The present protocol describes a reliable and straightforward method for culturing, collecting, and screening Ditylenchus dipsaci.
Plant-parasitic nematodes (PPNs) destroy over 12% of global food crops every year, which equates to roughly 157 billion dollars (USD) lost annually. With a growing global population and limited arable land, controlling PPN infestation is critical for food production. Compounding the challenge of maximizing crop yields are the mounting restrictions on effective pesticides because of a lack of nematode selectivity. Hence, developing new and safe chemical nematicides is vital to food security. In this protocol, the culture and collection of the PPN species Ditylenchus dipsaci are demonstrated. D. dipsaci is both economically damaging and relatively resistant to most modern nematicides. The current work also explains how to use these nematodes in screens for novel small molecule nematicides and reports on data collection and analysis methodologies. The demonstrated pipeline affords a throughput of thousands of compounds per week and can be easily adapted for use with other PPN species such as Pratylenchus penetrans. The techniques described herein can be used to discover new nematicides, which may, in turn, be further developed into highly selective commercial products that safely combat PPNs to help feed an increasingly hungry world.
Plant-parasitic nematodes (PPNs) are estimated to be responsible for the loss of 12.3% of global food production and cause an estimated 157 billion dollars in damage annually1,2,3. Unfortunately, the ability to control PPNs is waning because effective chemical nematicides have been banned or are facing escalating restrictions because of human safety and environmental concerns. This is primarily due to the poor nematode selectivity of previous generations of pesticides4. Over the last 25 years, six new chemical nematicides have been piloted or introduced into the market5. One of these has already been banned in Europe, and another has been discontinued while being investigated for its impact on human heatlh6,7. Hence, there is a pressing need for new nematicides that are highly selective for PPNs.
The stem and bulb nematode, Ditylenchus dipsaci (D. dipsaci) is an economically impactful PPN4. D. dipsaci infects nearly 500 plant species across 30 biological races and targets some of the most agriculturally important crops such rye, oats, garlic, onion, and leek8,9. For example, D. dipsaci has recently scourged garlic fields in Ontario and Quebec, resulting in losses of up to 90%10,11. Its geographical distribution is nearly ubiquitous and includes the Americas (including California and Florida), Europe, much of Asia (including China), and Oceania9. D. dipsaci is a migratory endoparasite that enters the stomata on leaves or wounds and lenticels where they release enzymes to break down the cell wall12. Compounding the impact of D. dipsaci on crops, the damage caused by the PPN makes the plant susceptible to secondary infection11. Unfortunately, D. dipsaci shows high tolerance levels to current nematicides compared to other nematode strains13,14.
This protocol describes the culturing of D. dipsaci, and its use in large-scale screens for small molecule candidate nematicides. Briefly, D. dipsaci populations are maintained and expanded on pea plants cultured in sterile Gamborg B-5 (GA) media15. Before growing seed sprouts on GA medium, the seeds must be sterilized through a series of washes and plated on nutrient agar (NA) to check for contamination. Seed sterilization is essential to detect bacterial and fungal contaminants that may be present. The non-contaminated seeds are then transferred to GA plates, where seed sprouts will grow in preparation for infection. The GA plates containing seed sprouts are infected with nematodes from a previous culture plate by transferring a piece of agar containing root tissue to the fresh plates. After 6-8 weeks, the nematodes are extracted from the GA media and are filtered through a coffee filter-lined funnel into a collection beaker. The nematodes can be used in various bioassays once a suitable number has been collected. The technique described in this protocol generates approximately 15,000 D. dipsaci per culture plate. Alternative protocols to cultivate D. dipsaci have been published16,17.
An in vitro small molecule screening assay based on previous work18 is also described here. As a proxy of worm health, the mobility of 20 nematodes per well is examined after 5 days of small molecule exposure. To better visualize worm mobility, NaOH is added to increase the movement of live worms19,20. This protocol allows medium-throughput screening and provides valuable data to assess the nematicidal potential of small molecules. If a different nematode collection technique is used16,17, the small molecule screening methodology described herein can nevertheless be implemented.
The D. dipsaci strain G-137 used for the present work was collected from Fish Lake 4 Variety garlic in Prince Edward County and was provided by Agriculture and Agri-food Canada. If starting a fresh culture, consult Poirier et al. for inoculation methodology15.
