help identify them, we have been guided by international experience, particularly in Canada and France, where pulse root disease research is relatively advanced."

She says the research team aims to 'isolate' or pinpoint particular pathogen species in situations where they discover the DNA sequences associated with pathogens known to be causing pulse crop losses overseas.

In this discovery process, SARDI scientists have been using next-generation sequencing (NGS) technology as a 'research tool'.

The NGS technology was able to detect the DNA sequences of soil-borne pathogens, which could not be identified with existing PREDICTA®B tests. New tests are being designed based on those sequences.

DNA CLUES

A faba bean seedling showing root disease damage from a Fusarium pathogen species. PHOTO Blake Gontar, SARDI

A faba bean seedling showing root disease damage from a Fusarium pathogen species. PHOTO Blake Gontar, SARDI

Dr Garrard says clues from the sequencing data enabled researchers to identify the mystery pathogen that caused the SA chickpea crop failures.

The SARDI pathology team initially thought the culprit might be a particular species of water mould, called Phytophthora medicaginis.

But existing species-specific PREDICTA®B tests were able to eliminate this pathogen as a suspect, and a genus-specific enzyme-linked immunosorbent assay (ELISA) confirmed the presence of another unknown pathogen from the Phytophthora genus.

DNA sequences from the elusive pathogen detected with NGS technology were then used to pinpoint another water mould species: Phytophthora megasperma.

Its signature DNA sequence was also used as the basis for generating a new test for this species as part of a GRDC-SARDI Bilateral project.

"Isolating this pathogen has proved difficult," Dr Garrard says, adding that they can now run the new test on all root samples contributed to the national survey.

She says the research team also suspects some Fusarium and Phoma pathogen species, for which there are currently no specific tests, could be economically important in terms of the crop losses they might be causing.

"As the evidence increases for which species are economically important, further tests may be developed," she says.

NATIONAL TRENDS 

A SARDI controlled environment test showing a healthy lentil plant without root disease (centre), compared with plants infected with a Fusarium pathogen species (left) and the Phoma pinodella pathogen (right). PHOTO Blake Gontar, SARDI

A SARDI controlled environment test showing a healthy lentil plant without root disease (centre), compared with plants infected with a Fusarium pathogen species (left) and the Phoma pinodella pathogen (right). PHOTO Blake Gontar, SARDI

Leading SARDI's soil biology and molecular diagnostics group, Dr Alan McKay explores the 'national trends' in pulse root pathogens that have surfaced from early findings of the study to date.

Dr McKay says the preliminary findings indicate Phoma species of soil-borne fungi are common in Australian pulse crops.

The SARDI team found that one fungus species, Phoma pinodella, was present in most of the pulse crops sampled across SA, Victoria, southern NSW and WA.

Providing a snapshot of its prevalence, the survey in south-eastern SA showed P. pinodella was the most prevalent root pathogen identified from 100 samples of low-performing crops.

For instance, researchers detected P. pinodella on all lentil and field pea samples, and almost 90 per cent of chickpea and faba bean samples.

"P. pinodella is known to infect a wide range of grain crops and causes foot rot in field peas and subclover, but its economic importance as a root pathogen on pulse crops, particularly in terms of yield impacts, is unknown," Dr McKay says.

"While further research is required, we have seen it cause lesions on primary roots, so it could be causing losses in pulse crops and may be more significant than previously thought."

Preliminary results from the national survey also showed Rhizoctonia solani AG8 was a prevalent root pathogen in the pulse crops sampled across the country, he says.

In the SA survey, this Rhizoctonia species, which causes bare patch in cereals, was detected on all lupin samples, half the lentil samples and about one-third of chickpea and faba bean samples.

"The high incidence of Rhizoctonia solani AG8 was not totally unexpected, even though cereals are its preferred hosts," Dr McKay says.

"It can also infect pulse roots, but its yield impact on pulse crops is not yet known."

Pythium species of soil-borne pathogens (water moulds or oomycetes) and root lesion nematode species, such as Pratylenchus neglectus, appeared to be common across the country in high, medium and low-rainfall zones.

"However, Rhizoctonia and Fusarium species might mainly occur in low and medium-rainfall areas," he says.

REGIONAL PATTERNS

SARDI's Blake Gontar will replace Tara Garrard as the leader and primary contact for the research project unmasking pulse root pathogens. PHOTO SARDI

SARDI's Blake Gontar will replace Tara Garrard as the leader and primary contact for the research project unmasking pulse root pathogens. PHOTO SARDI

Dr McKay says the national study could also help gauge patterns of root disease, which, at this stage, appear to be regionally specific.

For example, early findings of the research showed Sclerotinia infection may be more prevalent on the roots of pulse and canola crops grown in southern NSW, compared with those grown in SA, Victoria and WA.

Another preliminary finding of the 2019 survey was that two water mould species, Aphanomyces euteiches and Aphanomyces trifolii, may be linked to high rainfall regions in SA.

However, further analysis is needed to clarify the findings to date since one year of national data is not enough to define the distribution of pathogens, he says.

Dr McKay urges growers and agronomists to contribute samples collected from pulse crops to the survey being repeated this season.

"We can provide kits to ensure the samples arrive in good condition," he says.

In 2020, Blake Gontar from SARDI, a division of Primary Industries and Regions South Australia (PIRSA), will replace Dr Garrard as the leader and primary contact for the research project.

For sampling kits, contact:

SA - Blake Gontar, blake.gontar@sa.gov.au; WA - Carla Wilkinson, Carla.wilkinson@dpird.wa.gov.au; Victoria - Josh Fanning, Joshua.fanning@agriculture.vic.gov.au; southern NSW - Kurt Lindbeck, kurt.lindbeck@dpi.nsw.gov.au; northern NSW - Sean Bithell, sean.bithell@dpi.nsw.gov.au; Queensland - Kirsty Owen, kirsty.owen@usq.edu.au

GRDC Research Codes DAS1907-001BLX, DAS1802-011BLX, DAS1707-006BLX,DJP1907-002RMX

More information: Dr Tara Garrard, 08 8429 2247, Tara.garrard@sa.gov.au; Dr Alan McKay, 08 8429 2216,alan.mckay@sa.gov.au; Blake Gontar, 0430 597 811, blake.gontar@sa.gov.au

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