Revolutionising Greenhouse Pest Management with Environmental DNA: Early Detection of Pests in Tomato Plants

In the pursuit of more efficient and sustainable agriculture, finding innovative ways to detect crop pests is crucial. A groundbreaking study has shown how environmental DNA (eDNA) technology could transform pest monitoring in agriculture, especially in greenhouses.

What Is Environmental DNA (eDNA)?

Environmental DNA is a modern method for detecting different species without seeing them directly. Instead of relying on visual identification, eDNA technology detects organisms through the genetic material they leave behind—tiny traces of DNA shed into their environment. This DNA can be collected from places like soil, water, and plant surfaces.

The study focuses on two pests that significantly harm tomato plants grown in greenhouses:

1. Sweetpotato Whitefly (Bemisia argentifolii)- previously B. tabaci Biotype B
2. Twospotted Spider Mite (Tetranychus urticae)

Meet the Pests

Sweetpotato Whitefly

The Sweetpotato Whitefly is a tiny insect, about 0.9 millimetres long, but it can cause big problems. It is considered a “supervector,” meaning it can spread many different plant viruses when it feeds on plants. These viruses can lead to significant crop losses. Because the whiteflies are so small and tend to hide, they are hard to spot early on. Early detection is important to prevent damage. For example, in Georgia, USA, whitefly infestations in 2017 led to over $100 million in crop losses.

Twospotted Spider Mite

The Twospotted Spider Mite is a minuscule creature, about 0.4 millimetres in size, that feeds on a wide variety of plants—over 1,100 species, including 150 types of crops. When they feed on tomato plants, they can reduce yields by up to 50%. They reproduce quickly, and heavy infestations can kill plants. Their small size and ability to adapt make them hard to control and identify early, highlighting the need for advanced monitoring methods like eDNA.

Both pests thrive in greenhouse environments because of the favourable conditions and abundant food. Detecting these pests early using eDNA methods could help reduce economic losses and lessen the need for chemical pesticides, leading to more sustainable tomato farming.

The Study’s Goals and Methods

The research aimed to develop better ways to detect these pests by:

• Testing DNA Detection Tools: Evaluating how well current and newly designed DNA primers work. Primers are short strands of DNA that start the copying process in DNA detection.
• Comparing Detection Methods: Looking at the sensitivity of standard PCR (Polymerase Chain Reaction) versus real-time PCR (qPCR). PCR, or Polymerase Chain Reaction, is like a photocopier for DNA. Scientists use it to make millions of copies of a specific piece of DNA because the original amount is usually too small to study directly. This is helpful for things like diagnosing diseases, studying genes, or identifying organisms.
• Improving DNA Extraction: Developing faster methods to extract DNA from environmental samples.
• Ensuring Accuracy: Making sure the new methods specifically target the pests without picking up DNA from other species.

How Was the Experiment Conducted?

Growing the Plants and Pests

Tomato plants were grown for four weeks, first in controlled growth chambers and then moved to a greenhouse. The Sweetpotato Whitefly and Twospotted Spider Mite were also raised in controlled conditions. They were then introduced to the tomato plants for 24 hours using special clip-on cages attached to the leaves.

Amplifying the DNA with PCR

After the pests had time to infest the plants, scientists collected eDNA by rinsing the leaves with clean water to wash off any genetic material left by the pests. This water was then filtered to collect the DNA on tiny membrane filters, which were stored in a freezer until it was time to extract the DNA.

Amplifying the DNA with PCR

In this study, two types of PCR were used:

1. Conventional PCR (cPCR): This is the standard method where DNA is copied in cycles, and the results are seen at the end. Primers targeting a specific gene (the mitochondrial CO1 gene) were used. However, this method was not sensitive enough to detect very small amounts of DNA.
2. Real-Time PCR (qPCR): This method allows scientists to see the DNA amplification as it happens in real-time. It proved to be more sensitive and reliable, especially for detecting low levels of DNA. The researchers developed new primers specifically for this study to improve accuracy and avoid detecting other pests by mistake.

Testing for Accuracy and Sensitivity

The new primers were designed to be highly specific, meaning they would only amplify DNA from the target pests and not from other common greenhouse insects. They focused on specific gene regions:

• For Whiteflies: The 18S ribosomal RNA gene region.
• For Spider Mites: The mitochondrial CO1 gene.

Key Findings and Innovations

The study revealed several important points:

• Improved Primers: The newly developed primers were much better at specifically detecting the target pests. They were more sensitive and accurate than the existing primers.
• Better Detection Methods: Real-time PCR (qPCR) was more effective than conventional PCR (cPCR), especially for finding pests when their numbers were low.
• Efficient DNA Extraction: The QuickExtract kit was more effective for extracting DNA from samples with low pest infestations compared to the Qiagen kit.
• High Specificity: The new primers did not react with DNA from non-target species, ensuring that the detection was precise and reliable.

What Does This Mean for Agriculture?

This research has significant implications for modern farming:

Early Detection: The high sensitivity of the eDNA methods means pests can be detected earlier, allowing farmers to act quickly and potentially save their crops.

Cost-Effective Monitoring: Using eDNA is both accurate and affordable, making it practical for commercial greenhouses.

Reduced Labour: This method can reduce the need for time-consuming visual inspections, making pest monitoring more efficient.

Environmental Benefits: Early and accurate detection can lead to reduced use of pesticides, promoting more sustainable and eco-friendly farming practices.

Practical Applications for Industry

For farmers and greenhouse managers, this study suggests several practical steps:

• Implement eDNA Monitoring: Regularly using eDNA sampling can serve as an early warning system for pest infestations.
• Targeted Pest Control: With precise detection, pest control measures can be more focused, reducing the need for widespread pesticide application.
• Improve Crop Quality: Keeping a close eye on pest levels can help maintain healthier plants and better yields.

Future Perspectives

The study points to exciting possibilities ahead:

Advancing Technology: Further refining these detection methods could make them even more effective and easier to use. Developing tests that can detect multiple pests at once (multiplex assays) would be highly beneficial.

Wider Use: The eDNA approach could be adapted for outdoor farming and used to detect a variety of pests and diseases in different crops.

Integration with Smart Agriculture: Combining eDNA detection with smart technology like sensors, automated monitoring systems, and real-time data analysis could revolutionise pest management. Farmers could receive instant alerts about pest levels, allowing for immediate action.

Conclusion

This research marks a significant step forward in agricultural pest management. By using environmental DNA to detect pests early and accurately, farmers have a powerful new tool to protect their crops. As agriculture moves toward more sustainable and efficient practices, innovations like eDNA detection will be essential.

The success of this study in greenhouse tomatoes lays the groundwork for broader applications in farming. Staying informed about such technological advances will help agricultural professionals remain competitive and ensure the future of sustainable crop production.