Protecting WA crops

Impacts of mechanical soil amelioration on weeds, soilborne nematode pests and fungal pathogens

Dr Sarah Collins inspecting plants visibly impacted by plant parasitic nematodes and rhizoctonia bare patch at Yerecoin site
Dr Sarah Collins (DPIRD) inspecting plants visibly impacted by plant parasitic nematodes and rhizoctonia bare patch at Yerecoin trial site. Photo courtesy of: Dr Sarah Collins (DPIRD).

Growers in Western Australia (WA) have widely adopted both mechanical soil amelioration and liming to manage sub-soil constraints like acidity, compaction, water repellence and herbicide-resistant weeds. 

Common mechanical soil amelioration techniques include soil mixing (e.g. ripping and spading), soil inversion (e.g. mouldboarding or one-way plough) and deep ripping. These techniques create a changed soil profile as a result of soil mixing. These techniques also mix and redistribute the living components of soil, but little is known about the changes in diversity, distribution and long-term survival of the soil's biology including soilborne pathogens, nematodes and weed seeds that occur after mechanical deep soil amelioration. 

Physical soil constraints are found in most soils in the WA grainbelt:

  • Soil acidity affects 75% of topsoils and 45% of subsurface layers.
  • Water repellence affects 30% of soils, and
  • Soil compaction affects 75% of soils.

From scientific research by the Department of Primary Industries and Regional Development (DPIRD) and others, we know that these soil constraints can be successfully alleviated by major soil disturbance techniques that incorporate lime, bury repellent soils or physically disrupt compacted layers of soil.

Soilborne pathogens and plant parasitic nematodes are major constraints to WA grain production. As growers increasingly employ mechanical soil amelioration, it is vital to understand what is likely to happen to the soils biology in the process to make the most of potential soil profile changes. DPIRD research aims to identify the deep tillage techniques that best alleviate common soilborne disease or plant parasitic nematode issues in soil types typical for WA’s central growing region.

Mechanical deep soil amelioration can significantly affect weeds though physical movement of the weed seed bank, altered soil conditions affecting weed and crop emergence times, growth, and response to pre-seeding herbicides, and altered weed-crop competitive interaction during the growing season. DPIRD research is investigating how mechanical soil amelioration impacts weeds and weed seed longevity.

This issue of Protecting WA Crops will address the impacts of mechanical soil amelioration on weed ecology, soilborne nematode pests (root lesion and cereal cyst nematodes) and Rhizoctonia solani (AG8), the soilborne fungal pathogen that causes rhizoctonia bare patch. The impact of adding ameliorants such as lime on these biological constraints to maximising crop productivity will be outlined in another issue.

How does mechanical soil amelioration impact nematode pests in susceptible cereal crops? 

At a glance

Soil amelioration is a costly process, and the Australian grains industry will benefit from a better understanding of the effect of deep soil amelioration on soilborne diseases, parasitic nematodes and soil health.

DPIRD research scientists Sarah Collins, Daniel Huberli and Carla Wilkinson are exploring whether soil amelioration can alleviate our major soilborne diseases and nematode pest constraints and improve soil health. This has not been studied before.

This project compares the prevalence and distribution of soil biological communities, soilborne pathogen and nematode pests in the seasons following three mechanical amelioration treatments with a non-ameliorated control. 

Establishing a soil amelioration experiment is time consuming and costly. To increase the information gathered from field sites, treatments were evaluated for their impacts on weeds in addition to soil biological activity, soilborne pathogen and nematode pests. The results for weeds is discussed later in this issue and the biological activity studies will be reported in future.

Field experiments were established at Yerecoin and Darkan in WA prior to the 2019 cropping season. Barley and wheat varieties suited to the central cropping region were then sown for the 2019 and 2020 season; 90kg/ha of barley (cv. La Trobe) in 2019, and 90kg/ha of wheat (cv. Ninja) in 2020.

The soil type at the Yerecoin site was a deep yellow earth, and at the Darkan site it was a very dark brown humic loamy sand with medium water repellence and up to 40% gravel throughout the profile.

Figure 1. From left to right: Nil; Deep mix – 4m wide rotary spader; Deep rip – 2m wide Agroplow deep ripper; Inversion – 3 furrow Kverneland mouldboard plough.
Figure 1. From left to right: Nil; Deep mix – 4m wide rotary spader; Deep rip – 2m wide Agroplow deep ripper; Inversion – 3 furrow Kverneland mouldboard plough (©DPIRD 2021).

