We describe the use of thin-layer chromatography direct bioautography assay and liquid chromatography-mass spectrometry to identify microbial natural products that display antagonism against fungal pathogens using the pathogen Sclerotinia sclerotiorum and biopesticidal Bacillus isolates as a model system.
Thin layer chromatography-direct bioautography (TLC-DB) is a well-established bioassay used to separate and identify natural products (NPs) that are antagonistic against a target pathogen. It is a rapid, inexpensive, and simple option for the bioassay-guided isolation and identification of NPs that hinges on separation by TLC coupled with the direct application of a target pathogen to examine bioactivity. It is typically used for the analysis of bioactive plant extracts, detecting inhibitory activity against bacteria, fungi, and enzymes. That being said, it has great potential in bacterial NP discovery, particularly for evaluating bacterial NPs against pertinent agricultural pathogens, which is valuable for discovering and developing novel biopesticides for the agriculture industry. Furthermore, it is a tunable protocol that could be applied to other target pathogens or sources of NPs in research programs concerning the discovery and identification of bioactive compounds. Herein, we describe a model system for discovering and identifying biopesticide NPs using TLC-DB with Bacillus spp. and the agricultural pathogen Sclerotinia sclerotiorum.
Fungal agricultural pathogens cause significant losses in crop quality and yields worldwide, contributing to the economic and supply challenges of a stable global food production system1,2. Pathogen damage can be prevented by breeding cultivars resistant to infection and using integrated crop management systems, including crop rotations and land management practices to suppress pathogen proliferation3,4. Though these methods reduce damage to crops, chemical pesticides are generally used in tandem to actively kill fungal reproductive structures in the field and further prevent damage and yield reductions. Although effective, chemical pesticide usage has many drawbacks, including damage to surrounding ecosystems, a decline in soil fertility, associated human health risks, and the development of pathogen resistance, the latter causing higher doses of pesticides to be required each year5,6,7.
Microbial-based pest and pathogen management products have long been considered potential alternatives or complementary to synthetic pesticides. Since the early 1900s, Bacillus thuringiensis has been widely used to control agricultural pests and pathogens as a seed treatment, as a foliar spray, and in direct soil treatment8. Such products have been named biopesticides and are characterized as naturally occurring microorganisms or biochemicals that can kill, suppress, or reduce the vigor of a target pest or pathogen. Biopesticides can control the growth of a pathogen through various mechanisms but most commonly do so through the secretion of secondary metabolites9. Secondary metabolites, often referred to as natural products, are not involved in primary metabolism but are produced as an evolutionary advantage to outcompete other microorganisms10.
Biopesticides offer many advantages over their synthetic counterparts. They pose a low toxicity risk to the environment, fauna, and humans compared to synthetic pest management products9,10. Since most biopesticides have existed naturally in the environment for millennia, biodegradation pathways for microbial metabolites exist in the environment, limiting the possibility of soil or ecosystem contamination and reducing residence times that contribute to synthetic pesticides being so environmentally destructive11. Additionally, many biopesticides used for mitigating pathogen infection also exhibit plant growth-promoting properties, which can increase nutrient bioavailability and induce plant systemic resistance12.
Most commonly, biopesticides are applied in the form of microbial inoculum, and NPs are secreted by live microorganisms in situ12,13. In such a case, identifying the source of the activity of a biopesticide is of great value. Doing so provides insight into the mechanism of action of the biopesticide, aids with building a case for the protection of a microorganism with a patent, and can have a significant scientific impact if their structures are novel. Most importantly, however, identification of the bioactive source informs formulation possibilities for a downstream biopesticide product. If the NP itself is active, one can use the microorganism as a biomolecule factory for large-scale biopesticide production. Additionally, many NPs that have been explored for biocontrol also have potential applications in human medicine, making them even more economically valuable8.
Thin layer chromatography-direct bioautography (TLC-DB) assays are an inexpensive and straightforward method for the bioactivity-guided isolation and identification of biopesticidal metabolites. Although the technique is commonly used for separating bioactivity testing of phytochemicals from crude plant extracts, it also has great potential for the analysis of microbial extracts14. TLC provides fast and inexpensive separation of NPs in a crude microbial extract, and after coating with a media pathogen suspension, zones that contain active metabolites are easily visualized. Those zones can be scraped from the plate and extracted for chemical analysis by ultra-high-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) to identify known metabolites. Metabolites that do not match previously reported compounds can be isolated in larger quantities via liquid chromatography to undergo structure elucidation studies using techniques such as nuclear magnetic resonance spectroscopy and X-ray crystallography15.
This article describes a model system for discovering and identifying biopesticide NPs using TLC-DB with Bacillus spp. and the agricultural pathogen Sclerotinia sclerotiorum. Figure 1 provides a schematic overview of the TLC-DB procedure.
Figure 1: Schematic overview of steps 4-7 of the procedure of TLC-DB. Please click here to view a larger version of this figure.
The details of the reagents and the equipment used in this study are listed in the Table of Materials.