1. Culturing of D. dipsaci
2. Extraction and collection of D. dipsaci
3. In vitro small molecule screen
4. Data collection and analysis
Independent replicates reveal reproducible hits
To illustrate the expected variation between the replicate screens, the means and variation in sample mobility are plotted from three representative plates from a recent screen (Figure 1). Three replicates of the screen were performed on three different days. All three plates have negative (solvent-only) controls (darker bars), and samples within the set contained established nematicides. The remaining compounds are from a custom library currently being characterized in the Roy lab. Compared to similar screens done with C. elegans with the same molecules (SC, JK, PJR, unpublished results), the hit rate with D. dipsaci is significantly lower, and many drug plates exhibit no activity (Figure 1A). Some plates have fully reproducible hits (Figure 1B,C), while others vary in activity (Figure 1C). Relative to other species screened (not shown), D. dipsaci shows less variability in its response to compounds. Regardless, replicates are considered necessary in the identification of reproducible hits.
Nematicides vary in their ability to immobilize Ditylenchus dipsaci
Of the seven characterized nematicides tested against D. dipsaci, only Fluopyram exhibits robust activity in the assay described herein (Figure 1C). This is consistent with previous work showing that D. dipsaci is tolerant of nematicides13,14. Fluopyram inhibits complex II of the electron transport chain in a nematode-selective manner and is a commercial nematicide used to control a variety of PPNs, including Rotylenchulus reniformis and Meloidogyne incognita4,21,22. Fluopyram and one of the nematicides that lacked activity at the concentration tested (Oxamyl)23 were investigated in more detail through a dose-response analysis with D. dipsaci. Fluopyram induces an apparent dose-dependent effect on D. dipsaci mobility with an EC50 of 9.3 μM (with a 95% confidence interval between 8.2 to 10.5 μM) (Figure 2A,B). This result is expected based on published in vitro results from Storelli et al., 202013. Oxamyl has no significant effect on mobility up to a concentration of 120 µM (p = 0.3632, unpaired t-test) (Figure 2C,D).
Sodium hydroxide improves assay sensitivity
In contrast to the near-continuous swimming activity of C. elegans in liquid culture18, D. dipsaci animals are dramatically less mobile. This is not uncommon among parasitic nematodes in culture16. To help distinguish 'resting' worms from sick worms, 40 mM of NaOH is used at the assay endpoint to stimulate movement in those individuals who are capable (Figure 3)19,20. This technique allows for the clear identification of small molecules that immobilize worms, given that all worms in negative control wells move and yield an exceptionally low background of false positives in the screen.
Figure 1: Examples of screen output. Three biological replicates (open circles) with D. dipsaci were performed against the small molecules (60 µM) in each of the three plates shown. All three plates have 0.6% of DMSO solvent-only controls (darker bars). Except where otherwise noted with solvent controls or known nematicides, the wells of the three plates contain relatively uncharacterized drug-like compounds purchased from vendors (see Burns et al., 2015)18. (A) A 96 well plate from the small molecule library lacks any molecule with observable bioactivity against D. dipsaci. (B) A 96 well plate from the small molecule library has a single molecule that reproducibly disrupts D. dipsaci mobility. (C) A 96 well drug plate containing the characterized nematicides fluopyram (fluo), iprodione (ipro), abamectin (abam), fluensulfone (flue), tioxazafen (tiox), oxamyl (oxam), and wact-11. The error bars represent the standard error of the mean. Please click here to view a larger version of this figure.
Figure 2: Example of positive and negative results using mobility assay. (A) Examples of the terminal phenotypes after the exposure of D. dipsaci to increasing concentrations of fluopyram after 5 days before addition of NaOH. (B) A dose-response analysis of the movement of D. dipsaci after 5 days of exposure to the indicated concentrations of fluopyram. (C,D) The same as A,B, except for oxamyl. Each graph shows trials done on two separate days with three replicates each day. The y-axis of each graph indicates the fraction mobile of the worms in each well calculated as the number of animals moving relative to the total number of animals in the well. The error bars on both graphs represent the standard error of the mean. The scale bar represents 1 mm. Please click here to view a larger version of this figure.
Figure 3: Mobility of D. dipsaci after adding 40 mM of NaOH. The effect of NaOH addition to D. dipsaci samples in the presence of solvent-only control (A), tioxazafen (B), or fluopyram (C) after 5 days of co-incubation. The scale bar represents 1 mm. Please click here to view a larger version of this figure.