The soil amelioration techniques used at the trial sites included: 

  • deep ripping (using an Agroplow)
  • deep mixing (using an Imants rotary spader)
  • soil inversion (using a 3-furrow Kverneland mouldboard plough), and
  • a control (no tillage) (Figure 1).

At the beginning of 2019, and at the end of each cropping season, soil samples were taken at the trial sites at depths of 0-10, 10-20, 20-30 and 30-40cm. The DNA levels of the major nematode pests and soilborne pathogens present at each site were also measured.

Soil sampling at Yerecoin trial site (Photo courtesy: Dr Sarah Collins, DPIRD).
Soil sampling to 40 cm depths at Yerecoin trial site. Photo courtesy of: Dr Sarah Collins (DPIRD).

Deep soil amelioration resulted in improved crop performance

Soil amelioration affected crop establishment, with deep mixing and soil inversion resulting in fewer crop plants per m2 in both years than the control for both sites (Table 1). Conversely, barley (2019) and wheat (2020) grain yield (t/ha) and protein (%) were increased after soil inversion in both years at both sites (Table 1). 

Soil inversion was the most effective amelioration treatment to improve crop performance at both sites in the two 'transition' seasons, directly following amelioration, even though the sites have different soil types, constraints, and environmental conditions.    

Table 1. Effect of mechanical soil amelioration on crop establishment, yield and grain protein at Darkan and Yerecoin sites for La Trobe barley (2019) and Ninja wheat (2020). Letters indicate significantly different means when compared within a year (P<0.05), with treatments significantly different when they share no common letters.









Plant establishment (plants/m2











Grain Yield  











Grain protein  












Plant establishment (plants/m2











Grain Yield  











Grain protein  











Deep soil amelioration resulted in changes in soil biology in a changed soil profile

The degree of change in nematode pests and R. solani varied with the type of mechanical amelioration treatment (Table 2). The longevity of changes in R. solani and nematode pest levels over the two seasons was dependant on site. In these trials, the nematodes moved back into the topsoil in the sandy soils at Yerecoin more rapidly than in the gravelly Darkan soils, indicating that renovation may have a longer impact on RLN in gravelly soils than in sandy soils.  

R. solani, CCN, and both species of RLN nematode pests investigated survived and persisted at depth. Previous studies have shown that Pratylenchus thornei, a species of root lesion nematode, can thrive in soils to a depth of 0.6m but this is the first record of the three pathogens investigated here persisting and multiplying at depth in WA soils. It is also the first time that our investigation has included assessment of the impact of mechanical renovation on the soil biological community. Continued research is required to improve our understanding of the mechanisms at play.  

Overall soil amelioration reduced R. solani inoculum and nematode pests in the topsoil (0-10 cm) but increased them at 10-40 cm depth in both years and sites (data not shown). The redistribution of R. solani and nematode pests differed by the type of amelioration, with the magnitude increasing with tillage intensity in the order: deep ripping then soil mixing then soil inversion.  

Soil inversion buried the R. solani and nematode laden topsoil and brought up pathogen/pest-free subsoil to the surface at both sites. The new topsoil remained significantly lower in R. solani than the control over the two years at the Darkan and Yerecoin sites.

Rotary spading mixes soil within the implement's working depth, although the different layers may to some extent remain segregated throughout the profile. The resulting heterogeneity can be observed as patches of high organic matter content in the topsoil in a pattern that corresponds to each 'spade' action. Soil mixing (rotary spading) resulted in decreased R. solani inoculum levels in the topsoil and increasing levels at depth. Nematode pests reacted in the same way as soil mixing at Yerecoin, but the effects were less apparent at Darkan. 

Deep ripping mechanically breaks up compacted soil layers, with minimal soil mixing or soil translocation. Deep ripping redistributed both R. solani and nematode pests in the soil profile the least, due to limited soil movement by the technique. The effects of deep ripping on R. solani levels were no longer evident two years after amelioration. However, inoculum introduced at depth sometimes persisted over the two years.  