1. Selecting the microbial biocontrol candidates
2. Media preparation
3. Pathogen preparation
4. Natural product extract preparation
5. TLC plate preparation
6. Direct bioautography assay
7. Liquid chromatography mass spectrometry analysis
Upon the separation of microbial extracts by TLC, metabolites should be dispersed along the TLC plate vertically. Under visible light, it can be difficult to view metabolites that do not absorb in the visible light range. Thus, imaging under UV light can help view the separation of metabolites, as seen in Figure 2A,B. After the incubation period, the pathogen should appear to grow evenly across the entire plate except over the positive controls and the inhibition zones where active metabolites reside, pictured in Figure 2C.
Figure 2: Separation of microbial extracts by TLC. (A) Developed TLC plate containing nine Bacillus extracts imaged under visible light and (B) under 320 nm UV light prior to the application of fungal inoculum. (C) Completed bioautography assay with pathogen growth observed across the plate except for where growth is inhibited around the positive controls, and ZOI of each extract. Please click here to view a larger version of this figure.
Metabolites extracted from the zones of inhibition are analyzed by LC-MS and compared to the crude extract to determine the NPs responsible for the antagonism against the pathogen. Matching metabolites should have the same retention time and molecular ion species to be considered a match. Once the active metabolites are identified, the bacterial culture can be grown in bulk to isolate active metabolites of interest for structural chemistry or biological study.
TLC-DB is a valuable and well-established NP research tool and a simple and inexpensive alternative to microplate bioassay-guided isolation methods17. It requires minimal time and material resources compared to microplate assays, which require metabolite separation using liquid chromatography techniques. It is a highly versatile assay that can be used to detect antibacterial, antifungal, anti-parasitic, and antioxidant NPs in addition to enzyme inhibitors18,19,20,21,22,23. Though most commonly used for detecting and identifying bioactive phytochemicals, the same method can be applied for bacterial NPs as explored in this protocol18. Additionally, the protocol can be optimized for use with a variety of NP sources and target pathogens to aid in discovering and assessing novel bioactive NPs.
The media used for bacterial growth and solvent used for extraction can greatly impact natural product discovery results. The media used in this protocol is optimized for bacteria that produce cyclic lipopeptides, including Pseudomonas and Bacillus spp. but other media and nutrient sources should be considered if exploring other genera. One may choose to complete TLC-DB using the same microorganism grown in a range of media to evaluate the full breadth of metabolite diversity from one isolate or use identical growth conditions for a wider range of isolates. The choice of extraction solvent also impacts the natural products detected. It is generally understood that most bioactive NPs have low to moderate polarity, making ethyl acetate a suitable choice due to its low boiling point, which makes it easy to remove. However, if one also wishes to examine the polar and non-polar fractions, multiple extractions with other solvents can be carried out. Alternatively, the cell-free extract can be lyophilized and used in the assay to see all metabolites released into the media. However, more material will often need to be loaded onto the TLC plate to account for the dried media components in the lyophilized material. Similarly, if this method is used with a different pathogen, such as inoculum, the media used and incubation conditions must be optimized to obtain the 5 agar plates of mycelium used for the TLC-DB assay.
TLC-DB is advantageous compared to contact and immersion bioautography as it uses the thinnest layer of agar and inoculum, minimizing the reliance on the diffusion of metabolites into the agar layer, which can allow smaller amounts of natural products to induce pathogen inhibition17. Previously published findings using TLC bioautographic methods have used a spore suspension of the pathogen to complete the assay17. Although this does allow for precise control over the suspension concentration, it can be exceedingly difficult and time-consuming to induce the sporulation of certain fungi24. This modification greatly simplifies the assay and allows for the completion of the assay using fungal pathogens that are difficult to sporulate and may have previously been avoided for this method.
The mass of bacterial extract used in the assay can impact results. If too little extract is applied to the TLC plate, it is possible that the minimum inhibitory concentration of an active compound will not be surpassed, and bioactivity will not be detected. As a result, in some cases, and as seen in Figure 1 and Figure 2, it is worthwhile to overload the TLC plate, compromising separation for the ability to easily detect activity. Similarly, the pathogen load sprayed onto the plate must not be too low, as there will not be enough media applied to support pathogen growth. This method can be easily tuned to accommodate a variety of bacterial extracts and pathogens, and the quantities of microbial extract and inoculum outlined in the protocol have ensured bioactivity can be detected for multiple pathogens and microbial extracts. If no zones of inhibition are observed upon the completion of the assay, it may indicate one of the following. First, active metabolites may not be present in the extract applied due to incompatible media being used for bacterial growth or due to the activity of the bacteria not being a result of the NP production. A disc diffusion assay with the extract can be completed to confirm or deny the existence of active NPs in the extract. If the disk diffusion assay shows no pathogen suppression, other media can be tested to determine if other conditions produce bioactive NPs. If the disk diffusion assay does indicate that the extract suppresses the pathogen, then a larger mass of the bacterial extract may need to be applied to the TLC plate, in which case another assay can be attempted.