Critical steps
Despite the protocol's simplicity, there are critical steps in the protocol that deserve additional attention to maximize the likelihood of success. First, overbleaching the seeds can disrupt their growth. Therefore, limiting the seeds' time in the bleaching solution to 20 minutes or less is essential. Second, as previously noted by Storelli et al., the apparent health of the nematodes decreases over time when stored at 4 °C16. Using the nematodes soon after their collection provides additional confidence that optimal screening conditions can be achieved. Should longer-term storage be necessary, ensure that the tube's lid is not tight to allow oxygen exchange. Third, ensuring that the peas grow on the NA plates for the suggested time enables the experimenter to judge which seeds are contaminated. Fourth, overgrowing the peas on the GA plates before adding the nematodes will weaken infection and reduce the nematode yield. Finally, many factors that are difficult to control can impact screening results. Therefore, it is essential to perform multiple independent replicate screens on different days and ideally with PPNs collected from different culture plates to ensure the reproducibility of results.
Limitations of method
A limitation to the protocol is that it fails to synchronize the developmental stage of the collected worms, which range from juveniles to adults. Hence, strong hits revealed by any screen are likely effective at multiple stages. However, the protocol increases the risk of overlooking effective stage-specific hits. A second consideration is that in vitro screening should be considered the first step in a nematicide-discovery pipeline; soil-based assays are an excellent addition to a pipeline to test the translatability of the hits.
Significance and application of the protocol
The protocols described herein are simple and easily replicated. Furthermore, this protocol has been successfully applied to other PPNs in the lab, including Pratylenchus penetrans, by making only slight modifications. Developing new and safe PPN control measures is essential to ensure global food security. This is especially true for species like D. dipsaci that are generally tolerant to a wide variety of currently acceptable chemical nematicides13,14. Hence, the protocols outlined here have the potential to make an important contribution to human health on a global scale.
The authors have nothing to disclose.
The authors acknowledge Dr. Qing Yu (Agriculture and Agri-Food Canada) for providing the Ditylenchus dipsaci culture and for advice on culture methods; Dr. Benjamin Mimee (Agriculture and Agri-Food Canada) and Nathalie Dauphinais (Agriculture and Agri-Food Canada) for advice on in vitro culture of plant-parasitic nematodes; Dr. Andrew Burns and Sean Harrington for helpful suggestions on the project and the manuscript. JK is an NSERC Alexander Graham Bell Canada Graduate Scholar. PJR is supported by a CIHR project grant (313296). PJR is a Canada Research Chair (Tier 1) in Chemical Genetics.
15 mL tube | Sarstedt | 62.554.205 | |
2 forceps | Almedic | 7747-A10-108 | |
2L beaker | Pyrex | CLS10002L | |
50mL beaker | Pyrex | CLS100050 | |
96 well plate | Sarstedt | 83.3924 | |
aluminium foil | Alcan Plus | ||
bacteriological agar | BioShop | AGR001.5 | |
coffee filter | No name brand | 716 | |
commercial bleach 6% | Lavo Pro 6 | DIN102358107 | |
disposable petri dishes (10cm x 1.5cm) | Fisherbrand | FB0875712 | |
disposable petri dishes (10cm x 2.5cm) | Sigma-Aldrich | Z358762 | |
dissecting scope | Leica | Leica MZ75 | |
DMSO | Sigma-Aldrich | 472301-500ML | |
Funnel | VWR | 414004-270 | |
Gamborg B5 | Sigma-Aldrich | G5893-10L | |
glass petri dish | VWR | 75845-546 | |
glass slide | MAGNA | 60-1200 | |
Lint-Free Blotting Paper | V&P Scientific | VP 522-100 | |
mutlichannel pipette | Eppendorf research plus | 3125000036 | |
NaOH | Sigma-Aldrich | S8045-500G | |
nutrient agar | Sigma-Aldrich | 70148-100G | |
parafilm | Bemis | PM-996 | |
pea seeds | Ontario Seed Company | D-1995-250G | |
pin cleaning solutions | V&P Scientific | VP110A | |
pinner | V&P Scientific | VP381N | |
pinner rinse trays | V&P Scientific | VP 421 | |
pipette tips- low retention ? Reg. 200uL | LABFORCE | 1159M44 | |
reagent reservoir with lid for multichannel pipettes | Sigma-Aldrich | BR703459 | |
shaking incubator | New Brunswick Scientific | I26 | |
sterile surgical blade | MAGNA | sb21-100-a | |
stir bar | Fisherbrand | 2109 – 1451359 | |
sucrose | BioShop | SUC507.1 |