Table 2: Nematode pests and soilborne pathogen inoculum densities in the topsoil (0-10cm) measured at Darkan and Yerecoin using PREDICTA®B and their associated wheat yield loss risk categories over two seasons, post amelioration. Green, orange and red colours represent low, medium and high risk for yield loss. Note: *end DNA densities may have been impacted by delayed transit due to COVID-19 related travel restrictions
Treatment Nematodes and pathogen tested Darkan Yerecoin
2019 2020 2019 2020
Soil Inversion Pratylenchus quasitereoides  8.7 4.4    
Pratylenchus neglectus  4.0 4.0 3.1 10.9
Rhizoctonia solani (AG8) 2.2 1.4 1.7 1.7
Heterodera avenae     1.2 1.6
Soil Mixing Pratylenchus quasitereoides  14.5 10.0    
Pratylenchus neglectus  3.9 6.6 4.0 15.5
Rhizoctonia solani (AG8) 2.5 2.3 2.0 2.1
Heterodera avenae     1.3 3.3
Deep Ripping Pratylenchus quasitereoides  20.2 13.0    
Pratylenchus neglectus  10.6 12.3 8.2 12.2
Rhizoctonia solani (AG8) 2.7 2.4 2.3 2.5
Heterodera avenae     1.3 7.4
nil Pratylenchus quasitereoides  18.3 9.4    
Pratylenchus neglectus  11.2 13.4 8.3 11.0
Rhizoctonia solani (AG8) 2.7 2.3 2.5 2.3
Heterodera avenae     1.3 5.8

Impact of mechanical soil amelioration on weed management

In a DPIRD project, conducted in collaboration with other DPIRD, GRDC and SoilsWest Alliance soil/disease projects, research scientists Sultan Mia and Catherine Borger are investigating how soil amelioration changes the weed population, including the weed seed bank, emergence times, weed response to pre-emergent herbicides, and weed-crop competition.

These research findings will benefit growers by maximising the benefits of amelioration as a weed control technique. Potential weed management opportunities include:

  • burying the existing weed seed bank
  • simulating germination of weeds for future control, and/or
  • acting as a ‘knockdown’ nonselective weed control technique (depending on the method of soil incorporation).

Understanding optimal rotation choice following soil renovation will enable best practice for long term weed control and a fuller understanding of changes in crop-weed competition following the removal of soil constraints.

How does soil amelioration affect weed dynamics and weed seed burial?

At a glance

DPIRD Research Scientist, Sultan Mia, outlines setting up the screen house experiment.
DPIRD Research Scientist, Sultan Mia, outlines setting up the screen house experiment (©DPIRD 2021).

The sites at Yerecoin and Darkan, described above, were used for this experiment. At both sites, weed density was assessed approximately six weeks after sowing. At maturity, weed heads from two similar quadrats per plot were assessed.  Additionally, 20 random mature weed heads were collected from each plot. Seeds were separated from the heads and the number of seeds counted to determine weed seed production/m2

Annual ryegrass and great brome were the most prevalent weeds, with capeweed, clover and Afghan melon present in low numbers. Soil amelioration affected weed density in 2019 and 2020 (Table 3). 

At Yerecoin, a full soil inversion reduced weed emergence for the two years, with early season weed numbers reduced by up to 90-100%, compared with the control. Grass seed head numbers in soil inversion plots were 5 and 10 heads/m2 in 2019 and 2020, compared to 113 and 202 heads/m2 in the control plots. At Darkan, effective weed control was also observed in the soil inversion treatment, with 3 plants/m2 in both years, and 4-7 seed heads/m2 (Table 3). 

Deep ripping at Yerecoin had nearly four times greater weed density than deep mixing and the highest number of seed heads (163/m2 in 2019 and 324/m2 in 2020) in both years. Deep ripping at Darkan had greater weed density than other treatments in 2019. 

Soil inversion effectively reduced weed density at both trial sites. Deep ripping in Yerecoin stimulated weed emergence in the year after amelioration.

Table 3. Effect of soil amelioration on weed density and subsequent seed head production at Yerecoin and Darkan, WA, in 2019 and 2020. Letters indicate where means are significantly different (P<0.05).



Grass weed density (plants/m2) 

Grass weed head (number/m2) 







88 bc 

115 bc 

113 b 

202 b 

Deep ripping 

120 c 

207 c 

163 c 

324 c 

Deep mixing 

32 ab 

57 b 

97 b 

100 ab 

Soil inversion 


12 a 


10 a 



32 b 

26 bc 

20 b 

68 b 

Deep ripping 

42 c 

20 b 

23 b 

87 bc 

Deep mixing 

27 b 

33 c 

21 b 

105 c 

Soil inversion 





Results from these trials suggest that a full soil inversion provides long-term weed control. This is mainly achieved due to burial of the weed seeds to a depth that prevents successful emergence by the mouldboard. However, other soil renovation techniques may stimulate weed growth in the short term. Growers should plan an adequate weed management program, such as delayed sowing with use of a non-selective herbicide to control early weed cohorts. 