Comparing metabolites in the ZOI to the crude extract is essential for identifying active NPs. In the assay, metabolites from the crude extract can be metabolized or modified by the pathogen, which can be observed via LC-MS. Thus, only metabolites that occur in both the crude extract and the ZOI can be considered as NPs produced by the bacteria under study. If one cannot correlate the metabolites extracted from the ZOI to metabolites in the crude extract, a TLC plate can be prepared, as described in step 5. Without completing the bioautography assay, extract the metabolites from the TLC plate at the same retention time observed in the completed assay. This should allow for an easier correlation between the metabolites in the ZOIs and crude extract, causing pathogen suppression.
One drawback of TLC-DB is that the resolution of TLC is considerably less than that achieved when using traditional microwell screening techniques, which require liquid chromatography for separation. Thus, it is common for multiple metabolites to exist in the zone of inhibition where some metabolites may not be contributing to the bioactivity. This issue can be further caused by the practice of overloading the TLC plate to observe bioactivity more clearly. Recent work has been published using high-performance TLC (HP-TLC), which greatly improves resolution and can allow for the automation of TLC development that is otherwise impossible when using conventional TLC14,21,22,23. Also, plates can be developed in a second dimension (2D-TLC) to further separate metabolites with similar retention times. That being said, one should evaluate whether the increased time and material cost is a worthwhile compromise for increased resolution obtained from HP- and 2D-TLC25.
The authors have nothing to disclose.
We gratefully acknowledge Agriculture and Agri-Food Canada for the funding under which this research was made possible (projects J-001843 and J-002021). We thank Brett van Heyningen for filming the video content for this protocol. We would also like to thank former graduate students (Jennifer Vacon and Mark Nabuurs) for their insights into the methods described in this manuscript.
0.5-5 mL single channel Pipette | VWR | CA11020-004 | |
10 mL Thin Layer Chromatography Sprayer | VWR | KT422530-0010 | |
100 x 15 mm Petri plates | VWR | 89038-970 | |
100-1000 µL pipette tips | VWR | 76322-164 | |
100-1000 µL single channel pipette | VWR | 76169-240 | |
15 mL sterile centrifuge tubes | VWR | CA21008-918 | |
1 L glass bottle | Millipore Sigma | CLS13951L | Must be autoclave safe |
1 mL sterile syringe with needle | Thomas Scientific | 8935L75 | Detachable needle is recommended |
2 mL Microcentrifuge tube | VWR | 87003-298 | |
50 mL sterile centrifuge tubes | VWR | CA21008-940 | |
5 mL pipette tips | VWR | CA11020-008 | |
7 mL scintilation vials | VWR | 76538-962 | |
95% ethanol | Thermo Fisher Scientific | A412-500 | |
Autoclave | Cole-Parmer | UZ-01850-34 | 8 L, 115 VAC |
Bacteriological agar | VWR | 97064-336 | |
bin | Thomas Scientific | 1216H91 | |
D-Glucose | VWR | BDH9230-500G | |
Dichloromethane ≥99.8% ACS | VWR | BDH1113-4LG | |
Ethyl Acetate ≥99.8% ACS | VWR | BDH1123-4LG | |
Filter paper | VWR | CA28297-846 | |
Grinding Beads | VWR | 12621-148 | |
Hygromycin B | VWR | CA80501-074 | |
Iron Sulfate Heptahydrate | VWR | 97061-542 | |
Laminar flow hood | CleanTech | 1000-6-A | |
LC-MS | Waters | LITR10064178 | UPLC/MS/MS TQD system |
Lyophilizer | Labconco | 700201000 | Temperature collector -50 °C |
Manganese Sulfate Hydrate | VWR | CAAA10807-14 | |
Methanol ≥99.8% ACS | VWR | BDH2018-5GLP | |
Paper towel | VWR | 89402-824 | |
Potato Dextrose Agar | VWR | CA90000-758 | |
Potato Dextrose Broth | VWR | CA90003-494 | |
Potsasium Phosphate Dibasic | VWR | 470302-246 | |
Potsasium Phosphate Monobasic | VWR | 470302-252 | |
Pressure Gauge 6mm Union Straight 0-10 bar (0-145 psi) | Tameson | F25U6 | |
Pseudomonas F Agar | VWR | 90003-352 | Also known as Flo Agar |
PTFE Tubing | Sigma Aldrich | 58697-U | 1/16 inch inner diameter |
Sodium Chloride | VWR | BDH9286-500G | |
Spatula | VWR | 82027-490 | |
Sterile Inoculation loops with needle | VWR | 76534-512 | |
Tinfoil | Thomas Scientific | 1086F24 | Can be purchased from supermarket |
TLC Silica Gel 60 RP-18 F254S 25 Glass Plates 20 X 20 cm | Thomas Scientific | 1205Q12 | |
Vacuum Pump | Labconco | 1472100 | 98 L/min |
Vortex | VWR | 76549-928 | Must accomadate 15 mL and 50 mL centrifuge tubes |
Whatman in-line HEPA-VENT | Millipore Sigma | WHA67235000 | 10 filters, 1/4 to 3/8 inch inlet/outlet |
VWR | 97063-370 |