Emergence pattern of the weeds in the screen house  

An additional experiment was conducted in a screen house at Northam. 

Soil samples were collected from the field plots at both sites using a soil corer. Samples were collected at various depths (0-10, 10-20, 20-30 and 30-40cm) from Yerecoin and Darkan trial sites, put in trays and irrigated. Weed emergence was monitored for a year. 

Annual ryegrass and great brome had the highest emergence at Yerecoin and Darkan sites. 

In the control plots (no tillage system) at Darkan and Yerecoin, most weed seeds remained at the surface (0-10cm), although a few annual ryegrass emerged from soil collected at a depth of 10-20cm at Yerecoin (Figure 2A). 

Following deep mixing, emergence was observed in soil from all four depths (0-10, 10-20, 20-30, and 30-40cm), which indicates that weed seeds were distributed throughout the soil profile. The emergence pattern in the deep ripped sample trays was variable and the soil inversion treatment placed most seed at 10-20cm. (Figure 2A and 2B). 

Cumulative emergence of weeds from soil samples collected at Yerecoin site
Figure 2A.  Cumulative emergence of weeds from soil samples collected from increasing depths (0-40 cm) in each amelioration treatment at Yerecoin. 
Cumulative emergence of weeds from soil samples collected from increasing depths (0-40cm) in each amelioration treatment at Darkan. 
Figure 2B.  Cumulative emergence of weeds from soil samples collected from increasing depths (0-40cm) in each amelioration treatment at Darkan. 

Weed seed burial beyond the top 10cm is generally sufficient to prevent seeds from successfully emerging. A risk of seed burial is that it may induce dormancy, resulting in these seeds lasting longer in the seed bank. Seeds buried in the upper 0-10cm of soil might be returned to the soil surface in subsequent crop sowing events. Even deeply buried but viable seed (that have not degraded) can become a problem if they are returned to the surface following subsequent amelioration events.   

Soil inversion provides effective weed control by burying weed seeds, mostly in the middle layers of the ploughing depth, whereas deep ripping, and deep mixing, in some cases, stimulate weed emergence and seed head production. Deep mixing also distributes weed seeds throughout the soil profile. 

Emergence pattern of weeds after long-term seed burial using soil inversion (mouldboard plough) - 30 sites across the WA grainbelt investigated

At a glance

Soil inversion can bury 100% of weed seed. It can also transfer buried weed seeds back to the soil surface if practised on previously renovated soil.

The time taken for weed seeds to degrade following burial by inversion needs further investigation.

As a rule of thumb, growers are advised to leave seeds at depth for at least 10 years. However, some studies have indicated that seeds buried at depth may retain viability for as long as 120 years.

Because it is necessary to occasionally practice strategic tillage, even in conservation farming systems, we need to understand the seed degradation process, to be ready for potential weed problems if viable seeds are returned to the surface after previous soil inversion. 

DPIRD’s Sultan Mia, Catherine Borger and Gaus Azam have sampled sites that have previously been mouldboarded to determine weed seed viability following burial.

Thirty mouldboarded sites were identified throughout WA. Soil samples were collected from each site at four depths (0-10, 10-20, 20-30, and 30-40cm).

The sites ranged from Geraldton in the northern region to Esperance in the southern region. The time of soil inversion varied, with sites ameliorated between 2009 to 2020, and categorised as short (1-5 years), medium (5-10 years) and long (>10 years) based on the duration since soil inversion. Depth of inversion ranged from 10 to 38cm. Sites with sandy soils had deeper inversion depths (≥30n cm), whereas sites with heavy or gravel soils had shallower inversion. Ryegrass, bromegrass, wild radish, and capeweed were the major weeds onsite at the time of soil sampling. 

DPIRD Research Scientists Gaus Azam and Catherine Borger inspect a soil profile.
DPIRD Research Scientists Gaus Azam and Catherine Borger inspect a soil profile (© DPIRD 2021).

Emergence trays were set up in the screen house to monitor emergence. 

A total of 296 weed seedlings, of 16 species, covering both winter and summer weeds, emerged from the trays of the collected soil samples (Table 4). Among them, annual ryegrass, subterranean clover, wireweed, crumb weed, capeweed and bromegrass were the most common .

Table 4. Cumulative emergence of different weed species.

Serial no.

Common name 

Scientific name 

Cumulative emergence


Annual ryegrass 

Lolium rigidum  



Subterranean clover 

Trifolium subterraneum 




Polygonum aviculare  



Crumb weed 

Dysphania pumilio  




Arctotheca calendula  



Brome grass 

Bromus diandrus  



Stink grass 

Eragrostis cilianensis  



Summer grass 

Digitaria ciliaris 



Afgan melon 

Citrullus lanatus  




Digitaria sanguinalis 




Crassula sieberiana 




Erodium cicutarium 



Solanum sp 

Solanum nigrum 




Hordeum leporinum  




Tribulus terrestris 




Salvia reflexa 




Ornithopus spp. 




The emergence pattern of the six major weeds at different depths was also investigated. In the case of annual ryegrass and capeweed, more of these weeds emerged from 0-10cm depth, while more bromegrass and crumb weed emerged from 10-20cm depth (Figure 3). 

Figure 4. Depth-wise emergence distribution of the six major weeds, cumulative emergence.
Figure 3. Depth-wise emergence distribution of the six major weeds, cumulative emergence.  

Further analysis was conducted to determine seed degradation process by looking at time since burial, and viable seed number/m3 soil at 10-20cm, the depth where most of the seeds are buried after mould boarding. Seed viability reduced drastically when seeds were buried for longer periods. However, a portion of the seedbank remained viable even after 10 years of burial (Figure 4).  Another round of soil renovation can bring these viable seeds to a depth that induces germination and emergence. Growers should therefore consider best practices of IWM in reintroducing deep tillages following soil inversion.

Figure 5. Relationship of seed viability and duration of burial following soil inversion
Figure 4. Relationship of seed viability and duration of burial following soil inversion

Continued research is required to improve our understanding of the biological mechanisms at play following changes to soil profiles with mechanical deep soil amelioration.

This is the first time that the impact of mechanical soil amelioration on weeds, plant parasitic nematodes, soilborne diseases and other soil biology has been conducted in WA, and the results have implications for growers across our grainbelt. This research commenced in the ‘transition phase’ directly following the amelioration practices. This is the period of flux when the newly created soil profile is expected to go through the greatest physical and chemical changes. We know much less about the soil biological changes in the soil profile, so this research has been extended to include the 2021 season and potentially beyond.

A result common to both Yerecoin and Darkan sites was the ability of the soilborne pathogen (R. solani) and plant parasitic nematodes (P. neglectus, P. quasitereoides and Heterodera avenae) to survive when moved to greater depths in the profile than they naturally inhabit. The results also suggest that R. solani and the nematode pests impact roots systems at these depths.

It is clear that at these central grainbelt sites, soil inversion improved grain yield, with lower weed densities and soilborne disease constraints. Mixing and deep ripping soils had fewer positive impacts.

The relationship of weeds as hosts for soilborne nematodes and pathogens requires attention, particularly as weeds are often prolific in paddocks with soilborne disease and nematode pest constraints. 

More information

For more information, refer to:

Murphy D, Hoyle F, Collins S, Huberli D, and Geelson D (2021) Soil Biology. Soil Quality EBook. Soils West. Download from Apple Books.

Collins S, Mwenda G, Wilkinson C, Hüberli D,  Kelly S, Reynolds C, Kupsch M, Wickramarachchi K, Hunter H, Zaicou-Kunesch C, van Burgel A, Linsell K, and Davies S (2021) Soil amelioration alters soil biology, soilborne disease and nematode pests of cereal crops. What are the implications? In: 2021 Grains Research Updates, 22 - 23 February, Perth, Western Australia.

Mia S, Azam G, Borger G (2021) Weed management and control under different soil amelioration practices. In: 2021 Grains Research Updates, 22 - 23 February, Perth, Western Australia.


This work was a collaboration between the DPIRD soils, disease and weed science teams, including Dr Steve Davies, Dr Gaus Azam, Dr George Mwenda, Dr Sarah Collins, Dr Daniel Huberli, Dr Sultan Mia and Dr Catherine Borger. External collaborators include Professor Hugh Beckie (AHRI, UWA) and SoilsWest Alliance. Funding was provided by Royalties For Regions WA: Impact of soil amelioration on weed ecology and control (SPP-SP01) and Dynamic changes in the biological, physical and chemical characteristics of soils after amelioration that affect soilborne pathogens (SPP-SP03) and GRDC funded project Increasing farming system profitability and longevity of benefits following soil amelioration (DAW1901-006RTX).